More test fixes and code simplification #1259

Workflow file for this run

	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 docs (python ${{ matrix.python-version }})
	if: "!contains(github.event.head_commit.message, '[skip ci]') && github.actor != 'allcontributors'"
	runs-on: ubuntu-22.04
	strategy:
	matrix:
	python-version: [ "3.10", "3.11" ]
	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 install --with docs

	- name: Compile the documentation
	run: \|
	poetry run sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
	mkdir -p docs-src/_static
	poetry run 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: Set up the environment
	uses: ./.github/actions/setup-poetry-env
	with:
	python-version: ${{ matrix.python-version }}

	# update Identifiers.org namespaces
	- name: Update Identifiers.org namespaces
	run: poetry run python -c "from biosimulators_utils.utils.identifiers_org import get_identifiers_org_namespaces; get_identifiers_org_namespaces(reload=True);"

	- name: Test the updated Identifiers.org namespaces
	uses: GabrielBB/xvfb-action@v1
	env:
	MPLBACKEND: PDF
	with:
	run: poetry 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: poetry install --with docs

	- name: Compile the documentation
	run: \|
	poetry run sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
	mkdir -p docs-src/_static
	poetry run 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: Create packages to upload to PyPI
	run: \|
	poetry build

	- name: Upload packages to PyPI
	env:
	POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
	run: \|
	poetry publish --no-interaction --username __token__ --password $POETRY_PYPI_TOKEN_PYPI

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

More test fixes and code simplification #1259

Workflow file

More test fixes and code simplification #1259

Jobs

Run details

Workflow file for this run