Merge branch 'main' into 82-improve-cytoscape-graph-visualization #381

	name: checks
	on: [push, pull_request]
	jobs:
	test:
	name: test py${{ matrix.python-version }}
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ["3.11", "3.12", "3.13"]
	steps:
	- uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}

	- name: Install dependencies
	run: \|
	python3 -m pip install ".[tests]"

	- name: Run tests
	run: python3 -m pytest tests/test_dgidb.py tests/test_network_constructor.py
	lint:
	name: lint
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4

	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.11"

	- name: Install dependencies
	run: python3 -m pip install ".[dev]"

	- name: Check style
	run: python3 -m ruff check . && python3 -m ruff format --check .

	precommit_hooks:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	hook:
	- "end-of-file-fixer"
	- "trailing-whitespace"
	- "mixed-line-ending"
	steps:
	- uses: actions/checkout@v4
	- name: Set up Python 3.12
	uses: actions/setup-python@v5
	with:
	python-version: 3.12
	- uses: pre-commit/[email protected]
	with:
	extra_args: ${{ matrix.cmd }} --all-files
	docs:
	runs-on: ubuntu-latest
	env:
	SPHINX_GITHUB_CHANGELOG_TOKEN: ${{ secrets.SPHINX_GITHUB_CHANGELOG_TOKEN }}
	steps:
	- uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: 3.11

	- name: Install dependencies
	run: \|
	python3 -m pip install --upgrade pip
	python3 -m pip install '.[docs]'

	- name: Attempt docs build
	working-directory: ./docs
	run: make html

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