Merge pull request #2320 from MODFLOW-ORG/v6.6.2

Release 6.6.2

Author: wpbonelli

.build_rtd_docs/Doxyfile

@@ -37,7 +37,7 @@ PROJECT_NAME           = "MODFLOW 6"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = "version 6.6.1"
+PROJECT_NUMBER         = "version 6.6.2"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

.build_rtd_docs/MAINPAGE.md

@@ -2,6 +2,6 @@
 
 The documentation here is extracted from the source code by [doxygen](https://www.doxygen.nl/index.html).
 
-The source code repository is hosted [on GitHub](https://github.com/MODFLOW-USGS/modflow6).
+The source code repository is hosted [on GitHub](https://github.com/MODFLOW-ORG/modflow6).
 
 This documentation is intended for MODFLOW 6 contributors and users of the MODFLOW 6 library/API. MODFLOW 6 usage documentation can be found [on ReadTheDocs](https://modflow6.readthedocs.io/en/latest/).

.build_rtd_docs/conf.py

@@ -44,51 +44,64 @@
 # -- import version from doc/version.py -------------------------------------
 from version import __version__
 
-# -- copy run-time comparison markdown --------------------------------------
-print("Copy the run-time comparison table")
 dstdir = "_mf6run"
-fpth = "run-time-comparison.md"
-src = os.path.join("..", "distribution", fpth)
-dst = os.path.join(dstdir, fpth)
-# clean up an existing _mf6run directory
 if os.path.isdir(dstdir):
     shutil.rmtree(dstdir)
-# make the _mf6run directory
 os.makedirs(dstdir)
-# copy the file
+
+print(f"Copy run-time comparison table to {dstdir}")
+fpth = "run-time-comparison.md"
+src = os.path.join("..", "distribution", fpth)
+dst = os.path.join(dstdir, fpth)
 shutil.copy(src, dst)
 
-# -- copy developer docs
 dstdir = "_dev"
-fpth = "DEVELOPER.md"
-src = os.path.join("..", fpth)
-dst = os.path.join(dstdir, fpth.lower())
-# clean up an existing _mf6run directory
 if os.path.isdir(dstdir):
     shutil.rmtree(dstdir)
-# make the directory
 os.makedirs(dstdir)
-# copy the file
+
+print(f"Copy developer docs to {dstdir}")
+fpth = "DEVELOPER.md"
+src = os.path.join("..", fpth)
+dst = os.path.join(dstdir, fpth)
 shutil.copy(src, dst)
 
-# -- copy contributor docs
 fpth = "CONTRIBUTING.md"
 src = os.path.join("..", fpth)
-dst = os.path.join(dstdir, fpth.lower())
+dst = os.path.join(dstdir, fpth)
 shutil.copy(src, dst)
 
-# -- copy style guide
 fpth = "styleguide.md"
 src = os.path.join(fpth)
 dst = os.path.join(dstdir, fpth)
 shutil.copy(src, dst)
 
-# -- copy DFN spec
 fpth = "readme.md"
 src = os.path.join("..", "doc", "mf6io", "mf6ivar", fpth)
 dst = os.path.join(dstdir, "dfn.md")
 shutil.copy(src, dst)
 
+fpth = "EXTENDED.md"
+src = os.path.join("..", fpth)
+dst = os.path.join(dstdir, fpth)
+shutil.copy(src, dst)
+
+fpth = "CODE_OF_CONDUCT.md"
+src = os.path.join("..", fpth)
+dst = os.path.join(dstdir, fpth)
+shutil.copy(src, dst)
+
+dstdir = "_migration"
+if os.path.isdir(dstdir):
+    shutil.rmtree(dstdir)
+os.makedirs(dstdir)
+
+print(f"Copy migration guides to {dstdir}")
+fpth = "mf6_6_0_prt_migration_guide.md"
+src = os.path.join(fpth)
+dst = os.path.join(dstdir, fpth)
+shutil.move(src, dst)
+
 # -- build the deprecations table --------------------------------------------
 print("Build the deprecations markdown table")
 pth = os.path.join("..", "doc", "mf6io", "mf6ivar")
@@ -168,11 +181,13 @@
     "nbsphinx_link",
     "myst_parser",
     "sphinx_markdown_tables",
+    "sphinxcontrib.mermaid",
 ]
 
+myst_fence_as_directive = ["mermaid"]
+
 # # Tell sphinx what the pygments highlight language should be.
 # highlight_language = 'fortran'
-
 source_suffix = {".rst": "restructuredtext", ".md": "markdown"}
 
 # Add any paths that contain templates here, relative to this directory.
@@ -203,7 +218,7 @@
 ]
 
 # html_theme_options = {
-#     "github_url": "https://github.com/MODFLOW-USGS/modflow6",
+#     "github_url": "https://github.com/MODFLOW-ORG/modflow6",
 #     "use_edit_page_button": False
 # }
 

.build_rtd_docs/dev.rst

@@ -1,13 +1,15 @@
 Developer Guide
 ---------------
 
-This section includes developer instructions and conventions.
+This section contains developer documentation, including contributor conventions, instructions for common tasks, internal specifications, and more.
 
 .. toctree::
    :maxdepth: 1
    :glob:
 
-   _dev/contributing.md
-   _dev/developer.md
+   _dev/CODE_OF_CONDUCT.md
+   _dev/CONTRIBUTING.md
+   _dev/DEVELOPER.md
+   _dev/EXTENDED.md
    _dev/styleguide.md
    _dev/dfn.md

.build_rtd_docs/index.rst

@@ -11,9 +11,9 @@ Contents:
 .. toctree::
    :maxdepth: 2
 
-   API Reference <https://modflow-usgs.github.io/modflow6/>
+   API Reference <https://MODFLOW-ORG.github.io/modflow6/>
    _mf6run/run-time-comparison.md
    _mf6run/deprecations.md
    mf6io
    dev
-
+   migration

…leTracker/mf6_6_0_prt_migration_guide.md …_rtd_docs/mf6_6_0_prt_migration_guide.mdsrc/Solution/ParticleTracker/mf6_6_0_prt_migration_guide.md renamed to .build_rtd_docs/mf6_6_0_prt_migration_guide.md src/Solution/ParticleTracker/mf6_6_0_prt_migration_guide.md renamed to .build_rtd_docs/mf6_6_0_prt_migration_guide.md

@@ -2,7 +2,7 @@ Input Guide
 -----------
 
 The latest version of the complete MODFLOW 6 input/output guide can be found
-`here <https://github.com/MODFLOW-USGS/modflow6-nightly-build/releases/>`_.
+`here <https://github.com/MODFLOW-ORG/modflow6-nightly-build/releases/>`_.
 This section enumerates and describes MODFLOW 6 input files.
 
 Simulation

.build_rtd_docs/mf6io.rst

@@ -0,0 +1,10 @@
+Migration Guides
+----------------
+
+This section includes version-specific migration guides for particular models and/or capabilities.
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+
+   _migration/mf6_6_0_prt_migration_guide

.build_rtd_docs/migration.rst

@@ -2,6 +2,7 @@ numpy
 bmipy
 sphinx>=4
 sphinx_markdown_tables
+sphinxcontrib-mermaid
 nbsphinx
 nbsphinx_link
 ipython

.build_rtd_docs/requirements.rtd.txt

@@ -1,4 +1,4 @@
-# Fortran Style Guide
+# MODFLOW 6 Fortran style guide
 
 The goal of this guide is to provide a standard for MODFLOW 6 contributors to follow, in pursuit of consistent, readable, well-organized, and unsurprising source code.