Update pre-commit hooks and add CI action #852

	name: pytest

	on:
	push:
	branches:
	- "develop"
	- "master"
	pull_request:
	branches:
	- "*"
	schedule:
	# Nightly tests (on master)
	- cron: "0 0 * * *"

	defaults:
	run:
	# conda setup requires this special shell
	shell: bash -l {0}

	jobs:
	test:
	name: Test ${{ matrix.os }}-${{ matrix.python-version }}-${{ matrix.chemlib }}-${{ matrix.graphlib }}
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	os: [macOS-latest, ubuntu-latest, windows-latest]
	python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
	chemlib: [obabel, rdkit]
	graphlib: [nx, gt]
	# graph-tools does not work on Windows
	exclude:
	- {os: "windows-latest", graphlib: "gt"}

	steps:
	- uses: actions/checkout@v3

	- name: Info
	shell: bash
	run: \|
	uname -a
	df -h
	ulimit -a

	- uses: conda-incubator/setup-miniconda@v2
	with:
	python-version: ${{ matrix.python-version }}
	environment-file: devtools/conda-envs/spyrmsd-test-${{ matrix.chemlib }}-${{ matrix.graphlib }}.yaml
	channels: conda-forge,defaults
	activate-environment: spyrmsd
	auto-update-conda: true
	auto-activate-base: false
	show-channel-urls: true

	- name: Install
	run: \|
	python -m pip install . --no-deps
	conda list

	- name: Test
	run: \|
	pytest -v --benchmark --cov=spyrmsd --cov-report=xml --color=yes tests/

	- name: CodeCov
	uses: codecov/codecov-action@v3
	with:
	file: ./coverage.xml
	flags: unittests
	name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}-${{ matrix.chemlib }}-${{ matrix.graphlib }}

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