Add functionalities related to aromatic rings #811

Workflow file for this run

.github/workflows/test_and_deploy.yml at 172c35e

	---
	name: "CI & CD"

	on:
	workflow_dispatch:
	push:
	branches:
	- "main"
	pull_request:

	permissions:
	contents: write
	id-token: write

	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//interface
	--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: "3.11" # 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
	with:
	# Make sure to fetch the latest tag,
	# so 'switcher.py' works correctly in 'docs' job
	fetch-depth: 0
	fetch-tags: true
	- 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('src/biotite/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 -e .
	python -m biotite.setup_ccd
	- 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"}'
	} \| jq -sc
	)
	echo "include=$MATRIX" \| tee -a $GITHUB_OUTPUT
	env:
	CIBW_ARCHS_LINUX: "x86_64"
	CIBW_ARCHS_MACOS: "x86_64 arm64"
	CIBW_SKIP: "musllinux -manylinux_i686 -musllinux_i686 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

	- name: Checkout actions
	uses: actions/checkout@v4
	with:
	repository: aivant/actions
	token: ${{ secrets.COMPOSITE_ACTIONS_TOKEN }}
	ref: v4
	path: actions
	- name: Create tag for new internal release
	uses: ./actions/git/tag
	id: get-tag

	# 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
	- uses: actions/checkout@v4
	with:
	repository: aivant/actions
	token: ${{ secrets.COMPOSITE_ACTIONS_TOKEN }}
	ref: v4
	path: actions
	- uses: ./actions/git/tag
	id: get-tag
	- name: Build source distribution
	run: pipx run build --sdist
	- uses: actions/upload-artifact@v4
	with:
	name: release-sdist
	path: dist//*.tar.gz


	publish:
	name: Upload to internal package index
	if: github.ref == 'refs/heads/main'
	needs:
	- lint
	- test-and-build
	- sdist
	runs-on: ubuntu-latest
	environment:
	name: publish
	url: https://pypi.org/p/biotite
	steps:
	- name: Checkout actions
	uses: actions/checkout@v4
	with:
	repository: aivant/actions
	token: ${{ secrets.COMPOSITE_ACTIONS_TOKEN }}
	ref: v4
	path: actions
	- uses: actions/download-artifact@v4
	with:
	pattern: release-*
	merge-multiple: true
	# Cannot use 'dist' as it would indicate to py/publish
	# that it should build the wheels itself
	path: wheelhouse
	- name: List distributions to be uploaded
	run: ls wheelhouse
	- name: Upload to internal package index
	uses: ./actions/py/publish
	with:
	sa-name: default-gha
	wheel-directory: wheelhouse


	tag:
	name: Save updated git tag
	if: github.ref == 'refs/heads/main'
	needs: publish
	runs-on: ubuntu-latest
	steps:
	- name: Checkout repo
	uses: actions/checkout@v4
	- name: Checkout actions
	uses: actions/checkout@v4
	with:
	repository: aivant/actions
	token: ${{ secrets.COMPOSITE_ACTIONS_TOKEN }}
	ref: v4
	path: actions
	- name: Create tag for new internal release
	uses: ./actions/git/tag
	id: get-tag
	- name: Save git tag
	if: steps.get-tag.outputs.tag-name != ''
	run: git push origin ${{ steps.get-tag.outputs.tag-name }}

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Add functionalities related to aromatic rings #811

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Add functionalities related to aromatic rings #811

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