Merge branch 'open-atmos:main' into development

.github/workflows/pdoc.yml

@@ -0,0 +1,50 @@
+name: pdoc
+
+defaults:
+  run:
+    shell: bash
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  schedule:
+    - cron: '0 13 * * 4'
+
+jobs:
+  pdoc:
+    strategy:
+      matrix:
+        platform: [ubuntu-latest, macos-latest, windows-latest]
+    runs-on: ${{ matrix.platform }}
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: recursive
+          persist-credentials: false
+      - uses: actions/setup-python@v5.2.0
+        with:
+          python-version: 3.9
+      - env:
+          JUPYTER_PLATFORM_DIRS: 1
+        run: |
+          pip install pdoc nbformat gitpython
+          pip install -e . -e ./examples
+          python -We docs/generate_html.py . .
+
+          python - <<EOF
+          import glob, nbformat
+          for notebook_path in glob.glob('examples/PyMPDATA_examples/*/*.ipynb'):
+            with open(notebook_path, encoding="utf8") as fin:
+              with open(notebook_path + ".badges.md", 'w') as fout:
+                fout.write(nbformat.read(fin, nbformat.NO_CONVERT).cells[0].source)
+          EOF
+
+          PDOC_ALLOW_EXEC=1 python -We -m pdoc -o html PyMPDATA examples/PyMPDATA_examples -t docs/templates --math
+      - if: ${{ github.ref == 'refs/heads/main' && matrix.platform == 'ubuntu-latest' }}
+        uses: JamesIves/github-pages-deploy-action@4.1.1
+        with:
+          branch: pdoc
+          folder: html
+          clean: true

.github/workflows/projects.yml

@@ -0,0 +1,19 @@
+name: Add new issues and pull requests to project board
+
+on:
+  issues:
+    types:
+      - opened
+  pull_request_target:
+    types:
+      - opened
+
+jobs:
+  add-to-project:
+    name: Add to project
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/add-to-project@v1.0.2
+        with:
+          project-url: https://github.com/orgs/open-atmos/projects/6
+          github-token: ${{ secrets.ADD_TO_PROJECT_PAT }}

.github/workflows/pypi.yml

@@ -0,0 +1,57 @@
+name: pypi
+
+defaults:
+  run:
+    shell: bash
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  schedule:
+    - cron: '0 13 * * 4'
+  release:
+    types: [published]
+
+jobs:
+  dist:
+    strategy:
+      matrix:
+        package-dir: [".", "examples"]
+      fail-fast: false
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: recursive
+          fetch-depth: 0  # https://github.com/pypa/setuptools_scm/issues/480
+      - uses: actions/setup-python@v5.2.0
+        with:
+          python-version: "3.10"
+
+      - run: pip install twine build
+
+      - run: |
+          unset CI
+          cd ${{ matrix.package-dir }}
+          python -m build 2>&1 | tee build.log
+          exit `fgrep -v "warning: no previously-included files matching" buid.log | fgrep -i warning | wc -l`
+          twine check --strict dist/*
+          exit `tar tzf dist/*.tar.gz | fgrep ".ipynb" | wc -l`
+          cd ..
+
+      - if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+        uses: pypa/gh-action-pypi-publish@release/v1.12
+        with:
+          attestations: false
+          repository_url: https://test.pypi.org/legacy/
+          packages-dir: ${{ matrix.package-dir }}/dist
+
+      - if: startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@release/v1.12
+        with:
+          attestations: false
+          packages-dir: ${{ matrix.package-dir }}/dist

.github/workflows/readme_matlab.yml

@@ -14,19 +14,30 @@ on:
 
 jobs:
   matlab:
+    strategy:
+      matrix:
+        # https://www.mathworks.com/support/requirements/python-compatibility.html
+        include:
+          - matlab-version: "R2021b"
+            python-version: "3.9"
+          - matlab-version: "R2024b"
+            python-version: "3.12"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v1
+      - uses: actions/checkout@v4.2.2
+      - uses: actions/setup-python@v5.3.0
         with:
-          python-version: 3.8
+          python-version: ${{ matrix.python-version }}
       - run: pip install -e .
       - run: pip install pytest-codeblocks pytest
       - run: python -c "import pytest_codeblocks; code=pytest_codeblocks.extract_from_file('docs/markdown/pympdata_landing.md'); f=open('readme.m', 'w'); f.writelines(block.code for block in code if block.syntax=='Matlab'); f.close()"
       - run: cat readme.m
-      - uses: matlab-actions/setup-matlab@v0
+      - uses: matlab-actions/setup-matlab@v2.3.0
         with:
-          release: R2021a
-      - uses: matlab-actions/run-command@v0
+          release: ${{ matrix.matlab-version }}
+      - uses: matlab-actions/run-command@v2.1.1
+        with:
+          command: pe=pyenv; assert(pe.Version == "${{ matrix.python-version }}");
+      - uses: matlab-actions/run-command@v2.1.1
         with:
           command: readme