merge

.github/workflows/readme_rust.yml

@@ -0,0 +1,43 @@
+name: readme_rust
+
+defaults:
+  run:
+    shell: bash
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  schedule:
+    - cron: '0 13 * * 4'
+
+jobs:
+  rust:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: dtolnay/rust-toolchain@stable
+        with:
+          components: rust-src
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.9
+      - run: pip install -e .
+      - run: pip install pytest-codeblocks pytest
+
+      - run: |
+          cat >Cargo.toml <<EOF
+          [package]
+          name = "PyMPDATA"
+          version = "0.1.0"
+          edition = "2021"
+
+          [dependencies]
+          pyo3 = { version = "0.22.2", features=["auto-initialize"]}
+          EOF
+      - run: mkdir src
+      - run: python -c "import pytest_codeblocks; code=pytest_codeblocks.extract_from_file('docs/markdown/pympdata_landing.md'); f=open('src/main.rs', 'w'); f.writelines(block.code for block in code if block.syntax=='Rust'); f.close()"
+      - run: cat -n src/main.rs
+      - run: cargo run
+

.github/workflows/tests+pypi.yml

@@ -19,7 +19,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: actions/setup-python@v1
+      - uses: actions/setup-python@v5.2.0
         with:
           python-version: "3.10" 
       - run: |
@@ -37,7 +37,7 @@ jobs:
       with:
         submodules: recursive
         fetch-depth: 0 
-    - uses: actions/setup-python@master
+    - uses: actions/setup-python@v5.2.0
       with:
         python-version: 3.9
     - name: Generate coverage report
@@ -60,7 +60,7 @@ jobs:
         submodules: recursive
         fetch-depth: 0 
     - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5.2.0
       with:
         python-version: 3.9
     - name: Install dependencies
@@ -89,16 +89,24 @@ jobs:
         with:
           submodules: recursive
           persist-credentials: false
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5.2.0
         with:
           python-version: 3.9
       - env:
           JUPYTER_PLATFORM_DIRS: 1
         run: |
-          pip3 install pdoc
+          pip3 install pdoc nbformat
           pip install -e . -e ./examples
-          export PDOC_ALLOW_EXEC=1
-          python -We -m pdoc -o html PyMPDATA examples/PyMPDATA_examples -t docs/templates
+
+          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/[email protected]
         with:
@@ -120,38 +128,22 @@ jobs:
     needs: [nojit_and_codecov, pylint, pdoc, precommit, zenodo_json]
     strategy:
       matrix:
-        platform: [ubuntu-latest, macos-12, macos-14, windows-latest]
-        python-version: ["3.9", "3.12", "system"]
+        platform: [ubuntu-latest, macos-13, macos-14, windows-latest]
+        python-version: ["3.9", "3.12"]
         exclude:
-          - platform: ubuntu-latest
-            python-version: system
-          - platform: macos-12
-            python-version: system
-          - platform: windows-latest
-            python-version: system
           - platform: macos-14
             python-version: "3.9"
-          - platform: macos-14
-            python-version: "3.12"
     runs-on: ${{ matrix.platform }}
     steps:
       - uses: actions/checkout@v2
         with:
           submodules: recursive
           fetch-depth: 0 
 
-      - if: matrix.platform != 'macos-14'
-        uses: actions/setup-python@v1
+      - uses: actions/[email protected]
         with:
           python-version: ${{ matrix.python-version }}
 
-      - if: matrix.platform == 'macos-14'
-        run: |
-          sudo ln -s `which python3` /usr/local/bin/python
-          echo "PIP_INSTALL_ARGS=--break-system-packages" >> $GITHUB_ENV
-
-          # Python 3.12 workaround  
-          python -m pip install --break-system-packages setuptools
       - run: |
           python -m pip install $PIP_INSTALL_ARGS -e .  # to check if usable without test/example dependencies
           python -We -c "import PyMPDATA"
@@ -176,40 +168,20 @@ jobs:
     needs: [pylint, precommit]
     strategy:
       matrix:
-        platform: [ubuntu-latest, macos-12, macos-14, windows-latest]
+        platform: [ubuntu-latest, macos-13, macos-14, windows-latest]
         python-version: ["3.9", "3.12"]
-        exclude:
-          - platform: ubuntu-latest
-            python-version: system
-          - platform: macos-12
-            python-version: system
-          - platform: windows-latest
-            python-version: system
-          - platform: macos-14
-            python-version: "3.9"
-          - platform: macos-14
-            python-version: "3.12"
       fail-fast: false
     runs-on: ${{ matrix.platform }}
     steps:
       - uses: actions/checkout@v2
         with:
           submodules: recursive
-          fetch-depth: 0 
+          fetch-depth: 0
 
-      - if: matrix.platform != 'macos-14'
-        uses: actions/setup-python@v1
+      - uses: actions/[email protected]
         with:
           python-version: ${{ matrix.python-version }}
 
-      - if: matrix.platform == 'macos-14'
-        run: |
-          sudo ln -s `which python3` /usr/local/bin/python
-          echo "PIP_INSTALL_ARGS=--break-system-packages" >> $GITHUB_ENV
-
-          # Python 3.12 workaround
-          python -m pip install --break-system-packages setuptools
-
       - run: python -m pip install $PIP_INSTALL_ARGS -e .[tests] ./examples
       - run: python -m pip install $PIP_INSTALL_ARGS -r tests/devops_tests/requirements.txt
       - if: matrix.platform == 'ubuntu-latest'
@@ -223,6 +195,8 @@ jobs:
           sudo make install
           cd ../../../
           rm -rf libmpdataxx
+      - uses: julia-actions/setup-julia@v2
+      - run: julia --version
 
       # https://github.com/numba/numba/issues/6350#issuecomment-728174860
       - if: matrix.platform == 'ubuntu-latest'
@@ -279,7 +253,7 @@ jobs:
         with:
           submodules: recursive
           fetch-depth: 0  # https://github.com/pypa/setuptools_scm/issues/480
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5.2.0
         with:
           python-version: "3.10"
 
@@ -295,13 +269,15 @@ jobs:
           cd ..
 
       - if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-        uses: pypa/gh-action-pypi-publish@unstable/v1
+        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@unstable/v1
+        uses: pypa/gh-action-pypi-publish@release/v1.12
         with:
+          attestations: false
           packages-dir: ${{ matrix.package-dir }}/dist