CI Updates: Code coverage report, Ubuntu 24.04, PETSc 3.22 (#443)

Summary of changes:

- Integrate Codacy reporting
- Lock runner versions to `ubuntu-24.04` and `macos-14`. The
[`*-latest` runner
versions](https://github.com/actions/runner-images#available-images) are
moving targets; we wish to avoid surprise failing tests caused by runner
upgrades (e.g. see [macOS
issue](#421) from last year) .
- Upgrade PETSc to [v3.22](https://petsc.org/release/changes/322/).

.github/workflows/continuous-integration.yml

@@ -15,21 +15,25 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ ubuntu-latest ]
+        os: [ ubuntu-24.04 ]
         python-version: [ 3.9, '3.10', '3.11', '3.12' ]
         isMerge:
           - ${{ github.event_name == 'push' && github.ref == 'refs/heads/devel' }}
         exclude:
           - { isMerge: false, python-version: '3.10' }
           - { isMerge: false, python-version: '3.11' }
         include:
-          - os: macos-latest
+          - os: macos-14
             python-version: '3.10'
-          - os: macos-latest
+          - os: macos-14
             python-version: '3.11'
 
     name: ${{ matrix.os }} / Python ${{ matrix.python-version }}
 
+    env:
+      PSYDAC_MESH_DIR: ${{ github.workspace }}/mesh
+      OMP_NUM_THREADS: 2
+
     steps:
       - uses: actions/checkout@v4
 
@@ -44,7 +48,7 @@ jobs:
             requirements_extra.txt
 
       - name: Install non-Python dependencies on Ubuntu
-        if: matrix.os == 'ubuntu-latest'
+        if: matrix.os == 'ubuntu-24.04'
         uses: awalsh128/cache-apt-pkgs-action@latest
         with:
           packages: gfortran openmpi-bin libopenmpi-dev libhdf5-openmpi-dev
@@ -55,14 +59,14 @@ jobs:
       # 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: Set default MPI and HDF5 C compilers on Ubuntu
-        if: matrix.os == 'ubuntu-latest'
+      - 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
+          sudo apt-get install --reinstall openmpi-bin libhdf5-openmpi-dev liblapack-dev libblas-dev
 
       - name: Install non-Python dependencies on macOS
-        if: matrix.os == 'macos-latest'
+        if: matrix.os == 'macos-14'
         run: |
           brew install open-mpi
           brew install hdf5-mpi
@@ -89,9 +93,9 @@ jobs:
 
       - name: Determine directory of parallel HDF5 library
         run: |
-          if [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then
+          if [[ "${{ matrix.os }}" == "ubuntu-24.04" ]]; then
             HDF5_DIR=$(dpkg -L libhdf5-openmpi-dev | grep libhdf5.so | xargs dirname)
-          elif [[ "${{ matrix.os }}" == "macos-latest" ]]; then
+          elif [[ "${{ matrix.os }}" == "macos-14" ]]; then
             HDF5_DIR=$(brew list hdf5-mpi | grep "libhdf5.dylib" | xargs dirname | xargs dirname)
           fi
           echo $HDF5_DIR
@@ -104,12 +108,12 @@ jobs:
           cache-name: cache-PETSc
         with:
           path: "./petsc"
-          key: cache-${{ matrix.os }}-${{ matrix.python-version }}
+          key: petsc-${{ matrix.os }}-${{ matrix.python-version }}
 
       - if: steps.cache-petsc.outputs.cache-hit != 'true'
         name: Download a specific release of PETSc
         run: |
-          git clone --depth 1 --branch v3.21.4 https://gitlab.com/petsc/petsc.git
+          git clone --depth 1 --branch v3.22.2 https://gitlab.com/petsc/petsc.git
 
       - if: steps.cache-petsc.outputs.cache-hit != 'true'
         name: Install PETSc with complex support
@@ -157,7 +161,7 @@ jobs:
 
       - name: Install project
         run: |
-          python -m pip install .
+          python -m pip install .[test]
           python -m pip freeze
 
       - name: Test Pyccel optimization flags
@@ -169,35 +173,51 @@ jobs:
           mkdir pytest
           cp mpi_tester.py pytest
 
-      - name: Run single-process tests with Pytest
+      - name: Run coverage tests on macOS
+        if: matrix.os == 'macos-14'
+        working-directory: ./pytest
+        run: >- 
+          python -m pytest -n auto
+          --cov psydac
+          --cov-config $GITHUB_WORKSPACE/pyproject.toml
+          --cov-report xml
+          --pyargs psydac -m "not parallel and not petsc"
+
+      - name: Run single-process tests with Pytest on Ubuntu
+        if: matrix.os == 'ubuntu-24.04'
         working-directory: ./pytest
         run: |
-          export PSYDAC_MESH_DIR=$GITHUB_WORKSPACE/mesh
-          export OMP_NUM_THREADS=2
           python -m pytest -n auto --pyargs psydac -m "not parallel and not petsc"
 
+      - name: Upload coverage report to Codacy
+        if: matrix.os == 'macos-14'
+        uses: codacy/codacy-coverage-reporter-action@v1.3.0
+        with:
+          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
+          coverage-reports: ./pytest/coverage.xml
+
+      - name: Print detailed coverage results on macOS
+        if: matrix.os == 'macos-14'
+        working-directory: ./pytest
+        run: |
+          coverage report --ignore-errors --show-missing --sort=cover
+
       - name: Run MPI tests with Pytest
         working-directory: ./pytest
         run: |
-          export PSYDAC_MESH_DIR=$GITHUB_WORKSPACE/mesh
-          export OMP_NUM_THREADS=2
           python mpi_tester.py --mpirun="mpiexec -n 4 ${MPI_OPTS}" --pyargs psydac -m "parallel and not petsc"
 
       - name: Run single-process PETSc tests with Pytest
         working-directory: ./pytest
         run: |
-          export PSYDAC_MESH_DIR=$GITHUB_WORKSPACE/mesh
-          export OMP_NUM_THREADS=2
           python -m pytest -n auto --pyargs psydac -m "not parallel and petsc"
 
       - name: Run MPI PETSc tests with Pytest
         working-directory: ./pytest
         run: |
-          export PSYDAC_MESH_DIR=$GITHUB_WORKSPACE/mesh
-          export OMP_NUM_THREADS=2
           python mpi_tester.py --mpirun="mpiexec -n 4 ${MPI_OPTS}" --pyargs psydac -m "parallel and petsc"
 
       - name: Remove test directory
-        if: ${{ always() }}
+        if: always()
         run: |
           rm -rf pytest

pyproject.toml

@@ -26,8 +26,6 @@ dependencies = [
     'scipy >= 1.12',
     'sympy >= 1.5',
     'matplotlib',
-    'pytest >= 4.5',
-    'pytest-xdist >= 1.16',
     'pyyaml >= 5.1',
     'packaging',
     'pyevtk',
@@ -53,6 +51,13 @@ dependencies = [
     'igakit @ https://github.com/dalcinl/igakit/archive/refs/heads/master.zip'
 ]
 
+[project.optional-dependencies]
+test = [
+    "pytest-cov >= 5.0.0",
+    'pytest >= 4.5',
+    'pytest-xdist >= 1.16',
+]
+
 [project.urls]
 Homepage      = "https://github.com/pyccel/psydac"
 Documentation = "https://pyccel.github.io/psydac"
@@ -68,3 +73,41 @@ namespaces = false
 
 [tool.setuptools.package-data]
 "*" = ["*.txt"]
+
+[tool.coverage.run]
+branch = true
+omit = [
+    # Exclude pyccelised kernels
+    "*/__psydac__/*",
+
+    # Examples don't need to be covered
+    "*/examples/*",
+
+    # Unit tests shouldn't be included
+    "*/tests/*",
+    ]
+
+[tool.coverage.report]
+# Regexes for lines to exclude from consideration
+exclude_also = [
+    # Don't complain about missing debug-only code:
+    "def __repr__",
+    "if self\\.debug",
+
+    # Don't complain if tests don't hit defensive assertion code:
+    "raise AssertionError",
+    "raise NotImplementedError",
+
+    # Don't complain if non-runnable code isn't run:
+    "if False:",
+    "if __name__ == .__main__.:",
+
+    # Don't complain about abstract methods, they aren't run:
+    "@(abc\\.)?abstractmethod",
+    ]
+
+# Ignore source code that can’t be found, emitting a warning instead of an exception.
+ignore_errors = true
+
+[tool.coverage.html]
+directory = "coverage_html_report"