Merge pull request #157 from davidrudlstorfer/add_pytest_infrastructure

Add pytest framework to MeshPy

- Provide pytest infrastructure including
  - Tags/Markers for different test scenarious
  - Fixtures to simplify testing
  - Comparison utils for all sort of types

- Port rotation tests to pytest
- Port cosserat curve to pytest

- Update github actions
  - Simplify testing procedure
  - Update artifact upload

- Remove files from old testing framework

Author: davidrudlstorfer

.github/actions/run_performance_tests/action.yml

@@ -9,45 +9,27 @@ inputs:
     description: Command to source the virtual environment
     required: false
     default: ""
-  require_four_c:
-    description: Fail if the 4C tests can not be performed
+  additional-pytest-flags:
+    description: Additional flags to pass to pytest, i.e., markers
     required: false
-    default: 1
-  require_arborx:
-    description: Fail if the ArborX tests can not be performed
-    required: false
-    default: 1
-  require_cubitpy:
-    description: Fail if the CubitPy tests can not be performed
-    required: false
-    default: 1
-  coverage_config:
-    description: Config file to use for coverage analysis
-    required: false
-    default: "coverage.config"
+    default: ""
 runs:
   using: composite
   steps:
     - name: MeshPy testing
       shell: bash
       env:
         MESHPY_FOUR_C_EXE: /home/user/4C/build/4C
-        TESTING_GITHUB: 1
-        TESTING_GITHUB_4C: ${{ inputs.require_four_c }}
-        TESTING_GITHUB_ARBORX: ${{ inputs.require_arborx }}
-        TESTING_GITHUB_CUBITPY: ${{ inputs.require_cubitpy }}
         CUBIT_ROOT: /imcs/public/compsim/opt/cubit-15.2
         OMPI_MCA_rmaps_base_oversubscribe: 1
+        PERFORMANCE_TESTING_HOST: github-sisyphos-docker
       run: |
         cd ${GITHUB_WORKSPACE}
         ${{ inputs.source-command }}
         pip install ${{ inputs.install-command }}
         python --version
         pip list
-        cd tests
-        coverage run --rcfile=${{ inputs.coverage_config }} testing_main.py
-        coverage html
-        coverage report
-        coverage-badge -o htmlcov/coverage.svg
-        coverage run --rcfile=${{ inputs.coverage_config }} -m pytest pytest_testing_cosserat_curve.py
-        coverage report
+        TEMP_DIR="${RUNNER_TEMP}/meshpy_pytest"
+        mkdir -p "$TEMP_DIR"
+        echo "PYTEST_TMPDIR=$TEMP_DIR" >> $GITHUB_ENV
+        pytest  --basetemp="$TEMP_DIR" ${{ inputs.additional-pytest-flags}}

.github/actions/run_tests/action.yml

@@ -47,16 +47,12 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Run the test suite
         uses: ./.github/actions/run_tests
-        with:
-          require_four_c: 0
-          require_arborx: 0
-          require_cubitpy: 0
       - name: Upload test results on failure
         if: failure()
         uses: actions/upload-artifact@v4
         with:
           name: ${{github.job}}-${{ matrix.os-version }}-python${{ matrix.python-version }}-${{github.run_number}}
-          path: ${{github.workspace}}/tests/testing-tmp/
+          path: ${{ env.PYTEST_TMPDIR }}
 
   meshpy-testing-cubitpy:
     name: self-hosted with CubitPy
@@ -75,14 +71,13 @@ jobs:
         uses: ./.github/actions/run_tests
         with:
           source-command: "source python-testing-environment/bin/activate"
-          require_four_c: 0
-          require_arborx: 0
+          additional-pytest-flags: "--CubitPy"
       - name: Upload test results on failure
         if: failure()
         uses: actions/upload-artifact@v4
         with:
           name: ${{github.job}}-${{github.run_number}}
-          path: ${{github.workspace}}/tests/testing-tmp/
+          path: ${{ env.PYTEST_TMPDIR }}
 
   meshpy-testing-4C-arborx:
     name: ubuntu-latest with 4C and ArborX
@@ -106,14 +101,13 @@ jobs:
         with:
           source-command: "source python-testing-environment/bin/activate"
           install-command: "-e .[CI-CD]"
-          require_cubitpy: 0
-          coverage_config: "coverage_local.config"
+          additional-pytest-flags: "--4C --ArborX"
       - name: Upload test results on failure
         if: failure()
         uses: actions/upload-artifact@v4
         with:
           name: ${{github.job}}-${{github.run_number}}
-          path: ${{github.workspace}}/tests/testing-tmp/
+          path: ${{ env.PYTEST_TMPDIR }}
 
   meshpy-performance-testing:
     name: performance tests
@@ -129,5 +123,15 @@ jobs:
         uses: ./.github/actions/setup_virtual_python_environment
         with:
           python-exe: /home_local/github-runner/testing_lib/spack/opt/spack/linux-ubuntu20.04-icelake/gcc-9.4.0/python-3.12.1-qnjucxirxh534suwewl6drfa237u6t7w/bin/python
-      - name: Run the performance test suite
-        uses: ./.github/actions/run_performance_tests
+      - name: Run the test suite
+        uses: ./.github/actions/run_tests
+        with:
+          source-command: "source python-testing-environment/bin/activate"
+          install-command: ".[CI-CD]"
+          additional-pytest-flags: "--performance-tests --exclude-standard-tests"
+      - name: Upload test results on failure
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{github.job}}-${{github.run_number}}
+          path: ${{ env.PYTEST_TMPDIR }}

.github/workflows/testing.yml

@@ -86,16 +86,21 @@ tests with 4C
 export MESHPY_FOUR_C_EXE=path_to_4C
 ```
 
-To check if everything worked as expected, run the tests
+To check if everything worked as expected, run the standard tests with
 ```bash
-cd <path_to_meshpy>/tests
-python testing_main.py
+pytest
 ```
 
-Also run the performance tests (the reference time values and host name might have to be adapted in the file `<path_to_meshpy>/tests/performance_testing.py`)
+Further tests can be added with the following flags: `--4C`, `--ArborX`, `--CubitPy`, `--performance-tests`.
+These can be arbitrarily combined, for example
 ```bash
-cd <path_to_meshpy>/tests
-python performance_testing.py
+pytest --4C --CubityPy
+```
+executes the standard tests, the 4C tests and the CubitPy tests. Note that the reference time values for the performance tests might not suite your system.
+
+Finally, the base tests can be deactivated with `--exclude-standard-tests`. For example to just run the CubitPy tests execute
+```bash
+pytest --CubitPy --exclude-standard-tests
 ```
 
 Before you are ready to contribute to MeshPy, please make sure to install the `pre-commit hook` within the python environment to follow our style guides:
@@ -122,8 +127,8 @@ cd <path_to_meshpy>/build/geometric_search
 cmake ../../meshpy/geometric_search/src/
 make -j4
 ```
+
 If the ArborX extension is working correctly can be checked by running the geometric search tests
 ```bash
-cd <path_to_meshpy>/tests
-python testing_geometric_search.py
+pytest --ArborX
 ```

README.md

@@ -39,6 +39,7 @@ dependencies = [
   "numpy-quaternion",
   "pre-commit",
   "pytest",
+  "pytest-cov",
   "pyvista",
   "pyvista_utils@git+https://github.com/isteinbrecher/pyvista_utils.git@main",
   "scipy",
@@ -55,3 +56,13 @@ CI-CD = [
   "cubitpy@git+https://github.com/imcs-compsim/cubitpy.git@main",
   "setuptools" # Needed for coverage-badge
 ]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "-p pytest_cov --cov-report=term --cov-report=html --cov-fail-under=0 --cov=meshpy/ --cov=tutorial/ --cov-append"
+markers = [
+  "fourc: tests in combination with 4C",
+  "arborx: tests in combination with ArborX",
+  "cubitpy: tests in combination with CubitPy",
+  "performance: performance tests of MeshPy"
+]

pyproject.toml

@@ -28,4 +28,4 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 # -----------------------------------------------------------------------------
-"""This module defines testing functionality for MeshPy."""
+"""This module tests MeshPy."""