image: python:3.10 # Change pip's cache directory to be inside the project directory since we can # only cache local items. variables: PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip" LIBGL_ALWAYS_INDIRECT : 0 SREGISTRY_URL : "https://cloud.sylabs.io/" SREGISTRY_USERNAME : nyhuma # Pip's cache doesn't store the python packages # https://pip.pypa.io/en/stable/topics/caching/ # # If you want to also cache the installed packages, you have to install # them in a virtualenv and cache it as well. cache: paths: - .cache/pip - venv/ .before_script_template: &build_test before_script: - apt-get update -y && apt-get install libgl1-mesa-glx xvfb -y - python -m pip install --upgrade pip - python --version # For debugging - pip install virtualenv - virtualenv venv - source venv/bin/activate stages: # List of stages for jobs, and their order of execution - build - test - quality - docs - deploy build: stage: build <<: *build_test script: - pip install . test: # This job runs in the build stage, which runs first. stage: test <<: *build_test script: - pip install . - pip install -r requirements_dev.txt - pytest tests/. lint_test: # This job also runs in the test stage. stage: quality <<: *build_test # It can run at the same time as unit-test-job (in parallel). script: - pip install flake8 - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude='venv/' - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --exclude='venv/' jupyter_test: stage: quality <<: *build_test script: - apt-get install pandoc -y - apt-get install texlive-xetex texlive-fonts-recommended texlive-plain-generic -y - pip install nbconvert - cd examples # Loop through .ipynb files in the examples directory - for file in *.ipynb; do echo "Converting $file to PDF..."; jupyter nbconvert --execute "$file" --to pdf; done coverage_test: stage: quality <<: *build_test script: - pip install . - pip install -r requirements_dev.txt - python -m pytest --cov=ntrfc tests - coverage xml coverage: '/TOTAL.*\s+(\d+\%)/' artifacts: paths: - coverage.xml when: always pages: stage: docs <<: *build_test script: - pip install sphinx sphinx-rtd-theme - cd docs - make html - mv _build/html/ ../public/ artifacts: paths: - public rules: - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH build-singularity: image: name: quay.io/singularity/singularity:v3.7.0 entrypoint: [""] stage: deploy script: - echo $SYLABSTOKEN - singularity remote login --username $SREGISTRY_USERNAME --tokenfile $SYLABSTOKEN - singularity build --remote library://nyhuma/ntrflows/ntr.sif:latest singularitybuild/ntrfc_container.def only: - tags publish: stage: deploy <<: *build_test script: - pip install twine - python setup.py sdist bdist_wheel - twine upload --username $PYPI_USERNAME --password $PYPI_PASSWORD --verbose dist/* only: - tags