Integrate structural alphabets better into Biotite #589

Workflow file for this run

.github/workflows/test_and_deploy.yml at 226d7fb

	---
	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: cp310-* cp311-* cp312-* cp313-*
	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//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"
	# Configuration for the architecture-agnostic jobs
	PY_VERSION: "3.12" # Keep in sync with version in environment.yml


	jobs:
	lint:
	name: Check code style
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-python@v5
	with:
	python-version: "3.12"
	- name: Install ruff
	# Keep in sync with the ruff version in pyproject.toml
	run: pip install ruff==0.6.9
	- name: Check code formatting
	run: ruff format --diff
	- name: Lint code base
	run: ruff check


	build-internal:
	name: Build CCD and wheel for reusing it in several CI jobs
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-python@v5
	with:
	python-version: ${{ env.PY_VERSION }}
	- name: Get current CCD for hashing
	run: wget https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
	- name: Cache CCD
	uses: actions/cache@v4
	id: cache-ccd
	with:
	path: ./src/biotite/structure/info/components.bcif
	key: cache-${{ hashFiles('setup_ccd.py') }}-${{ hashFiles('components.cif.gz') }}
	- name: Remove CCD used for hashing
	run: rm components.cif.gz
	- name: Build internal CCD
	if: steps.cache-ccd.outputs.cache-hit != 'true'
	run: \|
	pip install .
	python setup_ccd.py
	- name: Install build backend
	run: pip install build
	- name: Build distribution
	run: python -m 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: ${{ steps.set-matrix.outputs.include }}
	steps:
	- uses: actions/checkout@v4
	- name: Install cibuildwheel
	# MAKE SURE THIS STAYS IN SYNC WITH THE LOWER GHA cibuildwheel
	run: pipx install cibuildwheel==2.20.0
	- id: set-matrix
	run: \|
	MATRIX=$(
	{
	cibuildwheel --print-build-identifiers --platform linux \
	\| jq -nRc '{"dist": inputs, "os": "ubuntu-latest"}' \
	&& 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"
	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
	- 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/[email protected]
	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
	defaults:
	run:
	shell: bash -l {0}

	steps:
	- uses: actions/checkout@v4
	- uses: actions/download-artifact@v4
	with:
	name: internal-build
	path: dist
	- uses: conda-incubator/setup-miniconda@v3
	with:
	environment-file: environment.yml
	miniforge-version: latest
	- name: Install distribution
	run: pip install ./dist/*.whl
	- name: "TEMP: Skip DSSP tests"
	# TEMP: Omit DSSP tests for now until conda-forge DSSP is functional
	# (https://github.com/conda-forge/dssp-feedstock/pull/4)
	run: mamba uninstall dssp
	- 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-latest
	needs:
	- build-internal
	defaults:
	run:
	shell: bash -l {0}

	steps:
	- uses: actions/checkout@v4
	- uses: actions/download-artifact@v4
	with:
	name: internal-build
	path: dist
	- uses: conda-incubator/setup-miniconda@v3
	with:
	activate-environment: biotite-dev
	miniforge-version: latest
	python-version: ${{ env.PY_VERSION }}
	- name: Install Muscle 5
	run: conda install -c bioconda "muscle=5"
	- name: Install distribution and pytest
	run: pip install .//dist//*.whl pytest
	- name: Test Muscle 5 interface
	run: pytest --durations=50 tests//application//test_msa.py


	docs:
	name: Build documentation

	runs-on: ubuntu-latest
	needs:
	- build-internal
	defaults:
	run:
	shell: bash -l {0}
	env:
	NCBI_API_KEY: ${{ secrets.NCBI_API_KEY }}

	steps:
	- uses: actions/checkout@v4
	with:
	# Make sure to fetch the latest tag, so 'switcher.py' works correctly
	fetch-depth: 0
	fetch-tags: true
	- uses: actions/download-artifact@v4
	with:
	name: internal-build
	path: dist
	- uses: conda-incubator/setup-miniconda@v3
	with:
	environment-file: environment.yml
	miniforge-version: latest
	- name: Install distribution
	run: pip install dist/*.whl
	- name: Build base documentation
	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: sphinx-build -a doc build//doc
	- 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: actions/setup-python@v5
	with:
	python-version: ${{ env.PY_VERSION }}
	- name: Install dependencies
	run: pip install dist//*.whl pytest pytest-codspeed
	- name: Run benchmarks
	uses: CodSpeedHQ/action@v3
	with:
	run: pytest --codspeed benchmarks


	upload-package:
	name: Upload package to GitHub Releases & PyPI
	permissions:
	contents: write
	needs:
	- lint
	- test-and-build
	- sdist
	- test-interfaces
	- test-muscle5
	runs-on: ubuntu-latest
	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/[email protected]
	if: github.event_name == 'release' && github.event.action == 'published'
	with:
	files: dist//*
	- name: Upload to PyPI
	uses: pypa/[email protected]
	if: github.event_name == 'release' && github.event.action == 'published'
	with:
	password: ${{ secrets.PYPI_TOKEN }}


	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/[email protected]
	if: github.event_name == 'release' && github.event.action == 'published'
	with:
	files: dist//components.bcif


	upload-docs:
	name: Upload documentation to GitHub Releases
	permissions:
	contents: write
	needs:
	- docs
	runs-on: ubuntu-latest
	steps:
	- uses: actions/download-artifact@v4
	with:
	name: documentation
	path: dist
	- uses: softprops/[email protected]
	if: github.event_name == 'release' && github.event.action == 'published'
	with:
	files: dist//doc.zip

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Integrate structural alphabets better into Biotite #589

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Integrate structural alphabets better into Biotite #589

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Workflow file for this run