Merge pull request #2216 from MODFLOW-USGS/v6.6.1

Release 6.6.1
MODFLOW-USGS · Feb 10, 2025 · 056cf5c · 056cf5c
2 parents 799088c + 8e717f3
commit 056cf5c
Show file tree

Hide file tree

Showing 291 changed files with 24,938 additions and 42,523 deletions.
diff --git a/.build_rtd_docs/Doxyfile b/.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 6.6.0"
+PROJECT_NUMBER         = "version 6.6.1"
 
 # 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

diff --git a/.codespellrc b/.codespellrc
@@ -1,3 +1,3 @@
 [codespell]
-skip = *.pdf,*.grb,*.bib,*.bst,*.log,./builddir,./src/Utilities/Libraries,./utils/mf5to6,./doc/ReleaseNotes/previous
+skip = *.pdf,*.grb,*.bib,*.bst,*.log,./builddir,./src/Utilities/Libraries,./utils/mf5to6,./doc/ReleaseNotes/previous,pixi.*
 ignore-words = .codespell.ignore
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -51,7 +51,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
 
       - name: Check Fortran source formatting
         run: pixi run check-format
@@ -66,7 +66,7 @@ jobs:
         run: pixi run check-python-format
 
       - name: Check CITATION.cff
-        uses: dieghernan/cff-validator@v3
+        run: pixi run check-citations
 
   build:
     name: Build
@@ -87,7 +87,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
 
       - name: Setup MF6
         run: pixi run setup -Dwerror=true builddir
@@ -132,7 +132,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
           manifest-path: "modflow6/pixi.toml"
 
       - name: Custom pixi install
@@ -249,7 +249,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
           manifest-path: "modflow6/pixi.toml"
 
       - name: Custom pixi install
@@ -259,11 +259,8 @@ jobs:
       - name: Set LDFLAGS (macOS)
         if: runner.os == 'macOS'
         run: |
-          os_ver=$(sw_vers -productVersion | cut -d'.' -f1)
-          if (( "$os_ver" > 12 )); then
-            ldflags="$LDFLAGS -Wl,-ld_classic"
-            echo "LDFLAGS=$ldflags" >> $GITHUB_ENV
-          fi
+          ldflags="$LDFLAGS -Wl,-ld_classic"
+          echo "LDFLAGS=$ldflags" >> $GITHUB_ENV
 
       - name: Build MF6
         working-directory: modflow6
@@ -412,7 +409,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
           manifest-path: "modflow6/pixi.toml"
 
       - name: Custom pixi install
@@ -515,7 +512,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
           manifest-path: "modflow6/pixi.toml"
 
       - name: Custom pixi install
@@ -547,5 +544,5 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@v4
         with:
-          name: failed-${{ matrix.os }}
+          name: failed-${{ matrix.os }}-ext
           path: modflow6/autotest/.failed
diff --git a/.github/workflows/compilers.yml b/.github/workflows/compilers.yml
@@ -18,29 +18,28 @@ jobs:
           - {os: ubuntu-22.04, compiler: gcc, version: 11}
           - {os: ubuntu-22.04, compiler: gcc, version: 12}
           - {os: ubuntu-22.04, compiler: gcc, version: 13}
+          - {os: ubuntu-22.04, compiler: gcc, version: 14}
+          - {os: ubuntu-24.04, compiler: gcc, version: 11}
+          - {os: ubuntu-24.04, compiler: gcc, version: 12}
+          - {os: ubuntu-24.04, compiler: gcc, version: 13}
+          - {os: ubuntu-24.04, compiler: gcc, version: 14}
           - {os: macos-13, compiler: gcc, version: 11}
           - {os: macos-13, compiler: gcc, version: 12}
           - {os: macos-13, compiler: gcc, version: 13}
           - {os: macos-14, compiler: gcc, version: 11}
           - {os: macos-14, compiler: gcc, version: 12}
           - {os: macos-14, compiler: gcc, version: 13}
+          - {os: macos-14, compiler: gcc, version: 14}
           - {os: windows-2022, compiler: gcc, version: 11}
           - {os: windows-2022, compiler: gcc, version: 12}
           - {os: windows-2022, compiler: gcc, version: 13}
           # ifx
-          - {os: ubuntu-22.04, compiler: intel, version: 2024.1}
+          - {os: ubuntu-22.04, compiler: intel, version: "2025.0"}
+          - {os: ubuntu-22.04, compiler: intel, version: "2024.1"}
           - {os: ubuntu-22.04, compiler: intel, version: "2024.0"}
-          - {os: ubuntu-22.04, compiler: intel, version: 2023.2}
-          - {os: ubuntu-22.04, compiler: intel, version: 2023.1}
-          - {os: ubuntu-22.04, compiler: intel, version: "2023.0"}
-          - {os: ubuntu-22.04, compiler: intel, version: 2022.2.1}
-          - {os: ubuntu-22.04, compiler: intel, version: 2022.2}
-          - {os: windows-2022, compiler: intel, version: 2024.1}
+          - {os: windows-2022, compiler: intel, version: "2025.0"}
+          - {os: windows-2022, compiler: intel, version: "2024.1"}
           - {os: windows-2022, compiler: intel, version: "2024.0"}
-          - {os: windows-2022, compiler: intel, version: 2023.2}
-          - {os: windows-2022, compiler: intel, version: 2023.1}
-          - {os: windows-2022, compiler: intel, version: "2023.0"}
-          - {os: windows-2022, compiler: intel, version: 2022.2}
           # ifort
           - {os: ubuntu-22.04, compiler: intel-classic, version: "2021.10"}
           - {os: ubuntu-22.04, compiler: intel-classic, version: 2021.9}
@@ -97,13 +96,19 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
           manifest-path: "modflow6/pixi.toml"
 
       - name: Custom pixi install
         working-directory: modflow6
         run: pixi run install
 
+      - name: Set LDFLAGS (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          ldflags="$LDFLAGS -Wl,-ld_classic"
+          echo "LDFLAGS=$ldflags" >> $GITHUB_ENV
+
       - name: Build modflow6
         working-directory: modflow6
         run: |
@@ -117,7 +122,7 @@ jobs:
 
       - name: Upload build log
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: meson-log.txt
           path: modflow6/builddir/meson-logs/meson-log.txt
@@ -176,9 +181,9 @@ jobs:
 
       - name: Upload reports
         if: success() || failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: compat
+          name: compat-${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.version }}
           path: compat/*.csv
 
   report:
@@ -203,10 +208,11 @@ jobs:
         run: pip install tabulate pandas
 
       - name: Download reports
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
-          name: compat
+          pattern: compat-*
           path: .github/compat/new
+          merge-multiple: true
 
       - name: Concatenate reports
         working-directory: .github/compat
@@ -226,7 +232,7 @@ jobs:
 
       # only upload wide CSVs and Markdown tables
       - name: Upload artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: compat
           path: |

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -28,7 +28,7 @@ jobs:
 
       - uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
 
       - name: Check spelling
         run: pixi run check-spelling
@@ -65,7 +65,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
           manifest-path: "modflow6/pixi.toml"
 
       - name: Custom pixi install
@@ -145,7 +145,7 @@ jobs:
         run: cat run-time-comparison.md
 
       - name: Upload benchmarks
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: run-time-comparison
           path: modflow6/distribution/run-time-comparison.md
@@ -159,7 +159,7 @@ jobs:
         run: cat deprecations.md
 
       - name: Upload deprecations
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: deprecations
           path: modflow6/doc/mf6io/mf6ivar/md/deprecations.md
@@ -169,7 +169,7 @@ jobs:
         run: pixi run sphinx
 
       - name: Upload RTD files
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: rtd-files-for-${{ github.sha }}
           path: |
@@ -186,7 +186,7 @@ jobs:
         run: pixi run build-docs
 
       - name: Upload PDF documents
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: mf6io.pdf
           path: |
@@ -237,7 +237,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
 
       - name: Custom pixi install
         run: pixi run install
@@ -253,14 +253,15 @@ jobs:
         working-directory: ${{env.working-directory}}
 
       - name: upload pages artifact
-        uses: actions/upload-pages-artifact@v2
+        uses: actions/upload-pages-artifact@v3
         with:
           path: ${{env.working-directory}}/html
 
   pages_deploy:
     if: github.ref == 'refs/heads/develop' && github.event_name == 'push'
     needs: doxygen_build
     permissions:
+      actions: read
       pages: write
       id-token: write
     environment:
@@ -270,4 +271,4 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v3
+        uses: actions/deploy-pages@v4
diff --git a/.github/workflows/large.yml b/.github/workflows/large.yml
@@ -69,7 +69,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
           manifest-path: "modflow6/pixi.toml"
 
       - name: Custom pixi install

diff --git a/.github/workflows/pixi_auto_update.yml b/.github/workflows/pixi_auto_update.yml
@@ -14,7 +14,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
           cache: false
 
       - name: Update pixi lock file

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -110,7 +110,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
           manifest-path: "modflow6/pixi.toml"
 
       - name: Custom pixi install
@@ -260,7 +260,7 @@ jobs:
           if exist rebuilt rd /s /q downloaded
 
       - name: Upload binaries
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: bin-${{ steps.ostag.outputs.ostag }}
           path: modflow6/bin
@@ -427,7 +427,7 @@ jobs:
           echo "ostag=$ostag" >> $GITHUB_OUTPUT
 
       - name: Download pre-built binaries
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: bin-${{ steps.ostag.outputs.ostag }}
           path: bin
@@ -464,7 +464,7 @@ jobs:
           cat md/deprecations.md
 
       - name: Upload deprecations
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: deprecations
           path: modflow6/doc/mf6io/mf6ivar/md/deprecations.md
@@ -493,7 +493,7 @@ jobs:
           mv "doc/ReleaseNotes.pdf" "doc/release.pdf"
 
       - name: Upload documentation artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: doc
           path: doc
@@ -572,7 +572,7 @@ jobs:
           echo "ostag=$ostag" >> $GITHUB_OUTPUT
 
       - name: Download artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           path: ${{ needs.build.outputs.distname }}_${{ steps.ostag.outputs.ostag }}
 
@@ -682,14 +682,14 @@ jobs:
           fi
 
       - name: Upload distribution
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: "${{ needs.build.outputs.distname }}_${{ steps.ostag.outputs.ostag }}"
           path: "${{ needs.build.outputs.distname }}_${{ steps.ostag.outputs.ostag }}.zip"
 
       - name: Upload release notes
         if: runner.os == 'Linux'
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: release_notes
           path: "${{ needs.build.outputs.distname }}_${{ steps.ostag.outputs.ostag }}/doc/release.pdf"

diff --git a/.github/workflows/release_dispatch.yml b/.github/workflows/release_dispatch.yml
@@ -252,7 +252,7 @@ jobs:
           cache-environment: true
 
       - name: Download artifacts
-        uses: dawidd6/action-download-artifact@v7
+        uses: dawidd6/action-download-artifact@v8
 
       - name: Draft release
         working-directory: modflow6

diff --git a/CITATION.cff b/CITATION.cff
@@ -2,8 +2,8 @@ cff-version: 1.2.0
 message: If you use this software, please cite the software itself.
 type: software
 title: MODFLOW 6 Modular Hydrologic Model
-version: 6.6.0
-date-released: '2024-12-19'
+version: 6.6.1
+date-released: '2025-02-10'
 doi: 10.5066/F76Q1VQV
 abstract: MODFLOW 6 is an object-oriented program and framework developed to provide
   a platform for supporting multiple models and multiple types of models within the