Adding containers logic #97
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| name: tests | |
| on: | |
| # workflow_dispatch | |
| push: | |
| branches: [ master ] | |
| paths-ignore: | |
| - '.gitignore' | |
| - '.readthedocs.yaml' | |
| - 'LICENSE' | |
| - 'setup.py' | |
| - 'README.md' | |
| - 'CITATION.cff' | |
| - 'references.jsonld' | |
| - '**/docs/**' | |
| - '**/json_schemas/**' | |
| - '.github/workflows/pr-tests.yml' | |
| - '**/test/data/**' | |
| - '**/test/references/**' | |
| - '.github/workflows/test_containers.yml' | |
| jobs: | |
| # Name of the Job | |
| lint_and_test: | |
| strategy: | |
| matrix: | |
| os: [mmbswarm] | |
| python-version: ["3.10", "3.11", "3.12"] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - run: echo "Repository -> ${{ github.repository }}" | |
| - run: echo "Branch -> ${{ github.ref }}" | |
| - run: echo "Trigger event -> ${{ github.event_name }}" | |
| - run: echo "Runner OS -> ${{ runner.os }}" | |
| - name: List files in the repository | |
| run: | | |
| ls ${{ github.workspace }} | |
| - name: Detect changed files and set test paths | |
| id: changes | |
| shell: bash | |
| run: | | |
| BEFORE="${{ github.event.before }}" | |
| AFTER="${{ github.sha }}" | |
| if [ "$BEFORE" = "0000000000000000000000000000000000000000" ]; then | |
| echo "New branch detected – running full test suite" | |
| echo "test_paths=" >> "$GITHUB_OUTPUT" | |
| exit 0 | |
| fi | |
| CHANGED_FILES=$(git diff --name-only "$BEFORE" "$AFTER" 2>/dev/null || echo "") | |
| echo "Changed files:" | |
| echo "${CHANGED_FILES:-(none)}" | |
| TESTS="" | |
| while IFS= read -r FILE; do | |
| [ -z "$FILE" ] && continue | |
| if [[ "$FILE" =~ ^${{ github.event.repository.name }}/test/unitests/test_[^/]+/test_[^/]+\.py$ ]]; then | |
| # Direct test file change – run only this file (skip container tests) | |
| if [[ "$FILE" != *_container.py ]]; then | |
| [ -f "$FILE" ] && TESTS+=$'\n'"$FILE" | |
| fi | |
| elif [[ "$FILE" =~ ^${{ github.event.repository.name }}/([a-z][^/]+)/([^/]+)\.py$ ]]; then | |
| TOOL="${BASH_REMATCH[1]}" | |
| BASE="${BASH_REMATCH[2]}" | |
| if [[ "$BASE" == "__init__" || "$BASE" == "common" ]]; then | |
| # Run all tests for this tool | |
| TEST_DIR="${{ github.event.repository.name }}/test/unitests/test_${TOOL}" | |
| [ -d "$TEST_DIR" ] && TESTS+=$'\n'"$TEST_DIR" | |
| else | |
| # Run the matching test file for this source file | |
| TEST_FILE="${{ github.event.repository.name }}/test/unitests/test_${TOOL}/test_${BASE}.py" | |
| if [ -f "$TEST_FILE" ]; then | |
| TESTS+=$'\n'"$TEST_FILE" | |
| else | |
| TEST_DIR="${{ github.event.repository.name }}/test/unitests/test_${TOOL}" | |
| [ -d "$TEST_DIR" ] && TESTS+=$'\n'"$TEST_DIR" | |
| fi | |
| fi | |
| fi | |
| done <<< "$CHANGED_FILES" | |
| TESTS=$(echo "$TESTS" | grep -v '^$' | sort -u | tr '\n' ' ' | xargs || echo "") | |
| echo "Test paths: ${TESTS:-(none detected – will run full suite)}" | |
| echo "test_paths=$TESTS" >> "$GITHUB_OUTPUT" | |
| - name: Remove all micromamba installations | |
| run: | | |
| rm -rf $HOME/.bash_profile $HOME/.conda $HOME/micromamba $HOME/micromamba-bin 2>/dev/null | |
| touch $HOME/.bash_profile | |
| - name: setup-micromamba | |
| uses: mamba-org/setup-micromamba@v2.0.0 | |
| with: | |
| generate-run-shell: true | |
| micromamba-version: '2.0.2-2' | |
| post-cleanup: 'all' | |
| init-shell: bash | |
| environment-file: .github/env.yaml | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| pytest | |
| pytest-cov | |
| pytest-html | |
| flake8 | |
| pip | |
| - name: Install genbadge from pip | |
| shell: bash -l {0} | |
| run: pip install genbadge[all] | |
| - name: List installed package versions | |
| shell: bash -l {0} | |
| run: micromamba list | |
| - name: Lint with flake8 | |
| shell: bash -l {0} | |
| run: | | |
| # F Codes: https://flake8.pycqa.org/en/latest/user/error-codes.html | |
| # E Code: https://pycodestyle.pycqa.org/en/latest/intro.html#error-codes | |
| # Workflow fails: Stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # Create directory for flake8 reports | |
| mkdir -p ./reports/flake8 | |
| # Exit-zero treats all errors as warnings, workflow will not fail: | |
| flake8 . --exclude=docs --ignore=C901,E226 --count --exit-zero --max-complexity=10 --max-line-length=9999 --statistics --format=html --htmldir=./reports/flake8/ --tee --output-file=./reports/flake8/flake8stats.txt | |
| - name: Generate Flake8 badge | |
| shell: bash -l {0} | |
| run: | | |
| genbadge flake8 --name "Flake8" --input-file ./reports/flake8/flake8stats.txt --output-file ./reports/flake8/flake8badge.svg | |
| - name: Run tests | |
| shell: bash -l {0} | |
| run: | | |
| # Ignoring docker and singularity tests | |
| export PYTHONPATH=.:$PYTHONPATH | |
| # Create directory for tests reports | |
| mkdir -p ./reports/junit | |
| # Run only tests for modified tools, fall back to full suite when nothing specific detected | |
| TEST_PATHS="${{ steps.changes.outputs.test_paths }}" | |
| if [ -z "$TEST_PATHS" ]; then | |
| TEST_PATHS="${{ github.event.repository.name }}/test/unitests/" | |
| fi | |
| pytest $TEST_PATHS --cov=${{ github.event.repository.name }}/ --cov-report=xml --ignore-glob=*container.py --junit-xml=./reports/junit/junit.xml --html=./reports/junit/report.html | |
| - name: Generate Tests badge | |
| shell: bash -l {0} | |
| run: | | |
| genbadge tests --name "Tests" --input-file ./reports/junit/junit.xml --output-file ./reports/junit/testsbadge.svg | |
| - name: Generate Coverage badge | |
| shell: bash -l {0} | |
| run: | | |
| # Create directory for flake8 reports | |
| mkdir -p ./reports/coverage | |
| coverage xml -o ./reports/coverage/coverage.xml | |
| coverage html -d ./reports/coverage/ | |
| genbadge coverage --name "Coverage" --input-file ./reports/coverage/coverage.xml --output-file ./reports/coverage/coveragebadge.svg | |
| - name: Publish coverage report to GitHub Pages | |
| uses: JamesIves/github-pages-deploy-action@v4 | |
| with: | |
| folder: ./reports | |