Add type annotations to code base #1278

Workflow file for this run

.github/workflows/test_and_deploy.yml at a481072

	---
	name: "CI & CD"

	on:
	workflow_dispatch:
	push:
	branches:
	- "main"
	pull_request:
	release:
	types:
	- published

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

	env:
	CIBW_BUILD: cp312-* cp313-* cp314-*
	CIBW_TEST_EXTRAS: test
	CIBW_TEST_COMMAND: >
	pytest {project}
	--durations=50
	--ignore={project}//tests//sequence//align//test_statistics.py
	--ignore={project}//tests//application
	--ignore={project}//tests//interface
	--ignore={project}//tests//database
	--ignore={project}//tests//test_doctest.py
	--ignore={project}//tests//test_modname.py
	CIBW_DEPENDENCY_VERSIONS: "pinned"


	jobs:
	lint:
	name: Check code style
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- uses: prefix-dev/setup-pixi@v0.9.6
	with:
	environments: lint
	cache: true
	cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
	- name: Check code style and type annotations
	run: pixi run lint


	build-internal:
	name: Build CCD and wheel for reusing it in several CI jobs
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	with:
	# Make sure to fetch the latest tag,
	# so 'switcher.py' works correctly in 'docs' job
	fetch-depth: 0
	fetch-tags: true
	- uses: prefix-dev/setup-pixi@v0.9.6
	with:
	environments: test
	activate-environment: true
	cache: true
	cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
	- name: Build CCD and wheel
	run: pixi run build-wheel
	- uses: actions/upload-artifact@v4
	with:
	name: internal-build
	path: ./dist/*.whl
	- uses: actions/upload-artifact@v4
	with:
	name: ccd
	path: ./src/biotite/structure/info/components.bcif


	generate-wheels-matrix:
	name: "Generate wheels matrix"
	runs-on: "ubuntu-latest"
	outputs:
	include: ${{ steps.set-matrix.outputs.include }}
	steps:
	- uses: actions/checkout@v4
	- name: Install cibuildwheel
	# MAKE SURE THIS STAYS IN SYNC WITH THE LOWER GHA cibuildwheel
	run: pipx install cibuildwheel==3.3.0
	- id: set-matrix
	run: \|
	MATRIX=$(
	{
	cibuildwheel --print-build-identifiers --platform linux --archs x86_64 \
	\| jq -nRc '{"dist": inputs, "os": "ubuntu-latest"}' \
	&& cibuildwheel --print-build-identifiers --platform linux --archs aarch64 \
	\| jq -nRc '{"dist": inputs, "os": "ubuntu-24.04-arm"}' \
	&& cibuildwheel --print-build-identifiers --platform macos \
	\| jq -nRc '{"dist": inputs, "os": "macos-latest"}' \
	&& cibuildwheel --print-build-identifiers --platform windows \
	\| jq -nRc '{"dist": inputs, "os": "windows-latest"}'
	} \| jq -sc
	)
	echo "include=$MATRIX" \| tee -a $GITHUB_OUTPUT
	env:
	CIBW_ARCHS_LINUX: "x86_64 aarch64"
	CIBW_ARCHS_MACOS: "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
	- build-internal
	strategy:
	matrix:
	include: ${{ fromJson(needs.generate-wheels-matrix.outputs.include) }}
	runs-on: ${{ matrix.os }}
	steps:
	- uses: actions/checkout@v4
	- name: Add internal CCD to Biotite
	uses: actions/download-artifact@v4
	with:
	name: ccd
	path: src/biotite/structure/info

	# 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@v3
	with:
	platforms: all

	- name: Build & (optionally) test wheels
	# MAKE SURE THIS STAYS IN SYNC WITH THE UPPER pipx call to cibuildwheel
	uses: pypa/cibuildwheel@v3.3.0
	with:
	only: ${{ matrix.dist }}

	- uses: actions/upload-artifact@v4
	with:
	name: release-${{ matrix.dist }}
	path: ./wheelhouse/*.whl


	sdist:
	name: Build source distribution
	runs-on: ubuntu-latest
	needs:
	- build-internal
	steps:
	- uses: actions/checkout@v4
	- name: Add internal CCD to Biotite
	uses: actions/download-artifact@v4
	with:
	name: ccd
	path: src/biotite/structure/info
	- name: Build source distribution
	run: pipx run build --sdist
	- uses: actions/upload-artifact@v4
	with:
	name: release-sdist
	path: dist//*.tar.gz


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

	runs-on: ubuntu-latest
	needs:
	- build-internal

	steps:
	- uses: actions/checkout@v4
	- uses: actions/download-artifact@v4
	with:
	name: internal-build
	path: dist
	- uses: prefix-dev/setup-pixi@v0.9.6
	with:
	environments: test
	activate-environment: true
	cache: true
	cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
	- name: Install pre-built wheel into the pixi environment
	# `--no-deps` because conda already provides all runtime dependencies
	run: pixi run python -m pip install --no-deps ./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: >
	pixi 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
	tests//interface


	test-muscle5:
	name: Test interface to Muscle 5

	runs-on: ubuntu-latest
	needs:
	- build-internal

	steps:
	- uses: actions/checkout@v4
	- uses: actions/download-artifact@v4
	with:
	name: internal-build
	path: dist
	- uses: prefix-dev/setup-pixi@v0.9.6
	with:
	environments: test-muscle5
	activate-environment: true
	cache: true
	cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
	- name: Install pre-built wheel into the pixi environment
	run: pixi run python -m pip install --no-deps ./dist/*.whl
	- name: Test Muscle 5 interface
	run: pixi run pytest --durations=50 tests//application//test_msa.py


	docs:
	name: Build documentation

	runs-on: ubuntu-latest
	needs:
	- build-internal
	env:
	NCBI_API_KEY: ${{ secrets.NCBI_API_KEY }}

	steps:
	- uses: actions/checkout@v4
	- uses: actions/download-artifact@v4
	with:
	name: internal-build
	path: dist
	- uses: prefix-dev/setup-pixi@v0.9.6
	with:
	environments: doc
	cache: true
	activate-environment: true
	cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
	- name: Restore cached partially build docs from a failed previous build
	id: cache-docs-restore
	uses: actions/cache/restore@v4
	with:
	key: docs-${{ github.sha }}
	path: \|
	doc/examples/backreferences
	doc/examples/gallery
	build/doc
	build/jupyter_execute
	- name: Install pre-built wheel into the pixi environment
	run: pixi run python -m pip install --no-deps ./dist/*.whl
	# Calling `sphinx-build` directly instead of `doc` task
	# to avoid the time consuming call of the `install` task
	- name: Build base documentation
	run: pixi run sphinx-build -a -D plot_gallery=0 doc build/doc
	- name: Build tutorial and gallery
	if: >
	(
	github.event_name == 'release' &&
	github.event.action == 'published'
	)
	\|\| github.event_name == 'workflow_dispatch'
	run: pixi run sphinx-build -a doc build/doc
	- name: Cache partially built docs from failed build
	id: cache-docs-save
	if: failure()
	uses: actions/cache/save@v4
	with:
	key: ${{ steps.cache-docs-restore.outputs.cache-primary-key }}
	path: \|
	doc/examples/backreferences
	doc/examples/gallery
	build/doc
	build/jupyter_execute
	- name: Zip documentation
	run: \|
	cd build
	zip -r ../dist/doc.zip doc
	cd ..
	- uses: actions/upload-artifact@v4
	with:
	name: documentation
	path: dist/doc.zip


	benchmark:
	name: Run benchmarks
	runs-on: ubuntu-latest
	if: github.event_name != 'release'
	needs:
	- build-internal
	steps:
	- uses: actions/checkout@v4
	- uses: actions/download-artifact@v4
	with:
	name: internal-build
	path: dist
	- uses: prefix-dev/setup-pixi@v0.9.6
	with:
	environments: test
	cache: true
	cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
	- name: Install pre-built wheel into the pixi environment
	run: pixi run -e test python -m pip install --no-deps ./dist/*.whl
	- name: Run benchmarks
	uses: CodSpeedHQ/action@v3
	with:
	run: pixi run -e test pytest --codspeed benchmarks


	upload-package:
	name: Upload package to GitHub Releases & PyPI
	permissions:
	contents: write
	id-token: write
	needs:
	- lint
	- test-and-build
	- sdist
	- test-interfaces
	- test-muscle5
	- docs
	runs-on: ubuntu-latest
	environment:
	name: publish
	url: https://pypi.org/p/biotite
	steps:
	- uses: actions/download-artifact@v4
	with:
	pattern: release-*
	merge-multiple: true
	path: dist
	- name: List distributions to be uploaded
	run: ls dist
	- name: Upload to GitHub Releases
	uses: softprops/action-gh-release@v2.0.5
	if: github.event_name == 'release' && github.event.action == 'published'
	with:
	files: dist//*
	- name: Upload to PyPI
	uses: pypa/gh-action-pypi-publish@release/v1
	if: github.event_name == 'release' && github.event.action == 'published'


	upload-ccd:
	name: Upload CCD to GitHub Releases
	permissions:
	contents: write
	needs:
	- build-internal
	runs-on: ubuntu-latest
	steps:
	- uses: actions/download-artifact@v4
	with:
	name: ccd
	path: dist
	- name: Upload to GitHub Releases
	uses: softprops/action-gh-release@v2.0.5
	if: github.event_name == 'release' && github.event.action == 'published'
	with:
	files: dist//components.bcif


	upload-docs:
	name: Upload documentation to GitHub Releases and documentation website
	if: github.event_name == 'release' && github.event.action == 'published'
	permissions:
	contents: write
	needs:
	- lint
	- test-and-build
	- sdist
	- test-interfaces
	- test-muscle5
	- docs
	runs-on: ubuntu-latest
	steps:
	- uses: actions/setup-python@v5
	with:
	python-version: "3.12"
	- name: Install dependencies for documentation upload
	run: pip install requests
	- uses: actions/checkout@v4
	- uses: actions/download-artifact@v4
	with:
	name: documentation
	path: dist
	- uses: softprops/action-gh-release@v2.0.5
	with:
	files: dist/doc.zip
	- name: Unzip documentation
	run: unzip dist/doc.zip -d build
	- name: Assemble multi-version documentation
	run: >
	python .github/workflows/multiversion_docs.py
	build/doc/_static/switcher.json
	dist/assembled_doc
	- name: Upload documentation to website (skip for patch releases)
	if: endsWith(github.event.release.tag_name, 0)
	uses: easingthemes/ssh-deploy@v5.1.0
	with:
	SSH_PRIVATE_KEY: ${{ secrets.DOC_PRIVATE_KEY }}
	REMOTE_HOST: ${{ secrets.DOC_HOST }}
	REMOTE_USER: ${{ secrets.DOC_USER }}
	SOURCE: "dist/assembled_doc/*"
	TARGET: "biotite"
	SCRIPT_BEFORE: "rm -r biotite/*"

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Add type annotations to code base #1278

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Add type annotations to code base #1278

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Workflow file for this run