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Attempted hotfix to avoid docker api version error in singularity #1184

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Attempted hotfix to avoid docker api version error in singularity

Attempted hotfix to avoid docker api version error in singularity #1184

Workflow file for this run

.github/workflows/ci.yml at 073b10a
name: Continuous integration
on:
push:
pull_request:
jobs:
getVersionNumber:
name: Get version number
if: "startsWith(github.ref, 'refs/tags/') && !contains(github.event.head_commit.message, '[skip ci]') && github.actor != 'allcontributors'"
runs-on: ubuntu-22.04
outputs:
version: ${{ steps.get-version-number.outputs.version }}
steps:
- id: get-version-number
name: Get version number
env:
TAG: ${{ github.ref }}
run: |
version="${TAG/refs\/tags\//}"
echo "version=$version" >> $GITHUB_OUTPUT
build:
name: Lint, test, and compile documentation
if: "!contains(github.event.head_commit.message, '[skip ci]') && github.actor != 'allcontributors'"
runs-on: ubuntu-22.04
strategy:
matrix:
python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12" ]
fail-fast: false
defaults:
run:
shell: bash
steps:
- name: Checkout repository
uses: actions/checkout@v4
with:
fetch-depth: 1
- name: Install Java # for pyNeuroML
uses: actions/setup-java@v2
with:
distribution: 'adopt'
java-version: '15'
- name: Install Perl # for BioNetGen
run: |
sudo apt-get update -y
sudo apt-get install -y --no-install-recommends perl
- name: Install XPP
run: |
sudo apt-get install -y --no-install-recommends wget make gcc libx11-dev libc6-dev xppaut
- name: Install Singularity # to validate that the Docker image can be converted into a Singularity image
uses: eWaterCycle/setup-singularity@v5
with:
singularity-version: 3.7.1
# install package
- name: Set up the environment
uses: ./.github/actions/setup-poetry-env
with:
python-version: ${{ matrix.python-version }}
- name: Lint the package
run: poetry run python -m flake8
- name: Run the tests
uses: GabrielBB/xvfb-action@v1
env:
MPLBACKEND: PDF
# BIOSIMULATORS_API_ENDPOINT: https://api.biosimulators.dev/ # uncomment to execute tests with the dev deployment
with:
run: poetry run python -m pytest tests/ --cov=./biosimulators_utils --cov-report=xml
- name: Upload the coverage report to Codecov
uses: codecov/codecov-action@v2
with:
token: ${{ secrets.CODECOV_TOKEN }}
flags: unittests
file: ./coverage.xml
# compile documentation
#- name: Install the requirements for compiling the documentation
# run: poetry run python -m pip install -r docs-src/requirements.txt
#- name: Compile the documentation
# run: |
# sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
# mkdir -p docs-src/_static
# sphinx-build docs-src docs
release:
name: Release a new version
needs: [getVersionNumber, build]
runs-on: ubuntu-22.04
steps:
- name: Checkout code
uses: actions/checkout@v4
with:
fetch-depth: 1
ref: dev
- name: Configure Git
run: |
git config --local user.email "[email protected]"
git config --local user.name "biosimulatorsdaemon"
git config pull.rebase false
- name: Install Python
uses: actions/setup-python@v5
with:
python-version: '3.9'
- name: Setup pip cache
uses: actions/cache@v2
with:
path: /opt/hostedtoolcache/Python
key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('poetry.lock') }}
restore-keys: |
${{ runner.os }}-pip-
- name: Install pip and setuptools
run: |
python -m pip install pip==20.3.4
python -m pip install --upgrade setuptools
# install package
- name: Install the package
run: python -m pip install .[all]
# update Identifiers.org namespaces
- name: Update Identifiers.org namespaces
run: python -c "from biosimulators_utils.utils.identifiers_org import get_identifiers_org_namespaces; get_identifiers_org_namespaces(reload=True);"
- name: Install pytest
run: python -m pip install pytest
- name: Install the requirements for the tests
run: python -m pip install .[tests]
- name: Test the updated Identifiers.org namespaces
uses: GabrielBB/xvfb-action@v1
env:
MPLBACKEND: PDF
with:
run: python -m pytest tests/utils/test_identifiers_org_utils.py
- id: commit-identifiers-namespaces
name: Commit the Identifiers.org namespaces
run: |
git stash
git pull
set +e
git stash pop
git add biosimulators_utils/utils/identifiers_org.json
git commit -m "chore: Updated Identifiers.org namespaces [skip ci]"
if [[ $? = 0 ]]; then
changed=1
else
changed=0
fi
echo "changed=$changed" >> $GITHUB_OUTPUT
# compile and push documentation
- name: Install the requirements for compiling the documentation
run: python -m pip install -r docs-src/requirements.txt
- name: Compile the documentation
run: |
sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
mkdir -p docs-src/_static
sphinx-build docs-src docs
- id: commit-docs
name: Commit the compiled documentation
run: |
git stash
git pull
set +e
git stash pop
git add docs
git commit -m "chore: Updated compiled documentation [skip ci]"
if [[ $? = 0 ]]; then
changed=1
else
changed=0
fi
echo "changed=$changed" >> $GITHUB_OUTPUT
- name: Push the compiled documentation
if: steps.commit-identifiers-namespaces.outputs.changed == '1' || steps.commit-docs.outputs.changed == '1'
uses: ad-m/github-push-action@master
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
branch: dev
# Create GitHub release
- name: Create GitHub release
uses: actions/create-release@v1
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
tag_name: ${{ needs.getVersionNumber.outputs.version }}
release_name: Release ${{ needs.getVersionNumber.outputs.version }}
# Create PyPI release
- name: Install twine
run: |
python -m pip install wheel twine
- name: Create packages to upload to PyPI
run: |
python setup.py sdist
python setup.py bdist_wheel
- name: Upload packages to PyPI
env:
TWINE_USERNAME: __token__
TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
run: |
twine upload dist/*