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[CI/CD](linting_and_testing.yml): Update set-up micromamba.
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name: tests | ||
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on: | ||
# workflow_dispatch | ||
push: | ||
branches: [ master ] | ||
paths-ignore: | ||
- '.gitignore' | ||
- '.readthedocs.yaml' | ||
- 'LICENSE' | ||
- 'setup.py' | ||
- 'README.md' | ||
- 'CITATION.cff' | ||
- 'references.jsonld' | ||
- '**/docs/**' | ||
- '**/json_schemas/**' | ||
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jobs: | ||
# Name of the Job | ||
lint_and_test: | ||
strategy: | ||
matrix: | ||
os: [self-hosted] | ||
python-version: ["3.9", "3.10", "3.11", "3.12"] | ||
runs-on: ${{ matrix.os }} | ||
steps: | ||
- name: Check out repository code | ||
uses: actions/checkout@v4 | ||
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- run: echo "Repository -> ${{ github.repository }}" | ||
- run: echo "Branch -> ${{ github.ref }}" | ||
- run: echo "Trigger event -> ${{ github.event_name }}" | ||
- run: echo "Runner OS -> ${{ runner.os }}" | ||
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- name: List files in the repository | ||
run: | | ||
ls ${{ github.workspace }} | ||
- name: Remove all micromamba installations | ||
run: | | ||
rm -rf /home/user/.bash_profile /home/user/.conda /home/user/micromamba /home/user/micromamba-bin 2>/dev/null | ||
touch /home/user/.bash_profile | ||
- name: setup-micromamba | ||
uses: mamba-org/[email protected] | ||
with: | ||
generate-run-shell: true | ||
micromamba-version: '2.0.2-2' | ||
post-cleanup: 'all' | ||
init-shell: bash | ||
environment-file: .github/env.yaml | ||
create-args: >- | ||
python=${{ matrix.python-version }} | ||
pytest | ||
pytest-cov | ||
pytest-html | ||
flake8 | ||
pip | ||
- name: Install genbadge from pip | ||
shell: bash -l {0} | ||
run: pip install genbadge[all] | ||
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- name: List installed package versions | ||
shell: bash -l {0} | ||
run: micromamba list | ||
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- 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=999 --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: Checkout biobb_common | ||
uses: actions/checkout@v4 | ||
with: | ||
repository: bioexcel/biobb_common | ||
path: './biobb_common' | ||
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- name: Run tests | ||
shell: bash -l {0} | ||
run: | | ||
# Ignoring docker and singularity tests | ||
export PYTHONPATH=.:./biobb_common:$PYTHONPATH | ||
# Create directory for tests reports | ||
mkdir -p ./reports/junit | ||
# Producction one | ||
pytest biobb_pmx/test/unitests/ --cov=biobb_pmx/ --cov-report=xml --ignore-glob=*container.py --ignore-glob=*docker.py --ignore-glob=*singularity.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 |