Merge branch 'dev' into biotools #1

	name: Python linting
	on:
	push:
	paths:
	- '**.py'
	- '.github/workflows/lint.yaml'
	- lib/galaxy/dependencies/**
	- mypy.ini
	pull_request:
	paths:
	- '**.py'
	- '.github/workflows/lint.yaml'
	- lib/galaxy/dependencies/**
	- mypy.ini
	concurrency:
	group: ${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: true
	jobs:
	test:
	name: Test
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: ['3.8', '3.12']
	env:
	LINT_PATH: 'lib/galaxy/dependencies/pinned-lint-requirements.txt'
	TYPE_PATH: 'lib/galaxy/dependencies/pinned-typecheck-requirements.txt'
	CORE_PATH: 'lib/galaxy/dependencies/pinned-requirements.txt'
	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	- name: Get full Python version
	id: full-python-version
	shell: bash
	run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
	- name: Cache pip dir
	uses: actions/cache@v4
	with:
	path: ~/.cache/pip
	key: pip-cache-${{ matrix.python-version }}-${{ hashFiles(env.LINT_PATH, env.TYPE_PATH, env.CORE_PATH) }}
	- name: Cache tox env
	uses: actions/cache@v4
	with:
	path: .tox
	key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles(env.LINT_PATH, env.TYPE_PATH, env.CORE_PATH) }}-lint
	- name: Install tox
	run: pip install tox
	- name: Run linting
	run: tox -e lint
	- name: Run docstring linting
	run: tox -e lint_docstring_include_list
	- name: Run mypy checks
	run: tox -e mypy
	- uses: psf/black@stable
	- uses: isort/isort-action@v1

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