references #14
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name: tests | |
on: | |
# workflow_dispatch | |
push: | |
branches: [ master ] | |
paths-ignore: | |
- '.gitignore' | |
- '.readthedocs.yaml' | |
- 'LICENSE' | |
- 'setup.py' | |
- 'README.md' | |
- 'references.jsonld' | |
- '**/docs/**' | |
- '**/json_schemas/**' | |
jobs: | |
# Name of the Job | |
lint_and_test: | |
strategy: | |
matrix: | |
os: [self-hosted] | |
python-version: ["3.8", "3.9", "3.10"] | |
runs-on: ${{ matrix.os }} | |
steps: | |
- name: Check out repository code | |
uses: actions/checkout@v3 | |
- 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 ${{ github.workspace }} | |
- name: Remove all micromamba installations | |
run: | | |
rm -rf /home/user/.bash_profile /home/user/.conda /home/user/micromamba /home/user/micromamba-bin 2>/dev/null | |
touch /home/user/.bash_profile | |
- name: provision-with-micromamba | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
generate-run-shell: true | |
post-cleanup: all | |
environment-file: .github/env.yaml | |
create-args: >- | |
python=${{ matrix.python-version }} | |
pytest | |
pytest-cov | |
pytest-html | |
flake8 | |
pip | |
- name: Install genbadge from pip | |
shell: micromamba-shell {0} # necessary for conda env to be active | |
run: pip install genbadge[all] | |
- name: List installed package versions | |
shell: micromamba-shell {0} # necessary for conda env to be active | |
run: micromamba list | |
- name: Lint with flake8 | |
shell: micromamba-shell {0} # necessary for conda env to be active | |
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 | |
# Do not check for undefined names fix_pdb_utils.py should be fixed | |
flake8 . --count --select=E9,F63,F7 --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: micromamba-shell {0} # necessary for conda env to be active | |
run: | | |
genbadge flake8 --name "Flake8" --input-file ./reports/flake8/flake8stats.txt --output-file ./reports/flake8/flake8badge.svg | |
- name: Checkout biobb_common | |
uses: actions/checkout@v3 | |
with: | |
repository: bioexcel/biobb_common | |
path: './biobb_common' | |
- name: Run tests | |
shell: micromamba-shell {0} # necessary for conda env to be active | |
run: | | |
# Ignoring docker and singularity tests | |
export PYTHONPATH=.:./biobb_common:$PYTHONPATH | |
# Create directory for tests reports | |
mkdir -p ./reports/junit | |
# Producction one | |
# pytest biobb_model/test/unitests/ --cov=./ --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 | |
# Avoiding fix_backbone because of the modeller installation | |
pytest biobb_model/test/unitests/ --cov=./ --cov-report=xml --ignore-glob=*fix_backbone.py --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: micromamba-shell {0} # necessary for conda env to be active | |
run: | | |
genbadge tests --name "Tests" --input-file ./reports/junit/junit.xml --output-file ./reports/junit/testsbadge.svg | |
- name: Generate Coverage badge | |
shell: micromamba-shell {0} # necessary for conda env to be active | |
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 | |