Prepare release

.github/actions/macos_install/action.yml

@@ -0,0 +1,24 @@
+name: 'MacOS installation commands'
+
+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 "MPI_OPTS=--oversubscribe" >> $GITHUB_ENV
+        echo "/opt/homebrew/opt/make/libexec/gnubin" >> $GITHUB_PATH
+      shell: bash

.github/actions/ubuntu_install/action.yml

@@ -0,0 +1,22 @@
+name: 'Ubuntu installation commands'
+
+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: [testing]
+    branches: [main]
+    types:
+      - completed
+
+jobs:
+  deployVersion:
+    runs-on: ubuntu-latest
+    if: github.repository == 'pyccel/psydac'
+    steps:
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - name: Install dependencies
+        uses: ./.github/actions/ubuntu_install
+
+      - 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}" >> $GITHUB_OUTPUT
+
+      - name: "Get release notes"
+        id: release_notes
+        run: |
+          echo "## What's Changed" > release_notes.md
+# TODO: CHANGELOG parsing can be enabled when file is ready
+#          START_LINE=$(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}..${tag_name}](https://github.com/pyccel/pyccel/compare/${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: ${{ steps.tag_name.outputs.TAG_NAME }}
+
+      - name: "Update releases"
+        run: |
+          gh api \
+            --method POST \
+            -H "Accept: application/vnd.github+json" \
+            -H "X-GitHub-Api-Version: 2022-11-28" \
+            /repos/pyccel/pyccel/releases \
+             -f "tag_name=${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 +1,101 @@
+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", "setup.py", ".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_install
+
+      - 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 "[email protected]"
+          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: 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
+          cp mpi_tester.py pytest
+
+      - name: Run single-process tests with Pytest
+        if: steps.duplicate_check.outputs.should_skip != 'true'
+        working-directory: ./pytest
+        run: |
+          pytest -n auto --pyargs psydac -m "not parallel and not petsc"

.github/workflows/documentation.yml

@@ -31,7 +31,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: '3.10'
     - name: Install non-Python dependencies on Ubuntu
       run: |
         sudo apt update

.github/workflows/testing.yml

@@ -9,7 +9,6 @@ on:
     paths:
       - 'psydac/**'
       - 'pyproject.toml'
-      - 'setup.py'
       - 'pytest.ini'
       - 'mpi_tester.py'
 
@@ -23,7 +22,6 @@ on:
     paths:
       - 'psydac/**'
       - 'pyproject.toml'
-      - 'setup.py'
       - 'pytest.ini'
       - 'mpi_tester.py'
 
@@ -36,15 +34,15 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-24.04, macos-14 ]
-        python-version: [ '3.9', '3.10', '3.11', '3.12', '3.13' ]
+        python-version: [ '3.10', '3.11', '3.12', '3.13', '3.14' ]
         isMerge:
           - ${{ github.event_name == 'push' && github.ref == 'refs/heads/devel' }}
         exclude:
-          - { isMerge: false, python-version: '3.9' , os:     macos-14 }
-          - { isMerge: false, python-version: '3.10', os: ubuntu-24.04 }
-          - { isMerge: false, python-version: '3.11', os:     macos-14 }
-          - { isMerge: false, python-version: '3.12', os: ubuntu-24.04 }
-          - { isMerge: false, python-version: '3.13', os:     macos-14 }
+          - { isMerge: false, python-version: '3.10', os:     macos-14 }
+          - { isMerge: false, python-version: '3.11', os: ubuntu-24.04 }
+          - { isMerge: false, python-version: '3.12', os:     macos-14 }
+          - { isMerge: false, python-version: '3.13', os: ubuntu-24.04 }
+          - { isMerge: false, python-version: '3.14', os:     macos-14 }
 
     name: ${{ matrix.os }} / Python ${{ matrix.python-version }}
 
@@ -62,45 +60,14 @@ jobs:
           cache: 'pip'
           cache-dependency-path: |
             pyproject.toml
-            requirements.txt
-            requirements_extra.txt
 
       - name: Install non-Python dependencies on Ubuntu
         if: matrix.os == 'ubuntu-24.04'
-        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
-        if: matrix.os == 'ubuntu-24.04'
-        run: |
-          sudo apt-get update
-          sudo apt-get install --reinstall openmpi-bin libhdf5-openmpi-dev liblapack-dev libblas-dev
+        uses: ./.github/actions/ubuntu_install
 
       - name: Install non-Python dependencies on macOS
         if: matrix.os == 'macos-14'
-        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 "MPI_OPTS=--oversubscribe" >> $GITHUB_ENV
-          echo "/opt/homebrew/opt/make/libexec/gnubin" >> $GITHUB_PATH
+        uses: ./.github/actions/macos_install
 
       - name: Print information on MPI and HDF5 libraries
         run: |
@@ -133,7 +100,7 @@ jobs:
       - if: steps.cache-petsc.outputs.cache-hit != 'true'
         name: Download a specific release of PETSc
         run: |
-          git clone --depth 1 --branch v3.23.2 https://gitlab.com/petsc/petsc.git
+          git clone --depth 1 --branch v3.24.2 https://gitlab.com/petsc/petsc.git
 
       - if: steps.cache-petsc.outputs.cache-hit != 'true'
         name: Install PETSc with complex support

.gitignore

@@ -32,4 +32,7 @@ __test__/
 .idea
 
 # Visual Studio Code workspace files
-*.code-workspace
+*.code-workspace
+
+# Meson lock files
+*/.wraplock

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "subprojects/igakit"]
+	path = subprojects/igakit
+	url = https://github.com/dalcinl/igakit/