Dropping DAE/ODE labels from many things. #199

Workflow file for this run

	name: Test and release

	on:
	push:

	jobs:
	test:
	name: Run unit tests on the ontology
	if: "!contains(github.event.head_commit.message, '[Skip CI]')"
	runs-on: ubuntu-latest
	steps:
	# Check out the repository
	- name: Checkout repo
	uses: actions/checkout@master
	with:
	fetch-depth: 1

	# Install the requirements for the tests
	- name: Install Python
	uses: actions/setup-python@v2
	with:
	python-version: '3.9'

	- name: Setup pip cache
	uses: actions/cache@v2
	with:
	path: /opt/hostedtoolcache/Python
	key: ${{ runner.os }}-pip-${{ hashFiles('libkisao/python/requirements.txt') }}-${{ hashFiles('libkisao/python/tests/requirements.txt') }}
	restore-keys: \|
	${{ runner.os }}-pip-

	- name: Install pip and setuptools
	run: \|
	python -m pip install --upgrade pip==23.0.0
	python -m pip install --upgrade pip==23.0.0

	- name: Install the Python KiSAO package
	working-directory: libkisao/python
	run: \|
	cp ../../kisao.owl kisao/
	python -m pip install .[all]

	# Lint the package
	- name: Install flake8
	run: python -m pip install flake8

	- name: Lint the package
	working-directory: libkisao/python
	run: python -m flake8

	# Run the tests
	- name: Install the requirements for the tests
	working-directory: libkisao/python
	run: \|
	python -m pip install pytest pytest-cov
	python -m pip install -r tests/requirements.txt

	- name: Run the tests
	working-directory: libkisao/python
	run: python -m pytest tests/ --cov

	# Compile documentation
	- name: Install the requirements for compiling the documentation
	working-directory: libkisao/python
	run: python -m pip install -r docs-src/requirements.txt

	- name: Compile the documentation
	working-directory: libkisao/python
	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

	- name: Compile a report of the substitutability among algorithms
	working-directory: libkisao/python
	shell: python
	run: \|
	import kisao.utils
	import os
	report = kisao.utils.get_algorithm_substitution_matrix()
	report.to_csv(os.path.join('docs', 'algorithm-substitutability.csv'))

	- name: Upload the coverage report to Codecov
	if: false
	uses: codecov/codecov-action@v2
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	flags: unittests
	file: ./libkisao/python/coverage.xml

	getMainBranchHeadRevision:
	name: Get the head revision of the main branch
	if: startsWith(github.ref, 'refs/tags/')
	runs-on: ubuntu-latest
	outputs:
	mainBranchHeadRevision: ${{ steps.get-main-branch.outputs.mainBranchHeadRevision }}
	steps:
	- name: Clone repository
	run: \|
	git clone https://${{ github.actor }}:${{ secrets.GITHUB_TOKEN }}@github.com/${{ github.repository }} .

	- id: get-main-branch
	name: Determine main branch
	run: \|
	mainBranch=$(git symbolic-ref refs/remotes/origin/HEAD \| cut -d '/' -f 4)
	mainBranchHeadRevision=$(git rev-parse refs/remotes/origin/${mainBranch})
	echo "mainBranchHeadRevision=$mainBranchHeadRevision" >> $GITHUB_OUTPUT

	determineIfReleaseNeeded:
	name: Determine if the package should be released
	needs:
	- getMainBranchHeadRevision
	if: startsWith(github.ref, 'refs/tags/')
	runs-on: ubuntu-latest
	outputs:
	release: ${{ steps.determine-if-release-needed.outputs.release }}
	steps:
	# Check out the repository
	- name: Checkout repo
	uses: actions/checkout@master
	with:
	fetch-depth: 1

	- id: determine-if-release-needed
	name: Determine if a release should be made
	run: \|
	release="0"

	if [[ "${{ github.ref }}" =~ ^refs/tags/ ]]; then
	echo "First check passed"
	tag_hash=$(git rev-parse "${{ github.ref }}")
	echo "tag_hash: $tag_hash"
	if [ "$tag_hash" == "${{ needs.getMainBranchHeadRevision.outputs.mainBranchHeadRevision }}" ]; then
	echo "Second check passed"
	release="1"
	fi
	fi

	echo "release=$release" >> $GITHUB_OUTPUT
	echo "release=$release"

	commitCompiledDocumentation:
	name: Commit and push compiled documentation to GitHub
	needs:
	- test
	- determineIfReleaseNeeded
	if: startsWith(github.ref, 'refs/tags/') && needs.determineIfReleaseNeeded.outputs.release == '1'
	runs-on: ubuntu-latest
	steps:
	# Check out the repository
	- name: Checkout repo
	uses: actions/checkout@master
	with:
	fetch-depth: 1
	# ref: dev
	# token: ${{ secrets.ADMIN_GITHUB_TOKEN }}

	# Install the requirements for the tests
	- name: Install Python
	uses: actions/setup-python@v2
	with:
	python-version: '3.9'

	- name: Setup pip cache
	uses: actions/cache@v2
	with:
	path: /opt/hostedtoolcache/Python
	key: ${{ runner.os }}-pip-${{ hashFiles('libkisao/python/requirements.txt') }}-${{ hashFiles('libkisao/python/tests/requirements.txt') }}
	restore-keys: \|
	${{ runner.os }}-pip-

	- name: Install pip and setuptools
	run: \|
	python -m pip install --upgrade pip==23.0.0
	python -m pip install --upgrade pip==23.0.0

	- name: Install the Python KiSAO package
	working-directory: libkisao/python
	run: \|
	cp ../../kisao.owl kisao/
	python -m pip install .[all]

	- name: Install the requirements for compiling the documentation
	working-directory: libkisao/python
	run: python -m pip install -r docs-src/requirements.txt

	- name: Compile the documentation
	working-directory: libkisao/python
	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

	- name: Compile a report of the substitutability among algorithms
	working-directory: libkisao/python
	shell: python
	run: \|
	import kisao.utils
	import os
	report = kisao.utils.get_algorithm_substitution_matrix()
	report.to_csv(os.path.join('docs', 'algorithm-substitutability.csv'))

	# If new tag, commit and push documentation
	- name: Configure Git
	run: \|
	git config --local user.email "[email protected]"
	git config --local user.name "SED-ML bot"
	git config pull.rebase false

	- id: commit-docs
	name: Commit the compiled documentation
	working-directory: libkisao/python
	run: \|
	git stash
	git pull
	set +e
	git stash pop
	git add docs
	git commit -m "Updated compiled documentation [Skip CI]"
	git checkout .
	git clean -f -d
	if [[ $? = 0 ]]; then
	docsChanged=1
	else
	docsChanged=0
	fi
	echo "docsChanged=$docsChanged" >> $GITHUB_OUTPUT

	- name: Push the compiled documentation
	if: startsWith(github.ref, 'refs/tags/') && steps.commit-docs.outputs.docsChanged == '1'
	uses: ad-m/github-push-action@master
	with:
	github_token: ${{ secrets.ADMIN_GITHUB_TOKEN }}
	branch: ${{ steps.get-main-branch.outputs.mainBranch }}

	createGitHubRelease:
	name: Create GitHub release
	needs:
	- test
	- determineIfReleaseNeeded
	if: startsWith(github.ref, 'refs/tags/') && needs.determineIfReleaseNeeded.outputs.release == '1'
	runs-on: ubuntu-latest
	steps:
	- name: Checkout repo
	uses: actions/checkout@master
	with:
	fetch-depth: 1
	# ref: dev
	# token: ${{ secrets.ADMIN_GITHUB_TOKEN }}

	- name: Merge dev branch into deploy branch
	uses: devmasx/[email protected]
	with:
	type: now
	target_branch: deploy
	github_token: ${{ secrets.ADMIN_GITHUB_TOKEN }}

	- id: get-version
	name: Get version number
	env:
	TAG: ${{ github.ref }}
	run: \|
	version="${TAG/refs\/tags\//}"
	echo "version=$version" >> $GITHUB_OUTPUT

	- name: Create GitHub release
	uses: "marvinpinto/action-automatic-releases@latest"
	with:
	repo_token: "${{ secrets.ADMIN_GITHUB_TOKEN }}"
	draft: false
	prerelease: false
	automatic_release_tag: ${{ steps.get-version.outputs.version }}

	releaseToBioPortal:
	name: Release version to BioPortal
	needs:
	- test
	- determineIfReleaseNeeded
	if: startsWith(github.ref, 'refs/tags/') && needs.determineIfReleaseNeeded.outputs.release == '1'
	runs-on: ubuntu-latest
	steps:
	- name: Checkout repo
	uses: actions/checkout@master

	- name: Install jq
	run: \|
	sudo apt-get update -y
	sudo apt-get install -y --no-install-recommends jq moreutils

	- name: Prepare BioPortal submission
	env:
	TAG: ${{ github.ref }}
	run: \|
	version="${TAG/refs\/tags\//}"
	released=$(date --iso-8601=second)
	cp .github/workflows/BioPortal-submission.json .github/workflows/BioPortal-submission-version.json
	jq \
	".pullLocation = \"https://raw.githubusercontent.com/SED-ML/KiSAO/${version}/kisao.owl\"" \
	.github/workflows/BioPortal-submission-version.json \| sponge .github/workflows/BioPortal-submission-version.json
	jq \
	".version = \"${version}\"" \
	.github/workflows/BioPortal-submission-version.json \| sponge .github/workflows/BioPortal-submission-version.json
	jq \
	".released = \"${released}\"" \
	.github/workflows/BioPortal-submission-version.json \| sponge .github/workflows/BioPortal-submission-version.json

	- name: Submit to BioPortal
	run: \|
	curl -X POST \
	-H "Authorization: apikey token=${{ secrets.BIOPORTAL_API_KEY }}" \
	-H "Content-Type: application/json" \
	-H "Accept: application/json" \
	-d @.github/workflows/BioPortal-submission-version.json \
	http://data.bioontology.org/ontologies/KISAO/submissions
	echo

	releaseToPyPI:
	name: Release version to PyPI
	needs:
	- test
	- determineIfReleaseNeeded
	if: startsWith(github.ref, 'refs/tags/') && needs.determineIfReleaseNeeded.outputs.release == '1'
	runs-on: ubuntu-latest
	steps:
	# Check out the repository
	- name: Checkout repo
	uses: actions/checkout@master
	with:
	fetch-depth: 1

	# Install the requirements for the tests
	- name: Install Python
	uses: actions/setup-python@v2
	with:
	python-version: '3.9'

	- name: Setup pip cache
	uses: actions/cache@v2
	with:
	path: /opt/hostedtoolcache/Python
	key: ${{ runner.os }}-pip-${{ hashFiles('libkisao/python/requirements.txt') }}-${{ hashFiles('libkisao/python/tests/requirements.txt') }}
	restore-keys: \|
	${{ runner.os }}-pip-

	- name: Install pip
	run: \|
	python -m pip install --upgrade pip==23.0.0
	python -m pip install --upgrade pip==23.0.0

	# Create PyPI release
	- name: Create PyPI release
	working-directory: libkisao/python
	env:
	TWINE_USERNAME: __token__
	TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
	run: \|
	# Install pandoc
	sudo apt-get update -y
	sudo apt-get install -y --no-install-recommends wget
	wget "https://github.com/jgm/pandoc/releases/download/3.1.3/pandoc-3.1.3-1-amd64.deb" -O /tmp/pandoc.deb
	sudo dpkg -i /tmp/pandoc.deb
	rm /tmp/pandoc.deb

	# Copy OWL file and LICENSE so it can be bundled into the Python package
	cp ../../kisao.owl kisao/
	cp ../../LICENSE .

	# Convert README to .rst format
	pandoc --from=gfm --output=README.rst --to=rst README.md

	# Install twine
	python -m pip install wheel twine

	# Create packages to upload to PyPI
	python setup.py sdist
	python setup.py bdist_wheel

	# Upload packages to PyPI
	twine upload dist/*

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Dropping DAE/ODE labels from many things. #199

Workflow file

Dropping DAE/ODE labels from many things. #199

Jobs

Run details

Workflow file for this run