Improve Geometry class

.github/actions/parallel_h5py/action.yml

@@ -20,6 +20,7 @@ runs:
       run: |
         export CC="mpicc"
         export HDF5_MPI="ON"
+        pip install 'mpi4py>=4.0.0'
         pip install h5py --no-cache-dir --no-binary h5py
         pip list
 

.github/workflows/documentation.yml

@@ -25,9 +25,11 @@ permissions:
 jobs:
   build_docs:
     runs-on: ubuntu-latest
+
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN}}
       OMP_NUM_THREADS: 2
+
     steps:
     - name: Checkout
       uses: actions/checkout@v5
@@ -36,18 +38,9 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: '3.10'
-    - 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
 
-    - 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
-        sudo apt install graphviz pandoc
+    - name: Install non-Python dependencies on Ubuntu
+      uses: ./.github/actions/ubuntu_install
 
     - name: Print information on MPI and HDF5 libraries
       run: |
@@ -68,9 +61,9 @@ jobs:
         key: petsc-${{ matrix.os }}-${{ matrix.python-version }}
 
     - if: steps.cache-petsc.outputs.cache-hit != 'true'
-      name: Download a specific release of PETSc
+      name: Download the latest release of PETSc
       run: |
-        git clone --depth 1 --branch v3.23.2 https://gitlab.com/petsc/petsc.git
+        git clone --depth 1 -b release https://gitlab.com/petsc/petsc.git
 
     - if: steps.cache-petsc.outputs.cache-hit != 'true'
       name: Install PETSc with complex support
@@ -107,6 +100,10 @@ jobs:
         pip install .[test]
         pip freeze
 
+    - name: Install non-Python dependencies for Documentation
+      run: |
+        sudo apt install graphviz pandoc
+
     - name: Install Python dependencies for Documentation
       run: |
         pip install -r docs/requirements.txt

.github/workflows/testing.yml

@@ -25,7 +25,8 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-24.04, macos-14 ]
-        python-version: [ '3.10', '3.11', '3.12', '3.13', '3.14' ]
+#        python-version: [ '3.9', '3.10', '3.11', '3.12', '3.13' ]
+        python-version: [ '3.11', '3.12' ]
         isMerge:
           - ${{ github.event_name == 'push' && github.ref == 'refs/heads/devel' }}
         exclude:
@@ -68,46 +69,46 @@ jobs:
         run: |
           pip install --upgrade pip setuptools wheel
 
-      - 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
-        run: |
-          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
-        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=$PETSC_ARCH" >> petsc.env
-
-      # This step is not really necessary and could be combined with PETSc install
-      # step; however it's good to verify if the cached PETSc installation really works!
-      - name: Test PETSc installation
-        working-directory: ./petsc
-        run: |
-          source petsc.env
-          make check
-          echo "PETSC_DIR=$PETSC_DIR" >> $GITHUB_ENV
-          echo "PETSC_ARCH=$PETSC_ARCH" >> $GITHUB_ENV
-
-      - name: Install petsc4py
-        working-directory: ./petsc
-        run: | 
-          pip install wheel Cython numpy
-          pip install src/binding/petsc4py
+#      - name: Cache PETSc
+#        uses: actions/cache@v4
+#        id: cache-petsc
+#        env:
+#          cache-name: cache-PETSc
+#        with:
+#          path: "./petsc"
+#          key: petsc-${{ matrix.os }}-${{ matrix.python-version }}
+#
+#      - if: steps.cache-petsc.outputs.cache-hit != 'true'
+#        name: Download a specific release of PETSc
+#        run: |
+#          git clone --depth 1 --branch v3.23.2 https://gitlab.com/petsc/petsc.git
+#
+#      - if: steps.cache-petsc.outputs.cache-hit != 'true'
+#        name: Install PETSc with complex support
+#        working-directory: ./petsc
+#        run: |
+#          export PETSC_DIR=$(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
+#        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
+#        working-directory: ./petsc
+#        run: | 
+#          pip install wheel Cython numpy
+#          pip install src/binding/petsc4py
 
       - name: Install h5py in parallel mode
         uses: ./.github/actions/parallel_h5py
@@ -125,54 +126,74 @@ jobs:
         run: |
           mkdir pytest
 
-      - name: Run coverage tests on macOS
-        if: matrix.os == 'macos-14'
-        working-directory: ./pytest
-        run: >-
-          pytest -n auto
-          --cov psydac
-          --cov-config $GITHUB_WORKSPACE/pyproject.toml
-          --cov-report xml
-          --pyargs psydac -m "not mpi and not petsc" -ra
-
-      - name: Run single-process tests with Pytest on Ubuntu
-        if: matrix.os == 'ubuntu-24.04'
+#      - name: Run single-process tests with Pytest and coverage 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: |
+#          psydac test
+
+      - name: Run single-process tests for CAD module
         working-directory: ./pytest
         run: |
-          psydac test
-
-      - 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
+          psydac test --mod psydac.cad -x -v
 
-      - name: Print detailed coverage results on macOS
-        if: matrix.os == 'macos-14'
+      - name: Run single-process tests for Mapping module
         working-directory: ./pytest
         run: |
-          coverage report --ignore-errors --show-missing --sort=cover
+          psydac test --mod psydac.mapping -x -v
 
-      - name: Run MPI tests with Pytest
+      - name: Run single-process tests for FEM module
         working-directory: ./pytest
         run: |
-          psydac test --mpi
+          psydac test --mod psydac.fem -x -v
 
-      - name: Run single-process PETSc tests with Pytest
+      - name: Run single-process tests for FEEC module
         working-directory: ./pytest
         run: |
-          psydac test --petsc
+          psydac test --mod psydac.feec -x -v
 
-      - name: Run MPI PETSc tests with Pytest
+      - name: Run single-process tests for API module
         working-directory: ./pytest
         run: |
-          psydac test --mpi --petsc
-
-      - name: Run single-process example tests with Pytest on Ubuntu
-        if: matrix.os == 'ubuntu-24.04'
-        run: |
-          python -m pytest examples/feec
+          psydac test --mod psydac.api -x -v
+
+#      - 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: |
+#          psydac test --mpi
+#
+#      - name: Run single-process PETSc tests with Pytest
+#        working-directory: ./pytest
+#        run: |
+#          psydac test --petsc
+#
+#      - name: Run MPI PETSc tests with Pytest
+#        working-directory: ./pytest
+#        run: |
+#          psydac test --mpi --petsc
 
       - name: Remove test directory
         if: always()

CHANGELOG.md

@@ -6,14 +6,18 @@ All notable changes to this project will be documented in this file.
 
 ### Added
 
+-   #567 : Improve `psydac test` command (with several new features)
+-   #565 : Expand editable install info in `README.md`
+
 ### Fixed
 
--   #570 : Optimize PSYDAC logo
--   #565 : Expand editable install info in `README.md`
+-   #567 : Fix parallel creation of folder `__psydac__` in `psydac.api.fem_bilinear_form`
 -   #566 : Fix command `psydac test --mpi` on Ubuntu machines
 
 ### Changed
 
+-   #527 : Improve `Geometry` class in module `psydac.cad.geometry`
+-   #570 : Optimize PSYDAC logo
 -   [DEVELOPER] Do not check file changes to trigger testing workflow on PRs
 -   [DEVELOPER] Run documentation workflow whenever `README.md` is modified
 -   [DEVELOPER] Run testing workflow on PRs only when set to "ready for review"

psydac/api/discretization.py

@@ -578,7 +578,7 @@ def discretize_domain(domain, *, filename=None, ncells=None, periodic=None, comm
         raise ValueError("Cannot provide both 'filename' and 'ncells'")
 
     elif filename:
-        return Geometry(filename=filename, comm=comm, mpi_dims_mask=mpi_dims_mask)
+        return Geometry.from_file(filename, comm=comm, mpi_dims_mask=mpi_dims_mask)
 
     elif ncells:
         return Geometry.from_topological_domain(domain, ncells, periodic=periodic, comm=comm, mpi_dims_mask=mpi_dims_mask)

psydac/api/tests/test_2d_complex.py

@@ -367,7 +367,7 @@ def test_complex_poisson_2d_multipatch():
     A = Square('A',bounds1=(0, 0.5), bounds2=(0, 1))
     B = Square('B',bounds1=(0.5, 1.), bounds2=(0, 1))
 
-    domain = Domain.join([A, B], [((0, 0, 1), (1, 0, -1))], 'domain')
+    domain = Domain.join([A, B], [((0, 0, 1), (1, 0, -1), 1)], 'domain')
 
     x, y = domain.coordinates
 
@@ -495,7 +495,7 @@ def test_maxwell_2d_2_patch_dirichlet_parallel_0():
     D1 = mapping_1(A)
     D2 = mapping_2(B)
 
-    domain = Domain.join([D1, D2], [((0, 1, 1), (1, 1, -1))], 'domain')
+    domain = Domain.join([D1, D2], [((0, 1, 1), (1, 1, -1), 1)], 'domain')
 
     x, y = domain.coordinates
 

psydac/api/tests/test_2d_multipatch_mapping_maxwell.py

@@ -126,7 +126,7 @@ def test_maxwell_2d_2_patch_dirichlet_0():
     D1     = mapping_1(A)
     D2     = mapping_2(B)
 
-    connectivity = [((0,1,1),(1,1,-1))]
+    connectivity = [((0, 1, 1), (1, 1,-1), 1)]
     patches = [D1,D2]
     domain = Domain.join(patches, connectivity, 'domain')
 
@@ -203,7 +203,7 @@ def test_maxwell_2d_2_patch_dirichlet_parallel_0():
     D1     = mapping_1(A)
     D2     = mapping_2(B)
 
-    connectivity = [((0,1,1),(1,1,-1))]
+    connectivity = [((0, 1, 1), (1, 1,-1), 1)]
     patches = [D1,D2]
     domain = Domain.join(patches, connectivity, 'domain')
     x,y    = domain.coordinates