Add workflow for building the docs #137

Workflow file for this run

.github/workflows/test_and_deploy.yml at ea3453e

	---
	name: "CI & CD"

	on:
	workflow_dispatch:
	pull_request:
	release:
	types:
	- published

	concurrency:
	group: ${{ github.workflow }}-${{ github.head_ref \|\| github.run_id }}
	cancel-in-progress: true

	env:
	CIBW_BUILD: cp39-* cp310-* cp311-*
	CIBW_TEST_EXTRAS: test
	CIBW_TEST_COMMAND: >
	pytest {project}
	--durations=50
	--ignore={project}//tests//structure//test_trajectory.py
	--ignore={project}//tests//sequence//align//test_statistics.py
	--ignore={project}//tests//application
	--ignore={project}//tests//database
	--ignore={project}//tests//test_doctest.py
	--ignore={project}//tests//test_modname.py
	CIBW_DEPENDENCY_VERSIONS: "pinned"
	# Once GHA and cibuildwheel are updated this can be removed
	# mussllinux takes 6+ hrs to build and test so ignore it
	CIBW_TEST_SKIP: "musllinux *-macosx_arm64"


	jobs:
	generate-wheels-matrix:
	name: "Generate wheels matrix"
	runs-on: "ubuntu-latest"
	outputs:
	include: ${{ steps.set-matrix.outputs.include }}
	steps:
	- uses: actions/checkout@v3
	- name: Install cibuildwheel
	# MAKE SURE THIS STAYS IN SYNC WITH THE LOWER GHA cibuildwheel
	run: pipx install cibuildwheel==2.11.4
	- id: set-matrix
	run: \|
	MATRIX=$(
	{
	cibuildwheel --print-build-identifiers --platform linux \
	\| jq -nRc '{"only": inputs, "os": "ubuntu-20.04"}' \
	&& cibuildwheel --print-build-identifiers --platform macos \
	\| jq -nRc '{"only": inputs, "os": "macos-11"}' \
	&& cibuildwheel --print-build-identifiers --platform windows \
	\| jq -nRc '{"only": inputs, "os": "windows-2019"}'
	} \| jq -sc
	)
	echo "include=$MATRIX" \| tee -a $GITHUB_OUTPUT
	env:
	CIBW_ARCHS_LINUX: "x86_64"
	CIBW_ARCHS_MACOS: "x86_64 arm64"
	CIBW_ARCHS_WINDOWS: "x86 AMD64"
	# Skip musllinux because it takes too long to compile on GHA
	# since it is emulated. (6+ hours)
	# note most of the build time is actually numpy for musllinux
	CIBW_SKIP: "musllinux -manylinux_i686 -musllinux_i686 -win32 pp"


	test-and-build:
	name: "Build & Test"
	needs: "generate-wheels-matrix"
	strategy:
	matrix:
	include: ${{ fromJson(needs.generate-wheels-matrix.outputs.include) }}
	runs-on: ${{ matrix.os }}
	steps:
	- uses: actions/checkout@v3

	# QEMU enables building/testing for non-native architectures (ie arm64)
	# at the cost of speed
	- name: Set up QEMU
	if: runner.os == 'Linux'
	uses: docker/setup-qemu-action@v2
	with:
	platforms: all

	- name: Build & (optionally) test wheels
	# MAKE SURE THIS STAYS IN SYNC WITH THE UPPER pipx call to cibuildwheel
	uses: pypa/[email protected]
	with:
	only: ${{ matrix.only }}

	- uses: actions/upload-artifact@v3
	with:
	name: release
	path: ./wheelhouse/*.whl


	test-interfaces:
	name: Test interfaces to databases and applications

	runs-on: ubuntu-20.04
	defaults:
	run:
	shell: bash -l {0}

	steps:
	- uses: actions/checkout@v3
	- uses: conda-incubator/setup-miniconda@v2
	with:
	environment-file: environment.yml
	# Use Mambaforge to circumvent conflict issue:
	# https://github.com/conda-incubator/setup-miniconda/issues/274
	miniforge-variant: Mambaforge
	- name: Build distribution
	run: pip wheel --no-deps -w dist .
	- name: Install distribution
	run: pip install .//dist//*.whl
	- name: Run tests
	# Running NCBI BLAST and SRA takes too long
	# The tests on the NCBI Entrez database are not reliable enough
	run: >
	pytest
	--durations=50
	--ignore="tests//application//test_blast.py"
	--ignore="tests//application//test_sra.py"
	--ignore="tests//database//test_entrez.py"
	tests//test_doctest.py
	tests//test_modname.py
	tests//database
	tests//application


	test-muscle5:
	name: Test interface to Muscle 5

	runs-on: ubuntu-20.04
	defaults:
	run:
	shell: bash -l {0}

	steps:
	- uses: actions/checkout@v3
	- uses: conda-incubator/setup-miniconda@v2
	with:
	activate-environment: biotite-dev
	miniforge-variant: Mambaforge
	python-version: "3.10"
	channels: conda-forge,defaults
	- name: Install Muscle 5
	run: conda install -c bioconda "muscle=5"
	- name: Build distribution
	run: pip wheel -w dist .
	- name: Install distribution
	run: pip install .//dist//*.whl pytest
	- name: Test Muscle 5 interface
	run: pytest --durations=50 tests//application//test_msa.py


	make-sdist:
	name: Build source distribution
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	with:
	fetch-depth: 0
	submodules: true
	- name: Build source distribution
	run: pipx run build --sdist
	- uses: actions/upload-artifact@v3
	with:
	name: release
	path: dist//*.tar.gz


	make-docs:
	name: Build documentation

	runs-on: ubuntu-20.04
	defaults:
	run:
	shell: bash -l {0}
	env:
	BUILD_GALLERY: >
	${{
	(
	github.event_name == 'release' &&
	github.event.action == 'published'
	)
	\|\| github.event_name == 'workflow_dispatch'
	}}

	steps:
	- uses: actions/checkout@v3
	- uses: conda-incubator/setup-miniconda@v2
	with:
	environment-file: environment.yml
	miniforge-variant: Mambaforge
	- name: Build distribution
	run: pip wheel --no-deps -w dist .
	- name: Install distribution
	run: pip install .//dist//*.whl
	- run: echo ${{ env.BUILD_GALLERY }}
	- name: Build documentation
	if: ${{ env.BUILD_GALLERY == 'false' }}
	run: sphinx-build -D plot_gallery=0 doc build//doc
	- name: Build documentation
	if: ${{ env.BUILD_GALLERY == 'true' }}
	run: sphinx-build doc build//doc
	- name: Zip documentation
	run: \|
	cd build
	zip -r ..//dist//doc.zip doc
	cd ..
	- uses: actions/upload-artifact@v3
	with:
	name: release
	path: dist//doc.zip
	# Put docs also into separate artifact to allow quicker download of docs
	- uses: actions/upload-artifact@v3
	with:
	name: documentation
	path: dist//doc.zip


	upload:
	name: Upload to GitHub Releases & PyPI
	permissions:
	contents: write
	needs:
	- test-and-build
	- make-sdist
	- make-docs
	- test-interfaces
	- test-muscle5
	runs-on: ubuntu-latest
	steps:
	- uses: actions/download-artifact@v3
	with:
	name: release
	path: dist
	- name: List distributions to be uploaded
	run: ls dist
	- name: Upload to GitHub Releases
	uses: softprops/action-gh-release@de2c0eb89ae2a093876385947365aca7b0e5f844
	if: github.event_name == 'release' && github.event.action == 'published'
	with:
	files: dist//*
	- name: Upload to PyPI
	uses: pypa/gh-action-pypi-publish@c7f29f7adef1a245bd91520e94867e5c6eedddcc
	if: github.event_name == 'release' && github.event.action == 'published'
	with:
	password: ${{ secrets.PYPI_TOKEN }}

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Add workflow for building the docs #137

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Add workflow for building the docs #137

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Workflow file for this run