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# Change pip's cache directory to be inside the project directory since we can
# only cache local items.
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:
.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
script:
- pip install .
test: # This job runs in the build stage, which runs first.
stage: test
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:
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
artifacts:
paths:
- public
rules:
- if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
name: quay.io/singularity/singularity:v3.7.0
entrypoint: [""]
- echo $SYLABSTOKEN
- singularity remote login --username $SREGISTRY_USERNAME --tokenfile $SYLABSTOKEN
- singularity build --remote library://nyhuma/ntrflows/ntr.sif:latest singularitybuild/ntrfc_container.def
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: