Allow bonds etc to be additively guessed when present #6208

Workflow file for this run

	name: GH Actions CI
	on:
	push:
	branches:
	- develop
	pull_request:
	branches:
	- develop
	workflow_dispatch:

	concurrency:
	# Probably overly cautious group naming.
	# Commits to develop will cancel each other, but PRs will only cancel
	# commits within the same PR
	group: "${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}"
	cancel-in-progress: true

	defaults:
	run:
	shell: bash -l {0}

	jobs:
	main_tests:
	if: "github.repository == 'MDAnalysis/mdanalysis'"
	runs-on: ${{ matrix.os }}
	timeout-minutes: 60
	strategy:
	fail-fast: false
	matrix:
	os: [ubuntu-latest, ]
	python-version: ["3.10", "3.11", "3.12"]
	full-deps: [true, ]
	codecov: [true, ]
	include:
	- name: python_313
	os: ubuntu-latest
	python-version: "3.13"
	full-deps: false
	codecov: true
	- name: macOS_monterey_py311
	os: macOS-12
	python-version: "3.12"
	full-deps: true
	codecov: true
	- name: macOS_14_arm64_py312
	os: macOS-14
	python-version: "3.12"
	full-deps: false
	codecov: true
	- name: numpy_min
	os: ubuntu-latest
	python-version: "3.10"
	full-deps: false
	codecov: true
	numpy: numpy=1.23.2
	- name: asv_check
	os: ubuntu-latest
	python-version: "3.10"
	full-deps: true
	codecov: false
	extra-pip-deps: asv
	env:
	CYTHON_TRACE_NOGIL: 1
	MPLBACKEND: agg

	steps:
	- uses: actions/checkout@v4

	- name: setup_os
	uses: ./.github/actions/setup-os
	with:
	os-type: ${{ matrix.os }}

	- name: setup_micromamba
	uses: mamba-org/setup-micromamba@v1
	with:
	environment-name: mda
	create-args: >-
	python=${{ matrix.python-version }}
	pip
	# using jaime's shim to avoid pulling down the cudatoolkit
	condarc: \|
	channels:
	- jaimergp/label/unsupported-cudatoolkit-shim
	- conda-forge
	- bioconda

	- name: install_deps
	uses: ./.github/actions/setup-deps
	with:
	micromamba: true
	full-deps: ${{ matrix.full-deps }}
	# disable GSD because it occasionally introduce hanging in testing #4209
	gsd: ''
	# in most cases will just default to empty, i.e. pick up max version from other deps
	numpy: ${{ matrix.numpy }}
	extra-pip-deps: ${{ matrix.extra-pip-deps }}

	- name: build_srcs
	uses: ./.github/actions/build-src
	with:
	build-tests: true
	build-docs: false
	# The standard mdanalysis deployment is to build with the
	# oldest supported numpy version and then use whatever new
	# numpy version we want at runtime. To do this we ensure
	# that we use build isolation
	isolation: true

	- name: check_deps
	run: \|
	micromamba list
	pip list

	- name: run_tests
	if: contains(matrix.name, 'asv_check') != true
	run: \|
	PYTEST_FLAGS="--disable-pytest-warnings --durations=50"
	if [ ${{ matrix.codecov }} = "true" ]; then
	PYTEST_FLAGS="${PYTEST_FLAGS} --cov-config=.coveragerc --cov=MDAnalysis --cov-report=xml"
	fi
	echo $PYTEST_FLAGS
	pytest -n logical --timeout=200 testsuite/MDAnalysisTests $PYTEST_FLAGS

	- name: run_asv
	if: contains(matrix.name, 'asv_check')
	run: \|
	cd benchmarks
	time python -m asv check -E existing

	- name: codecov
	if: matrix.codecov
	uses: codecov/codecov-action@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	file: coverage.xml
	fail_ci_if_error: False
	verbose: True


	build_docs:
	if: "github.repository == 'MDAnalysis/mdanalysis'"
	runs-on: ubuntu-latest
	timeout-minutes: 15
	env:
	CYTHON_TRACE_NOGIL: 1
	MPLBACKEND: agg

	steps:
	- uses: actions/checkout@v4

	- name: setup_micromamba
	uses: mamba-org/setup-micromamba@v1
	with:
	environment-name: mda
	create-args: >-
	python=3.10
	pip
	# using jaime's shim to avoid pulling down the cudatoolkit
	condarc: \|
	channels:
	- jaimergp/label/unsupported-cudatoolkit-shim
	- conda-forge
	- bioconda

	- name: install_deps
	uses: ./.github/actions/setup-deps
	with:
	micromamba: true
	full-deps: true
	gsd: ''
	extra-pip-deps: "docutils sphinx-sitemap sphinxcontrib-bibtex pybtex pybtex-docutils"
	extra-conda-deps: "mdanalysis-sphinx-theme>=1.3.0"

	- name: build_srcs
	uses: ./.github/actions/build-src
	with:
	build-tests: true
	build-docs: true
	isolation: true

	- name: doctests
	if: github.event_name == 'pull_request'
	continue-on-error: true
	run: \|
	cd package && sphinx-build -b doctest --keep-going ./doc/sphinx/source ./doc/html

	- name: deploy_docs
	if: github.event_name != 'pull_request'
	env:
	GH_USER: github-actions
	GH_EMAIL: "[email protected]"
	GH_REPOSITORY: "github.com/${{ github.repository }}.git"
	GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	URL: https://docs.mdanalysis.org

	run: \|
	# set up environment variables
	# cannot execute bash to make variables in env section
	# export URL for the Python script $UPDATE_JSON
	export URL
	export VERSION=$(cd package/MDAnalysis; python -c 'import version; print(version.__version__)')
	UPDATE_JSON=$(pwd)/maintainer/update_json_stubs_sitemap.py
	BRANCH="${GITHUB_REF#refs/heads/}"

	# the below turns off non-blocking as it causes large writes to stdout to fail
	# (see https://github.com/travis-ci/travis-ci/issues/4704)
	# commented out as this is not a problem with gh-actions
	# python -c 'import os,sys,fcntl; flags = fcntl.fcntl(sys.stdout, fcntl.F_GETFL); fcntl.fcntl(sys.stdout, fcntl.F_SETFL, flags&~os.O_NONBLOCK);'
	cd package/doc/html/

	# move docs into version subfolder
	mkdir ../${VERSION} && mv * ../${VERSION} && mv ../${VERSION} $VERSION

	# set up git
	REV=$(git rev-parse --short HEAD)
	git init
	git config user.name $GH_USER
	git config user.email $GH_EMAIL
	git remote add upstream "https://${GH_USER}:${GH_TOKEN}@${GH_REPOSITORY}"
	git fetch --depth 50 upstream $BRANCH gh-pages
	git reset upstream/gh-pages

	# redirects and copies
	mkdir latest
	python $UPDATE_JSON
	touch .
	touch .nojekyll

	git add -A ${VERSION}/
	git add .nojekyll versions.json .xml .html index.html latest

	for dirname in dev stable documentation_pages ; do
	if [ -d $dirname ]; then git add $dirname; fi
	done

	# check for anything to commit
	# https://stackoverflow.com/questions/3878624/how-do-i-programmatically-determine-if-there-are-uncommited-changes
	git diff-index --quiet HEAD -- \|\| git commit -m "rebuilt html docs for version ${VERSION} from branch ${BRANCH} with sphinx at ${REV}"
	git push -q upstream HEAD:gh-pages


	sdist_check_and_build:
	if: "github.repository == 'MDAnalysis/mdanalysis'"
	runs-on: ubuntu-latest
	timeout-minutes: 30

	steps:
	- uses: actions/checkout@v4

	- uses: actions/setup-python@v5
	with:
	python-version: 3.11

	- name: install_deps
	run: \|
	python -m pip install -U pip pipx wheel build
	python -m pip install twine "readme-renderer>=34.0" pytest-xdist pytest-timeout

	- name: build_package_sdist
	run: \|
	pipx run build --sdist --outdir dist package

	- name: build_testsuite_sdist
	run: \|
	pipx run build --sdist --outdir dist testsuite

	- name: check_package_build
	run: \|
	DISTRIBUTION=$(ls -t1 dist/mdanalysis-*.tar.gz \| head -n1)
	test -n "${DISTRIBUTION}" \|\| { echo "no distribution dist/MDAnalysis-*.tar.gz found"; exit 1; }
	twine check $DISTRIBUTION

	- name: check_testsuite_build
	run: \|
	DISTRIBUTION=$(ls -t1 dist/mdanalysistests-*.tar.gz \| head -n1)
	test -n "${DISTRIBUTION}" \|\| { echo "no distribution dist/MDAnalysisTests-*.tar.gz found"; exit 1; }
	twine check $DISTRIBUTION

	- name: install sdist
	working-directory: ./dist
	run: \|
	ls -a .
	python -m pip install mdanalysis-*.tar.gz
	python -m pip install mdanalysistests-*.tar.gz

	- name: check install
	run: pip list

	- name: run tests
	working-directory: ./dist
	run: python -m pytest --timeout=200 -n logical --pyargs MDAnalysisTests

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Allow bonds etc to be additively guessed when present #6208

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Allow bonds etc to be additively guessed when present #6208

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