Update from upstream 2026-07-23

.github/actions/install_h5py/action.yml

@@ -0,0 +1,35 @@
+name: 'Parallel h5py installation'
+description: 'Install h5py in parallel mode using the system MPI and HDF5 libraries'
+
+runs:
+  using: "composite"
+  steps:
+
+    - name: Determine directory of parallel HDF5 library
+      shell: bash
+      run: |
+        if [[ "$RUNNER_OS" == "Linux" ]]; then
+          HDF5_DIR=$(dpkg -L libhdf5-openmpi-dev | grep libhdf5.so | xargs dirname)
+        elif [[ "$RUNNER_OS" == "macOS" ]]; then
+          HDF5_DIR=$(brew list hdf5-mpi | grep "libhdf5.dylib" | xargs dirname | xargs dirname)
+        fi
+        echo $HDF5_DIR
+        echo "HDF5_DIR=$HDF5_DIR" >> $GITHUB_ENV
+
+    - name: Install h5py in parallel mode
+      shell: bash
+      run: |
+        export CC="mpicc"
+        export HDF5_MPI="ON"
+        pip install h5py --no-cache-dir --no-binary h5py
+        pip list
+
+    - name: Check parallel h5py installation
+      shell: bash
+      run: |
+        python -c "
+        from mpi4py import MPI
+        import h5py
+        # This particular instantiation of h5py.File will fail if parallel h5py isn't installed
+        f = h5py.File('parallel_test.hdf5', 'w', driver='mpio', comm=MPI.COMM_WORLD)
+        print(f)"

.github/actions/install_petsc4py/action.yml

@@ -0,0 +1,54 @@
+name: 'Install PETSc and petsc4py'
+description: 'Install PETSc and petsc4py with complex support'
+
+runs:
+  using: "composite"
+  steps:
+
+    - name: Cache PETSc
+      uses: actions/cache@v4
+      id: cache-petsc
+      env:
+        cache-name: cache-PETSc
+      with:
+        path: "./petsc"
+        key: petsc-${{ matrix.os }}-${{ matrix.python-version }}
+
+    - if: steps.cache-petsc.outputs.cache-hit != 'true'
+      name: Download a specific release of PETSc
+      shell: bash
+      run: |
+        git clone --depth 1 --branch v3.25.0 https://gitlab.com/petsc/petsc.git
+      # The branch "release" contains work towards the next version of PETSc,
+      # and it may not be stable. If necessary, it can be cloned as follows:
+      # git clone --depth 1 --branch release https://gitlab.com/petsc/petsc.git
+
+    - if: steps.cache-petsc.outputs.cache-hit != 'true'
+      name: Install PETSc with complex support
+      shell: bash
+      working-directory: ./petsc
+      run: |
+        export PETSC_DIR=$(pwd)
+        export PETSC_ARCH=petsc-cmplx
+        ./configure --with-scalar-type=complex --with-fortran-bindings=0 --have-numpy=1         
+        make all
+        echo "PETSC_DIR=$PETSC_DIR" > petsc.env
+        echo "PETSC_ARCH=$PETSC_ARCH" >> petsc.env
+
+    # This step is not really necessary and could be combined with PETSc install
+    # step; however it's good to verify if the cached PETSc installation really works!
+    - name: Test PETSc installation
+      shell: bash
+      working-directory: ./petsc
+      run: |
+        source petsc.env
+        make check
+        echo "PETSC_DIR=$PETSC_DIR" >> $GITHUB_ENV
+        echo "PETSC_ARCH=$PETSC_ARCH" >> $GITHUB_ENV
+
+    - name: Install petsc4py
+      shell: bash
+      working-directory: ./petsc
+      run: | 
+        pip install wheel Cython numpy
+        pip install src/binding/petsc4py

.github/actions/macos_installations/action.yml

@@ -0,0 +1,24 @@
+name: 'MacOS installation commands'
+description: 'Install non-Python dependencies on macOS'
+
+runs:
+  using: "composite"
+  steps:
+
+    - name: Install non-Python dependencies on macOS
+      run: |
+        brew install make
+        brew install open-mpi
+        brew install hdf5-mpi
+        brew install libomp
+        GFORTRAN_HOME=$(which gfortran || true)
+        echo "GFORTRAN_HOME : $GFORTRAN_HOME"
+        if [[ ! -f "$GFORTRAN_HOME" ]]; then
+          gfort=$(find ${PATH//:/\/ } -name 'gfortran-*' -exec basename {} \; | sort | tail -n 1 || true)
+          echo "Found $gfort"
+          gfort_path=$(which ${gfort})
+          folder=$(dirname ${gfort_path})
+          ln -s ${gfort_path} ${folder}/gfortran
+        fi
+        echo "/opt/homebrew/opt/make/libexec/gnubin" >> $GITHUB_PATH
+      shell: bash

.github/actions/ubuntu_installations/action.yml

@@ -0,0 +1,23 @@
+name: 'Ubuntu installation commands'
+description: 'Install non-Python dependencies on Ubuntu'
+
+runs:
+  using: "composite"
+  steps:
+
+    - name: Install non-Python dependencies on Ubuntu
+      uses: awalsh128/cache-apt-pkgs-action@latest
+      with:
+        packages: gfortran openmpi-bin libopenmpi-dev libhdf5-openmpi-dev
+        version: 1.0
+        execute_install_scripts: true
+
+    # When loading cached apt packages, the default MPI compiler isn't set.
+    # Workaround is to 'reinstall' openmpi-bin, which doesn't actually perform
+    # installation (since openmpi-bin already exists), but instead reruns
+    # `update-alternatives` which fixes the symlinks to mpicc/mpif90.
+    - name: Reconfigure non-Python dependencies on Ubuntu
+      run: |
+        sudo apt-get update
+        sudo apt-get install --reinstall openmpi-bin libhdf5-openmpi-dev liblapack-dev libblas-dev
+      shell: bash

.github/workflows/deploy.yml

@@ -0,0 +1,131 @@
+name: Deploy new version to PyPI
+
+on:
+  workflow_run:
+    workflows: ["Unit tests"]
+    branches: [main]
+    types:
+      - completed
+
+jobs:
+  deployVersion:
+    runs-on: ubuntu-latest
+    if: ${{ github.repository == 'pyccel/psydac' && github.event.workflow_run.conclusion == 'success' }}
+    steps:
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Checkout repository
+        uses: actions/checkout@v6
+        with:
+          ref: main
+          submodules: true
+
+      - name: Install dependencies
+        uses: ./.github/actions/ubuntu_installations
+
+      - name: Update build tools
+        run: |
+          pip install --upgrade pip
+          pip install --upgrade build
+          pip install --upgrade twine
+
+      - name: Build and deploy to PyPI
+        run: |
+          echo ${{ github.event.workflow_run.head_branch }}
+          python -m build --sdist
+          ls dist/*
+          twine upload --repository pypi dist/* --non-interactive
+        shell: bash
+        env:
+          TWINE_USERNAME: '__token__'
+          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+
+      - name: Install psydac package without extra components
+        run: |
+          pip install .
+
+      - name: "Get tag name"
+        id: tag_name
+        run: |
+          version=$(python -c "from psydac import __version__; print(__version__)")
+          echo "VERSION=${version}" >> $GITHUB_OUTPUT
+          echo "TAG_NAME=v${version}" >> $GITHUB_OUTPUT
+
+      - name: "Get release notes"
+        id: release_notes
+        run: |
+          echo "## What's Changed" > release_notes.md
+          START_LINE=$(grep "^## " CHANGELOG.md -n | head -1 | cut -d: -f -1)
+          END_LINE=$(grep "^## " CHANGELOG.md -n | head -2 | tail -1 | cut -d: -f -1)
+          START_LINE=$((${START_LINE}+1))
+          END_LINE=$((${END_LINE}-1))
+          echo "## What's Changed" > release_notes.md
+          sed -n ${START_LINE},${END_LINE}p CHANGELOG.md >> release_notes.md
+
+      - name: "Get contributors"
+        run: |
+          # Get relevant commits
+          LAST_RELEASE_COMMIT=$(git log -2 --pretty=%H | tail -1)
+          CURRENT_RELEASE_COMMIT=$(git log -1 --pretty=%H)
+
+          # Find any new lines in the AUTHORS file
+          NEW_CONTRIBUTORS=$(git diff --no-indent-heuristic --unified=0 --no-color ${LAST_RELEASE_COMMIT}..${CURRENT_RELEASE_COMMIT} AUTHORS | { grep "^\+[^+]" || true; } | cut -d ' ' -f 2-)
+          if [ -n "${NEW_CONTRIBUTORS}" ]
+          then
+            # If there are new contributors then add a section with their names
+            echo "## New Contributors" >> release_notes.md
+            while IFS= read -r c
+            do
+              echo "- ${c}" >> release_notes.md
+            done <<< "${NEW_CONTRIBUTORS}"
+            echo "" >> release_notes.md
+          fi
+
+          # Find the PR which created the release
+          PR_ID=$(gh api -H "Accept: application/vnd.github+json" -H "X-GitHub-Api-Version: 2022-11-28" /search/issues?q="${CURRENT_RELEASE_COMMIT}" | jq '.["items"][0]["number"]')
+          # Extract authors from all commits in the PR
+          CONTRIBUTORS=$(gh pr view ${PR_ID} --json commits | jq '.["commits"][]["authors"][]["login"]' | tr -d '"' | sort -u)
+
+          # Add a hidden section listing the user names of all authors on commits in this release
+          echo "<details>" >> release_notes.md
+          echo "" >> release_notes.md
+          echo "## Contributors" >> release_notes.md
+          for c in ${CONTRIBUTORS}
+          do
+            echo "- @$c" >> release_notes.md
+          done
+          echo "" >> release_notes.md
+          echo "</details>" >> release_notes.md
+
+          # Get the full changelog link
+          PREVIOUS_TAG=$(gh release list --limit 1 --json tagName | jq '.[]["tagName"]' | tr -d '"')
+
+          echo "" >> release_notes.md
+          echo "**Full list of changes**: [${PREVIOUS_TAG}..${tag_name}](https://github.com/pyccel/psydac/compare/${PREVIOUS_TAG}..${tag_name})" >> release_notes.md
+
+        shell: bash
+        env:
+          GH_TOKEN: ${{ github.token }}
+          tag_name: ${{ steps.tag_name.outputs.TAG_NAME }}
+
+      - name: "Update repo tags"
+        uses: EndBug/latest-tag@latest
+        with:
+          ref: ${{ steps.tag_name.outputs.TAG_NAME }}
+
+      - name: "Update releases"
+        run: |
+          gh api \
+            --method POST \
+            -H "Accept: application/vnd.github+json" \
+            -H "X-GitHub-Api-Version: 2022-11-28" \
+            /repos/pyccel/psydac/releases \
+             -f "tag_name=${tag_name}" -f "name=Version ${version}" -F "body=@release_notes.md" -F "draft=false" -F "prerelease=false" -F "generate_release_notes=false"
+        shell: bash
+        env:
+          tag_name: ${{ steps.tag_name.outputs.TAG_NAME }}
+          version: ${{ steps.tag_name.outputs.VERSION }}
+          GH_TOKEN: ${{ github.token }}

.github/workflows/deploy_check.yml

@@ -0,0 +1,110 @@
+name: Check deployment of new version to TestPyPI
+
+on:
+  pull_request:
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - ready_for_review
+    branches: [main]
+
+jobs:
+  deployTest:
+    runs-on: ubuntu-latest
+    if: github.repository == 'pyccel/psydac'
+    steps:
+      - id: duplicate_check
+        uses: fkirc/skip-duplicate-actions@v5
+        with:
+          skip_after_successful_duplicate: 'true'
+          paths: '["psydac/**", "pyproject.toml", ".github/workflows/deploy_check.yml", ".github/actions/**"]'
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Checkout repository
+        if: steps.duplicate_check.outputs.should_skip != 'true'
+        uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - name: Install dependencies
+        if: steps.duplicate_check.outputs.should_skip != 'true'
+        uses: ./.github/actions/ubuntu_installations
+
+      - name: Update build tools
+        if: steps.duplicate_check.outputs.should_skip != 'true'
+        run: |
+          pip install --upgrade pip
+          pip install --upgrade build
+          pip install --upgrade twine
+
+      - name: Build and deploy to TestPyPI
+        if: steps.duplicate_check.outputs.should_skip != 'true'
+        run: |
+          CURRENT_VERSION=$(grep 'version *= *"\([0-9\.]*\)"' pyproject.toml | grep '[0-9\.]*' -o)
+          TEST_VERSION=${CURRENT_VERSION}.dev$(date +%Y%m%d%H%M%S)
+          sed -i.bak "s/\"${CURRENT_VERSION}\"/\"${TEST_VERSION}\"/g" pyproject.toml && rm pyproject.toml.bak
+          echo "TEST_VERSION=${TEST_VERSION}" >> $GITHUB_ENV
+          # Setup dummy user to save temp version for meson
+          git config --global user.email "you@example.com"
+          git config --global user.name "Your Name"
+          git commit -m "Save temp version" pyproject.toml
+          python -m build --sdist
+          ls dist/*
+          twine check --strict dist/*
+          twine upload --repository testpypi dist/* --non-interactive --verbose
+          sleep 60
+        shell: bash
+        env:
+          TWINE_USERNAME: '__token__'
+          TWINE_PASSWORD: ${{ secrets.TEST_PYPI_API_TOKEN }}
+
+      - name: Install h5py in parallel mode
+        if: steps.duplicate_check.outputs.should_skip != 'true'
+        uses: ./.github/actions/parallel_h5py
+
+      - name: Download psydac package from TestPyPI and install it
+        if: steps.duplicate_check.outputs.should_skip != 'true'
+        timeout-minutes: 60
+        run: |
+          WAIT=20
+          SUCCESS=0
+          for i in {1..5}; do
+            echo "Attempt $i: Installing psydac==${TEST_VERSION}..."""
+            if pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ psydac[test]=="${TEST_VERSION}"
+            then
+              SUCCESS=1
+              break
+            else
+              echo "Install failed. Retrying in $WAIT seconds..."
+              sleep $WAIT
+            fi
+          done
+
+          # Final check
+          if [ "$SUCCESS" -ne 1 ]; then
+            echo "ERROR: Failed to install psydac==${TEST_VERSION}."
+            exit 1
+          fi
+        shell: bash
+
+      - name: Initialize test directory
+        if: steps.duplicate_check.outputs.should_skip != 'true'
+        run: |
+          mkdir pytest
+
+      - name: Run single-process tests with Pytest
+        if: steps.duplicate_check.outputs.should_skip != 'true'
+        working-directory: ./pytest
+        run: |
+          psydac test -x
+
+      - name: Run MPI tests with Pytest
+        if: steps.duplicate_check.outputs.should_skip != 'true'
+        working-directory: ./pytest
+        run: |
+          psydac test --mpi -x

.github/workflows/test-PR-psydac.yml

@@ -60,7 +60,7 @@ jobs:
       - name: Initialize test directory
         run: |
           mkdir pytest
-          cp mpi_tester.py pytest
+          cp scripts/mpi_tester.py pytest
 
       - name: Run single-process tests with Pytest on Ubuntu
         run: |