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

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.
 

.build_rtd_docs/styleguide.md

@@ -82,7 +82,7 @@
 # Settings for GitHub actions integration
 if on_rtd:
     extensions.append("rtds_action")
-    rtds_action_github_repo = "MODFLOW-USGS/modflow6"
+    rtds_action_github_repo = "MODFLOW-ORG/modflow6"
     rtds_action_path = "."
     rtds_action_artifact_prefix = "rtd-files-for-"
     rtds_action_github_token = os.environ.get("GITHUB_TOKEN", None)

.doc/conf.py

@@ -10,9 +10,9 @@ Checklist of items for pull request
 - [ ] Formatted new and modified Fortran source files with `fprettify`
 - [ ] Added doxygen comments to new and modified procedures
 - [ ] Updated meson files, makefiles, and Visual Studio project files for new source files
-- [ ] Updated [definition files](/MODFLOW-USGS/modflow6/tree/develop/doc/mf6io/mf6ivar)
-- [ ] Updated [develop.tex](/MODFLOW-USGS/modflow6/doc/ReleaseNotes/develop.tex) with a plain-language description of the bug fix, change, feature; required for changes that may affect users
-- [ ] Updated [input and output guide](/MODFLOW-USGS/modflow6/doc/mf6io)
+- [ ] Updated [definition files](/MODFLOW-ORG/modflow6/tree/develop/doc/mf6io/mf6ivar)
+- [ ] Updated [develop.toml](/MODFLOW-ORG/modflow6/doc/ReleaseNotes/develop.toml) with a plain-language description of the bug fix, change, feature; required for changes that may affect users
+- [ ] Updated [input and output guide](/MODFLOW-ORG/modflow6/doc/mf6io)
 - [ ] Removed checklist items not relevant to this pull request
 
-For additional information see [instructions for contributing](/MODFLOW-USGS/modflow6/.github/CONTRIBUTING.md) and [instructions for developing](/MODFLOW-USGS/modflow6/.github/DEVELOPER.md).
+For additional information see [instructions for contributing](/MODFLOW-ORG/modflow6/.github/CONTRIBUTING.md) and [instructions for developing](/MODFLOW-ORG/modflow6/.github/DEVELOPER.md).

.github/PULL_REQUEST_TEMPLATE.md

@@ -14,9 +14,6 @@ runs:
         cmakeVersion: latest
         ninjaVersion: latest
 
-    - name: Setup 7-zip
-      uses: milliewalky/setup-7-zip@v1
-
     - name: Download NetCDF-C
       shell: bash
       run: |
@@ -40,3 +37,10 @@ runs:
       shell: cmd
       run: |
         "%ONEAPI_ROOT%\setvars.bat" intel64 vs2022 && "%TEMP%\compile_netcdf.bat"
+
+    - name: Update path for NetCDF libs
+      shell: bash
+      run: |
+        echo "$GITHUB_WORKSPACE/netcdf/netCDF4.9.2-NC4-64/bin" >> $GITHUB_PATH
+        echo "$GITHUB_WORKSPACE/netcdf/netCDF4.9.2-NC4-64/lib" >> $GITHUB_PATH
+        echo "$GITHUB_WORKSPACE/netcdf/netcdf-fortran-4.6.1/build/fortran" >> $GITHUB_PATH

.github/actions/build-netcdf-win/action.yml

@@ -10,20 +10,11 @@ runs:
         version: 13
 
     - name: Checkout PETSc
-      if: runner.os == 'Linux'
       uses: actions/checkout@v4
       with:
         repository: petsc/petsc
         path: petsc
-        ref: release
-
-    - name: Checkout PETSc
-      if: runner.os == 'macOS'
-      uses: actions/checkout@v4
-      with:
-        repository: petsc/petsc
-        path: petsc
-        ref: v3.22.1
+        ref: v3.22.5
 
     - name: Configure environment
       shell: bash
@@ -57,7 +48,7 @@ runs:
       run: |
         brew install netcdf-fortran
         nc-config --all
-        nf-config
+        nf-config --all
 
     - name: Build modflow6
       shell: bash
@@ -73,6 +64,13 @@ runs:
       working-directory: modflow6
       run: cat builddir/meson-logs/meson-log.txt
 
+    - name: Build mf5to6
+      shell: bash
+      working-directory: modflow6
+      run: |
+        pixi run setup-mf5to6 builddir
+        pixi run build-mf5to6 builddir
+
     - name: Update flopy
       shell: bash
       working-directory: modflow6

.github/actions/test-extended/action.yml

@@ -3,3 +3,5 @@ cd "%GITHUB_WORKSPACE%\modflow6"
 pixi run setup -Dextended=true builddir
 pixi run build builddir
 pixi run test builddir
+pixi run setup-mf5to6 builddir
+pixi run build-mf5to6 builddir