diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml new file mode 100644 index 0000000..386461b --- /dev/null +++ b/.github/workflows/build.yml @@ -0,0 +1,64 @@ +name: build + +on: + push: + branches: + - main + pull_request: + branches: + - main + +jobs: + test: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ['3.9', '3.10', '3.11', '3.12', '3.13'] + steps: + - uses: actions/checkout@v4 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + + - name: Install uv + uses: astral-sh/setup-uv@v4 + + - name: Install dependencies + run: uv sync + + - name: Run pre-commit + run: | + uv run pre-commit run --all-files + + - name: Run tests + run: | + uv run python -m unittest discover -s tests -p "*.py" + + publish: + needs: test + runs-on: ubuntu-latest + if: github.event_name == 'push' && github.ref == 'refs/heads/main' + permissions: + id-token: write + steps: + - uses: actions/checkout@v4 + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: '3.9' + + - name: Install uv + uses: astral-sh/setup-uv@v4 + + - name: Install dependencies + run: uv sync + + - name: Build package + run: uv build + + - name: Publish to PyPI (production) + run: | + uv publish --trusted-publishing always diff --git a/.gitignore b/.gitignore index 3d5d821..216f74c 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,4 @@ -**/tests/**/*.bcif +tests/*.bcif ### VisualStudioCode template .vscode/* @@ -227,4 +227,3 @@ dmypy.json # Cython debug symbols cython_debug/ - diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..e6e0191 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,15 @@ +repos: +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v3.2.0 + hooks: + - id: trailing-whitespace + - id: end-of-file-fixer + - id: check-yaml + - id: check-added-large-files + +- repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.12.3 + hooks: + - id: ruff + args: [ --fix ] + - id: ruff-format diff --git a/LICENSE b/LICENSE index 9300acc..9edf377 100644 --- a/LICENSE +++ b/LICENSE @@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. \ No newline at end of file +SOFTWARE. diff --git a/README.md b/README.md index a5752a2..4e68bed 100644 --- a/README.md +++ b/README.md @@ -7,5 +7,5 @@ A library for reading and writing (Binary)CIF files in Python. ## Linting ``` -autoflake --remove-all-unused-imports --remove-unused-variables --ignore-init-module-imports -ir . && isort . && black . -``` \ No newline at end of file +pre-commit run -a +``` diff --git a/ciftools/binary/data.py b/ciftools/binary/data.py index 8ee206d..e783fbe 100644 --- a/ciftools/binary/data.py +++ b/ciftools/binary/data.py @@ -1,6 +1,7 @@ from typing import Any, Dict, List, Optional, Union import numpy as np + from ciftools.binary.decoder import decode_cif_data from ciftools.binary.encoded_data import EncodedCIFCategory, EncodedCIFColumn, EncodedCIFFile from ciftools.models.data import CIFCategory, CIFColumn, CIFDataBlock, CIFFile, CIFValuePresenceEnum diff --git a/ciftools/binary/decoder.py b/ciftools/binary/decoder.py index 906c719..f6d3148 100644 --- a/ciftools/binary/decoder.py +++ b/ciftools/binary/decoder.py @@ -1,4 +1,5 @@ import numpy as np + from ciftools.binary.data_types import DataType from ciftools.binary.encoded_data import EncodedCIFData from ciftools.binary.encoding_types import ( @@ -59,10 +60,10 @@ def _decode_integer_packing_signed(data: np.ndarray, encoding: IntegerPackingEnc value = 0 t = data[i] while t == upper_limit or t == lower_limit: - value += t + value += int(t) i += 1 t = data[i] - value += t + value += int(t) output[j] = value i += 1 j += 1 @@ -80,10 +81,10 @@ def _decode_integer_packing_unsigned(data: np.ndarray, encoding: IntegerPackingE value = 0 t = data[i] while t == upper_limit: - value += t + value += int(t) i += 1 t = data[i] - value += t + value += int(t) output[j] = value i += 1 j += 1 diff --git a/ciftools/binary/encoded_data.py b/ciftools/binary/encoded_data.py index 17b1ac8..43964d6 100644 --- a/ciftools/binary/encoded_data.py +++ b/ciftools/binary/encoded_data.py @@ -1,6 +1,7 @@ from typing import Optional, TypedDict, Union import numpy as np + from ciftools.binary.encoding_types import EncodingBase diff --git a/ciftools/binary/encoder.py b/ciftools/binary/encoder.py index 963cf95..102c9eb 100644 --- a/ciftools/binary/encoder.py +++ b/ciftools/binary/encoder.py @@ -1,8 +1,10 @@ import math import sys -from typing import Any, Dict, List, Protocol, Tuple, Union +from typing import Any, List, Protocol, Tuple, Union import numpy as np +from numba import jit + from ciftools.binary.data_types import DataType, DataTypeEnum from ciftools.binary.encoded_data import EncodedCIFData from ciftools.binary.encoding_types import ( @@ -15,12 +17,10 @@ RunLengthEncoding, StringArrayEncoding, ) -from numba import jit class BinaryCIFEncoder(Protocol): - def encode(self, data: Any) -> EncodedCIFData: - ... + def encode(self, data: Any) -> EncodedCIFData: ... class ComposeEncoders(BinaryCIFEncoder): @@ -109,7 +109,6 @@ def encode(self, data: np.ndarray, *args, **kwargs) -> EncodedCIFData: class IntegerPacking(BinaryCIFEncoder): def encode(self, data: np.ndarray) -> EncodedCIFData: - # TODO: must be 32bit integer? packing = _determine_packing(data) if packing.bytesPerElement == 4: @@ -325,8 +324,8 @@ def _pack_strings(data: List[str]) -> Tuple[str, np.ndarray, np.ndarray]: str_map = {s: i for i, s in enumerate(strings)} string_data = "".join(strings) - indices = np.array([str_map[s] for s in data], dtype=' Optional[str]: - ... + def get_string(self, row: int) -> Optional[str]: ... - def get_integer(self, row: int) -> int: - ... + def get_integer(self, row: int) -> int: ... - def get_float(self, row: int) -> float: - ... + def get_float(self, row: int) -> float: ... - def get_value_presence(self, row: int) -> CIFValuePresenceEnum: - ... + def get_value_presence(self, row: int) -> CIFValuePresenceEnum: ... - def are_values_equal(self, row_a: int, row_b: int) -> bool: - ... + def are_values_equal(self, row_a: int, row_b: int) -> bool: ... - def string_equals(self, row: int, value: str) -> bool: - ... + def string_equals(self, row: int, value: str) -> bool: ... def as_ndarray( self, *, dtype: Optional[Union[np.dtype, str]] = None, start: Optional[int] = None, end: Optional[int] = None @@ -40,11 +34,9 @@ def as_ndarray( """ ... - def __getitem__(self, idx: Any) -> Any: - ... + def __getitem__(self, idx: Any) -> Any: ... - def __len__(self) -> int: - ... + def __len__(self) -> int: ... @property def value_presences(self) -> Optional[np.ndarray]: @@ -56,29 +48,23 @@ def value_presences(self) -> Optional[np.ndarray]: class CIFCategory(Protocol): @property - def name(self) -> str: - ... + def name(self) -> str: ... @property - def n_rows(self) -> int: - ... + def n_rows(self) -> int: ... @property - def n_columns(self) -> int: - ... + def n_columns(self) -> int: ... @property - def field_names(self) -> List[str]: - ... + def field_names(self) -> List[str]: ... def __getattr__(self, name: str) -> CIFColumn: return self[name] - def __getitem__(self, name: str) -> CIFColumn: - ... + def __getitem__(self, name: str) -> CIFColumn: ... - def __contains__(self, key: str) -> bool: - ... + def __contains__(self, key: str) -> bool: ... # Category Helpers def get_matrix(self, field: str, rows: int, cols: int, row_index: int) -> np.ndarray: @@ -120,19 +106,15 @@ class CIFDataBlock(Protocol): def __getattr__(self, name: str) -> CIFCategory: return self[name] - def __getitem__(self, name: str) -> CIFCategory: - ... + def __getitem__(self, name: str) -> CIFCategory: ... - def __contains__(self, key: str): - ... + def __contains__(self, key: str): ... @property - def header(self) -> str: - ... + def header(self) -> str: ... @property - def categories(self) -> Dict[str, CIFCategory]: - ... + def categories(self) -> Dict[str, CIFCategory]: ... class CIFFile(Protocol): @@ -145,12 +127,10 @@ def __getitem__(self, index_or_name: Union[int, str]) -> CIFDataBlock: def __getattr__(self, name: str) -> CIFDataBlock: return self[name] - def __len__(self) -> int: - ... + def __len__(self) -> int: ... def __contains__(self, key: str) -> bool: return key in self._block_map @property - def data_blocks(self) -> List[CIFDataBlock]: - ... + def data_blocks(self) -> List[CIFDataBlock]: ... diff --git a/ciftools/models/writer.py b/ciftools/models/writer.py index b58c3d0..0b71124 100644 --- a/ciftools/models/writer.py +++ b/ciftools/models/writer.py @@ -2,6 +2,7 @@ from typing import Any, Callable, Collection, Generic, List, Optional, Protocol, TypeVar, Union import numpy as np + from ciftools.binary.encoder import BYTE_ARRAY, STRING_ARRAY, BinaryCIFEncoder from ciftools.models.data import CIFValuePresenceEnum @@ -87,24 +88,18 @@ def string_array( class CIFCategoryDesc(Protocol): @property - def name(self) -> str: - ... + def name(self) -> str: ... @staticmethod - def get_row_count(data: Any) -> int: - ... + def get_row_count(data: Any) -> int: ... @staticmethod - def get_field_descriptors(data: Any) -> Collection[CIFFieldDesc]: - ... + def get_field_descriptors(data: Any) -> Collection[CIFFieldDesc]: ... class CIFWriter(Protocol): - def start_data_block(self, header: str) -> None: - ... + def start_data_block(self, header: str) -> None: ... - def write_category(self, category: CIFCategoryDesc, data: List[Any]) -> None: - ... + def write_category(self, category: CIFCategoryDesc, data: List[Any]) -> None: ... - def encode(self) -> Union[str, bytes]: - ... + def encode(self) -> Union[str, bytes]: ... diff --git a/ciftools/serialization.py b/ciftools/serialization.py index 6b80768..c833c23 100644 --- a/ciftools/serialization.py +++ b/ciftools/serialization.py @@ -1,4 +1,5 @@ import msgpack + from ciftools.binary.data import BinaryCIFFile from ciftools.binary.writer import BinaryCIFWriter from ciftools.models.data import CIFFile diff --git a/mypy.ini b/mypy.ini index a14e76f..dc93bf7 100644 --- a/mypy.ini +++ b/mypy.ini @@ -9,4 +9,4 @@ ignore_missing_imports = True ignore_missing_imports = True [mypy-msgpack.*] -ignore_missing_imports = True \ No newline at end of file +ignore_missing_imports = True diff --git a/pyproject.toml b/pyproject.toml index 4ee7aa2..0482c05 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,20 +1,39 @@ [project] name = "ciftools" -version = "0.2.0" +version = "0.2.2" authors = [ - { name="Ravi Jose Tristao Ramos", email="souoravi@gmail.com" }, { name="David Sehnal", email="david.sehnal@gmail.com" }, + { name="Ravi Jose Tristao Ramos", email="souoravi@gmail.com" }, ] description = "A library for handling BinaryCIF files." readme = "README.md" -license = { file="LICENSE" } -requires-python = ">=3.9" +license = "MIT" +license-files = ["LICENSE"] +requires-python = ">=3.9,<3.14" classifiers = [ "Programming Language :: Python :: 3", - "License :: OSI Approved :: MIT License", + "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", "Operating System :: OS Independent", ] +dependencies = [ + "msgpack>=1.0.3", + "numba>=0.56.2", + "numpy>=1.11.1", +] -[tool.black] +[dependency-groups] +dev = [ + "pre-commit>=3.0.0", +] + +[tool.ruff] +target-version = "py39" line-length = 120 -target-version = ['py39'] +indent-width = 4 + +[tool.ruff.lint] +select = ["E4", "E7", "E9", "F", "I"] diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index aade9d2..0000000 --- a/requirements.txt +++ /dev/null @@ -1,2 +0,0 @@ -numpy >= 1.11.1 -msgpack >= 1.0.3 \ No newline at end of file diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 6b4d10c..0000000 --- a/setup.cfg +++ /dev/null @@ -1,9 +0,0 @@ -[isort] -line_length=120 -include_trailing_comma=True -force_grid_wrap=0 -use_parentheses=True -multi_line_output=3 -skip_glob = - */__init__.py -src_paths = ["ciftools"] \ No newline at end of file diff --git a/setup.py b/setup.py deleted file mode 100644 index 2f7a8a2..0000000 --- a/setup.py +++ /dev/null @@ -1,12 +0,0 @@ -from setuptools import find_packages, setup - -setup( - name="CifTools", - version="0.2.0", - url="https://github.com/molstar/ciftools-python", - author="Ravi Jose Tristao Ramos, David Sehnal", - author_email="souoravi@gmail.com, david.sehnal@gmail.com", - description="A library for handling (Binary)CIF files.", - packages=find_packages(exclude=["tests"]), - install_requires=["numpy >= 1.11.1", "msgpack >= 1.0.3", "numba >= 0.56.2"], -) diff --git a/tests/_decoding.py b/tests/_decoding.py index 3bc3f21..71831b2 100644 --- a/tests/_decoding.py +++ b/tests/_decoding.py @@ -1,16 +1,19 @@ import unittest -import urllib.request +from pathlib import Path from ciftools.models.data import CIFValuePresenceEnum from ciftools.serialization import loads +test_folder = Path(__file__).parent / "fixtures" + class TestEncodings_Decoding(unittest.TestCase): def test(self): # TODO: set assert expectations print("mmCIF test") - data = urllib.request.urlopen("https://models.rcsb.org/1tqn.bcif").read() + bcif_path = test_folder / "1tqn.bcif" + data = bcif_path.read_bytes() parsed = loads(data, lazy=False) atom_site = parsed["1TQN"].atom_site @@ -32,9 +35,8 @@ def test(self): # print([[f"_{c.name}.{f}" for f in c.field_names] for c in parsed[0].categories.values()]) print("Volume Data test") - data = urllib.request.urlopen( - "https://ds.litemol.org/x-ray/1tqn/box/-22.367,-33.367,-21.634/-7.106,-10.042,-0.937?detail=1" - ).read() + bcif_path = test_folder / "x-ray_1tqn-cartn_-22.4_-33.4_-21.6_-7.1_-10_-0.9_d1.bcif" + data = bcif_path.read_bytes() parsed = loads(data) print([b.header for b in parsed.data_blocks]) diff --git a/tests/_encoding.py b/tests/_encoding.py index e48b1ba..113ab0d 100644 --- a/tests/_encoding.py +++ b/tests/_encoding.py @@ -3,6 +3,7 @@ from typing import List import numpy as np + from ciftools.binary.encoder import DELTA, INTEGER_PACKING, ComposeEncoders, FixedPoint from ciftools.models.writer import CIFCategoryDesc from ciftools.models.writer import CIFFieldDesc as Field @@ -103,7 +104,6 @@ def get_row_count(data: TestVolumeData) -> int: class TestEncodings_Encoding(unittest.TestCase): def test(self): - # test test_data = prepare_test_data(5, 3) # print("Original data: " + str(test_data.__dict__)) diff --git a/tests/byte_array.py b/tests/byte_array.py index 316a343..bb52954 100644 --- a/tests/byte_array.py +++ b/tests/byte_array.py @@ -2,6 +2,7 @@ import msgpack import numpy as np + from ciftools.binary.data_types import DataTypeEnum from ciftools.binary.decoder import decode_cif_data from ciftools.binary.encoder import BYTE_ARRAY diff --git a/tests/delta.py b/tests/delta.py index 9b45c3a..76e7630 100644 --- a/tests/delta.py +++ b/tests/delta.py @@ -2,13 +2,14 @@ import msgpack import numpy as np + from ciftools.binary.decoder import decode_cif_data from ciftools.binary.encoder import BYTE_ARRAY, DELTA, ComposeEncoders class TestEncodings_Delta(unittest.TestCase): def test(self): - test_arr = np.array([1, 1, 2, 2, 10, -10]) + test_arr = np.array([1, 1, 2, 2, 10, -10], dtype=np.int32) encoder = ComposeEncoders(DELTA, BYTE_ARRAY) diff --git a/tests/fixed_point.py b/tests/fixed_point.py index 6af536e..a92bb7d 100644 --- a/tests/fixed_point.py +++ b/tests/fixed_point.py @@ -2,13 +2,13 @@ import msgpack import numpy as np + from ciftools.binary.decoder import decode_cif_data from ciftools.binary.encoder import BYTE_ARRAY, DELTA, ComposeEncoders, FixedPoint class TestEncodings_FixedPoint(unittest.TestCase): def test(self): - test_suite = [ (np.random.rand(100) * 1000, 1), (np.random.rand(100) * 1000, 2), @@ -26,7 +26,6 @@ def test(self): class TestEncodings_FixedPointDelta(unittest.TestCase): def test(self): - test_suite = [ (np.random.rand(100) * 1000, 1), (np.random.rand(100) * 1000, 2), diff --git a/tests/fixtures/1tqn.bcif b/tests/fixtures/1tqn.bcif new file mode 100644 index 0000000..81af16b Binary files /dev/null and b/tests/fixtures/1tqn.bcif differ diff --git a/tests/fixtures/x-ray_1tqn-cartn_-22.4_-33.4_-21.6_-7.1_-10_-0.9_d1.bcif b/tests/fixtures/x-ray_1tqn-cartn_-22.4_-33.4_-21.6_-7.1_-10_-0.9_d1.bcif new file mode 100644 index 0000000..51a47c6 Binary files /dev/null and b/tests/fixtures/x-ray_1tqn-cartn_-22.4_-33.4_-21.6_-7.1_-10_-0.9_d1.bcif differ diff --git a/tests/integer_packing.py b/tests/integer_packing.py index d23e0b9..c572b76 100644 --- a/tests/integer_packing.py +++ b/tests/integer_packing.py @@ -2,6 +2,7 @@ import msgpack import numpy as np + from ciftools.binary.decoder import decode_cif_data from ciftools.binary.encoder import INTEGER_PACKING diff --git a/tests/interval_quantization.py b/tests/interval_quantization.py index c15970d..75e1e4e 100644 --- a/tests/interval_quantization.py +++ b/tests/interval_quantization.py @@ -2,6 +2,7 @@ import msgpack import numpy as np + from ciftools.binary.data_types import DataTypeEnum from ciftools.binary.decoder import decode_cif_data from ciftools.binary.encoder import BYTE_ARRAY, ComposeEncoders, IntervalQuantization @@ -9,7 +10,6 @@ class TestEncodings_IntervalQuantization(unittest.TestCase): def test(self): - test_suite = [ (np.random.rand(100) * 100, 100, DataTypeEnum.Uint8), (np.random.rand(100) * 100, 2**8, DataTypeEnum.Uint8), diff --git a/tests/molstar/.gitignore b/tests/molstar/.gitignore index 2a53041..2e6ba49 100644 --- a/tests/molstar/.gitignore +++ b/tests/molstar/.gitignore @@ -1,2 +1,2 @@ node_modules -*.cif \ No newline at end of file +*.cif diff --git a/tests/molstar/README.md b/tests/molstar/README.md index d783f2e..298e505 100644 --- a/tests/molstar/README.md +++ b/tests/molstar/README.md @@ -4,4 +4,4 @@ To convert the lattice generated by the Python tests, run ``` npm node_modules/.bin/cif2bcif ../ciftools/tests/lattices.bcif lattices.cif -``` \ No newline at end of file +``` diff --git a/tests/molstar/index.js b/tests/molstar/index.js index afc3ba9..0873aaa 100644 --- a/tests/molstar/index.js +++ b/tests/molstar/index.js @@ -12,4 +12,4 @@ async function test() { console.log(annotation); } -test() \ No newline at end of file +test() diff --git a/tests/run_length.py b/tests/run_length.py index 70afccb..6bbccec 100644 --- a/tests/run_length.py +++ b/tests/run_length.py @@ -2,14 +2,14 @@ import msgpack import numpy as np + from ciftools.binary.decoder import decode_cif_data from ciftools.binary.encoder import BYTE_ARRAY, RUN_LENGTH, ComposeEncoders class TestEncodings_RunLength(unittest.TestCase): def test(self): - - suite = [np.array([-3] * 9 + [1] * 10 + [2] * 11 + [3] * 12), np.arange(10)] + suite = [np.array([-3] * 9 + [1] * 10 + [2] * 11 + [3] * 12, dtype=np.int32), np.arange(10, 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