Merge develop into main

.github/workflows/build_workflow.yml

@@ -22,12 +22,24 @@ jobs:
     name: test mpas_analysis - python ${{ matrix.python-version }}
     runs-on: ubuntu-latest
     timeout-minutes: 20
-    defaults:
-      run:
-        shell: bash -l {0}
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        include:
+          - python-version: "3.10"
+            pixi-environment: py310
+            variant-file: ci/python3.10.yaml
+          - python-version: "3.11"
+            pixi-environment: py311
+            variant-file: ci/python3.11.yaml
+          - python-version: "3.12"
+            pixi-environment: py312
+            variant-file: ci/python3.12.yaml
+          - python-version: "3.13"
+            pixi-environment: py313
+            variant-file: ci/python3.13.yaml
+          - python-version: "3.14"
+            pixi-environment: py314
+            variant-file: ci/python3.14.yaml
       fail-fast: false
     steps:
       - id: skip_check
@@ -37,53 +49,68 @@ jobs:
           paths_ignore: ${{ env.PATHS_IGNORE }}
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
-        name: Cache Conda
-        uses: actions/cache@v4
-        env:
-          # Increase this value to reset cache if conda-dev-spec.template has not changed in the workflow
-          CACHE_NUMBER: 0
+        name: Set up Pixi
+        uses: prefix-dev/setup-pixi@v0.9.5
         with:
-          path: ~/conda_pkgs_dir_py${{ matrix.python-version }}
-          key:
-            ${{ runner.os }}-${{ matrix.python-version }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('dev-spec.txt,pyproject.toml') }}
-
-      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
-        name: Set up Conda Environment
-        uses: mamba-org/setup-micromamba@v2
-        with:
-          environment-name: mpas_analysis_dev
-          init-shell: bash
-          condarc: |
-            channel_priority: strict
-            channels:
-                - conda-forge
-          create-args: >-
-            python=${{ matrix.python-version }}
-
-      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
-        name: Install mpas_analysis
-        run: |
-          conda install -y --file dev-spec.txt \
-            python=${{ matrix.python-version }}
-          python -m pip install --no-deps --no-build-isolation -vv -e .
+          environments: ${{ matrix.pixi-environment }}
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Run Tests
         env:
-           CHECK_IMAGES: False
+          CHECK_IMAGES: "False"
         run: |
           set -e
-          pip check
-          pytest --pyargs mpas_analysis
-          mpas_analysis --help
-          download_analysis_data --help
+          pixi run -e ${{ matrix.pixi-environment }} python -m pip check
+          pixi run -e ${{ matrix.pixi-environment }} pytest --pyargs mpas_analysis
+          pixi run -e ${{ matrix.pixi-environment }} mpas_analysis --help
+          pixi run -e ${{ matrix.pixi-environment }} download_analysis_data --help
 
-      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' && matrix.python-version == '3.14' }}
         name: Build Sphinx Docs
         run: |
-          cd docs
-          DOCS_VERSION=test make versioned-html
+          pixi run -e ${{ matrix.pixi-environment }} bash -lc '
+            cd docs
+            DOCS_VERSION=test make versioned-html
+          '
+
+  package:
+    name: build package - python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    strategy:
+      matrix:
+        include:
+          - python-version: "3.10"
+            pixi-environment: py310
+            variant-file: ci/python3.10.yaml
+          - python-version: "3.11"
+            pixi-environment: py311
+            variant-file: ci/python3.11.yaml
+          - python-version: "3.12"
+            pixi-environment: py312
+            variant-file: ci/python3.12.yaml
+          - python-version: "3.13"
+            pixi-environment: py313
+            variant-file: ci/python3.13.yaml
+          - python-version: "3.14"
+            pixi-environment: py314
+            variant-file: ci/python3.14.yaml
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Set up Pixi
+        uses: prefix-dev/setup-pixi@v0.9.5
+        with:
+          environments: ${{ matrix.pixi-environment }}
+
+      - name: Build Conda Package with rattler-build
+        run: |
+          pixi run -e ${{ matrix.pixi-environment }} \
+            rattler-build build \
+            -m ${{ matrix.variant-file }} \
+            -r ci/recipe/recipe.yaml \
+            --output-dir rattler-build-output

.github/workflows/docs_workflow.yml

@@ -10,98 +10,68 @@ on:
     types: [published]
 
 env:
-  PYTHON_VERSION: "3.13"
+  PYTHON_VERSION: "3.14"
 
 jobs:
   publish-docs:
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -l {0}
     timeout-minutes: 20
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           persist-credentials: false
           fetch-depth: 0
 
-      - name: Cache Conda
-        uses: actions/cache@v4
-        env:
-          # Increase this value to reset cache if deploy/conda-dev-spec.template has not changed in the workflow
-          CACHE_NUMBER: 0
+      - name: Set up Pixi
+        uses: prefix-dev/setup-pixi@v0.9.5
         with:
-          path: ~/conda_pkgs_dir
-          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('dev-spec.txt') }}
-
-      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
-        name: Set up Conda Environment
-        uses: mamba-org/setup-micromamba@v2
-        with:
-          environment-name: mpas_analysis_dev
-          init-shell: bash
-          condarc: |
-            channel_priority: strict
-            channels: 
-                - conda-forge
-          create-args: >-
-            python=${{ env.PYTHON_VERSION }}
-
-      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
-        name: Install mpas_analysis
-        run: |
-          git config --global url."https://github.com/".insteadOf "git@github.com:"
-          conda install -y --file dev-spec.txt \
-            python=${{ env.PYTHON_VERSION }}
-          python -m pip install -vv --no-deps --no-build-isolation -e .
+          environments: py314
 
       - name: Build Sphinx Docs
         run: |
           set -e
-          pip check
-          mpas_analysis sync diags --help
-          cd docs
-          DOCS_VERSION=${{ github.ref_name }} make versioned-html
+          git config --global url."https://github.com/".insteadOf "git@github.com:"
+          pixi run -e py314 python -m pip check
+          pixi run -e py314 mpas_analysis sync diags --help
+          pixi run -e py314 bash -lc '
+            cd docs
+            DOCS_VERSION=${{ github.ref_name }} make versioned-html
+          '
+
       - name: Copy Docs and Commit
         run: |
           set -e
-          pip check
-          mpas_analysis sync diags --help
-          cd docs
-          # gh-pages branch must already exist
-          git clone https://github.com/MPAS-Dev/MPAS-Analysis.git --branch gh-pages --single-branch gh-pages
+          pixi run -e py314 bash -lc '
+            cd docs
+            # gh-pages branch must already exist
+            git clone https://github.com/MPAS-Dev/MPAS-Analysis.git --branch gh-pages --single-branch gh-pages
 
-          # Only replace docs in a directory with the destination branch name with latest changes. Docs for
-          # releases should be untouched.
-          rm -rf gh-pages/${{ github.ref_name }}
+            # Only replace docs in a directory with the destination branch name with latest changes. Docs for
+            # releases should be untouched.
+            rm -rf gh-pages/${{ github.ref_name }}
 
-          # don't clobber existing release versions (in case we retroactively fixed them)
-          cp -r _build/html/${{ github.ref_name }} gh-pages/
+            # do not clobber existing release versions if they were updated manually
+            cp -r _build/html/${{ github.ref_name }} gh-pages/
 
-          mkdir -p gh-pages/shared
-          cp shared/version-switcher.js gh-pages/shared/version-switcher.js
+            mkdir -p gh-pages/shared
+            cp shared/version-switcher.js gh-pages/shared/version-switcher.js
 
-          # Update the list of versions with all versions in the gh-pages directory.
-          python generate_versions_json.py
+            # Update the list of versions with all versions in the gh-pages directory.
+            python generate_versions_json.py
+
+            cd gh-pages
+            touch .nojekyll
+            printf "<meta http-equiv=\"refresh\" content=\"0; url=./develop/index.html\" />" > index.html
+            git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+            git config --local user.name "github-actions[bot]"
+            git add .
+            git commit -m "Update documentation" -a || true
+          '
 
-          # Make sure we're in the gh-pages directory.
-          cd gh-pages
-          # Create `.nojekyll` (if it doesn't already exist) for proper GH Pages configuration.
-          touch .nojekyll
-          # Add `index.html` to point to the `develop` branch automatically.
-          printf '<meta http-equiv="refresh" content="0; url=./develop/index.html" />' > index.html
-          # Configure git using GitHub Actions credentials.
-          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
-          git config --local user.name "github-actions[bot]"
-          # The second command will fail if no changes were present, so we ignore it
-          git add .
-          git commit -m "Update documentation" -a || true
       - name: Push Changes
         uses: ad-m/github-push-action@master
         with:
           branch: gh-pages
           directory: docs/gh-pages
           github_token: ${{ secrets.GITHUB_TOKEN }}
           force: true
-

.gitignore

@@ -93,6 +93,8 @@ ENV/
 .ropeproject
 
 .DS_Store
+.pixi/
+pixi.lock
 
 # test suites
 /anvil_test_suite/
@@ -101,4 +103,7 @@ ENV/
 /compy_test_suite/
 
 # vscode settings
-.vscode/
+.vscode/
+
+# codex
+.codex

ci/python3.10.yaml

@@ -1,5 +1,5 @@
 channel_sources:
-- conda-forge,defaults
+- conda-forge
 pin_run_as_build:
   python:
     min_pin: x.x

ci/python3.11.yaml

@@ -1,5 +1,5 @@
 channel_sources:
-- conda-forge,defaults
+- conda-forge
 pin_run_as_build:
   python:
     min_pin: x.x

ci/python3.12.yaml

@@ -1,5 +1,5 @@
 channel_sources:
-- conda-forge,defaults
+- conda-forge
 pin_run_as_build:
   python:
     min_pin: x.x

ci/python3.13.yaml

@@ -1,5 +1,5 @@
 channel_sources:
-- conda-forge,defaults
+- conda-forge
 pin_run_as_build:
   python:
     min_pin: x.x

ci/python3.14.yaml

@@ -0,0 +1,8 @@
+channel_sources:
+- conda-forge
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.14.* *_cp314