.github/workflows/py-ci.yml #9903

Workflow file for this run

	on:
	push:
	branches:
	- master
	tags:
	- "*"
	pull_request:
	merge_group:
	jobs:
	linter:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-python@v5
	with:
	python-version: '3.11'
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip setuptools
	python -m pip install 'pylint==3.2.7' 'pycodestyle>=2.6.1'
	- name: Run pylint
	run: \|
	pylint .
	- name: Run pycodestyle
	run: \|
	pycodestyle $(find -name '.py' -not -path './venv/')

	isort:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-python@v5
	with:
	python-version: '3.11'
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip setuptools
	python -m pip install isort
	- name: Run isort
	run: \|
	isort --check --diff .

	test-gendocs:
	runs-on: ubuntu-latest
	env:
	QUILT_DISABLE_USAGE_METRICS: true
	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-python@v5
	with:
	# on newer versions it crashes with
	# TypeError: <classmethod(<function Package.install at 0x105219f30>)> is not a callable object
	python-version: '3.9'
	- name: install deps
	run: \|
	python -m pip install --upgrade pip setuptools
	python -m pip install api/python nbconvert git+https://github.com/quiltdata/[email protected]+quilt3.2
	- name: generate docs
	run: cd gendocs && python build.py
	- name: show invisible changes via cat
	run: git diff \| cat -A
	- name: check there are no changes
	run: git diff --exit-code

	test-testdocs:
	runs-on: ubuntu-latest
	env:
	QUILT_DISABLE_USAGE_METRICS: true
	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-python@v5
	with:
	python-version: '3.11'
	- name: install poetry
	run: python -m pip install poetry
	- name: install deps
	run: cd testdocs && poetry install
	- name: test codeblocks
	run: cd testdocs && poetry run pytest --codeblocks ../docs

	test-client:
	strategy:
	matrix:
	os: [ubuntu-latest, windows-latest]
	python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
	runs-on: ${{ matrix.os }}
	env:
	QUILT_DISABLE_USAGE_METRICS: true
	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip setuptools
	python -m pip install -e api/python[tests]
	- name: Run Pytest
	run: \|
	pytest --cov=api/python api/python
	- uses: codecov/codecov-action@v4
	env:
	CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
	OS: ${{ matrix.os }}
	PYTHON_VERSION: ${{ matrix.python-version }}
	with:
	flags: api-python
	name: ${{ github.job }}
	env_vars: OS,PYTHON_VERSION

	pypi-release-tag-check:
	needs: test-client
	runs-on: ubuntu-latest
	outputs:
	check: ${{ steps.check.outputs.check }}
	if: github.ref_type == 'tag'
	steps:
	- name: check git tag
	id: check
	run: \|
	if [[ ${{ github.ref_name }} =~ ^[0-9]+(\.[0-9]+)*([abrc]+[0-9]+)?$ ]]; then
	echo ::set-output name=check::true
	fi

	pypi-release:
	needs: pypi-release-tag-check
	if: github.ref_type == 'tag' && needs.pypi-release-tag-check.outputs.check == 'true'
	runs-on: ubuntu-latest
	defaults:
	run:
	working-directory: api/python
	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-python@v5
	with:
	python-version: '3.12'
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip setuptools
	python -m pip install build==1.2.2.post1 twine==5.1.1
	- name: verify git tag vs. version
	env:
	CIRCLE_TAG: ${{ github.ref_name }}
	run: python setup.py verify
	- name: build
	run: python -m build
	- name: upload to PyPI
	env:
	TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
	TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
	run: twine upload dist/*

	test-lambda:
	strategy:
	fail-fast: false
	matrix:
	path:
	- access_counts
	- indexer
	- pkgevents
	- pkgpush
	- preview
	- s3hash
	- shared
	- status_reports
	- tabular_preview
	- thumbnail
	- transcode
	runs-on: ubuntu-latest
	env:
	QUILT_DISABLE_USAGE_METRICS: true
	PYTHONPATH: deps
	JUPYTER_PATH: deps/share/jupyter # Jupyter is not smart enough to handle custom Python paths
	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-python@v5
	with:
	python-version-file: lambdas/${{ matrix.path }}/.python-version
	- name: Install dependencies
	run: \|
	if [ ${{ matrix.path }} == "thumbnail" ]
	then
	# Due to behavior change in pip>=23.1 installing tifffile==0.15.1
	# from thumbnail lambda fails whithout installed wheel.
	# See https://github.com/pypa/pip/issues/8559.
	# HACK: Pre-install numpy v1 as a build dependency for tifffile to prevent it from using v2 and failing to build
	python -m pip install wheel 'numpy<2'
	fi

	# Try to simulate the lambda .zip file:
	# - Use --no-deps to ensure that second-order dependencies are included in the requirements file
	# - Remove "tests" directories
	# - Run "strip" on shared libraries
	python -m pip install -t deps --no-deps -r lambdas/${{ matrix.path }}/requirements.txt lambdas/${{ matrix.path }}
	find deps -name tests -type d -exec rm -r \{} \+
	find deps $ -name '.so.' -o -name '*.so' $ -type f -exec strip \{} \+

	python -m pip install -r lambdas/${{ matrix.path }}/test-requirements.txt
	- name: Pytest
	run: \|
	pytest --cov=lambdas lambdas/${{ matrix.path }}
	- uses: codecov/codecov-action@v4
	env:
	CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
	LAMBDA: ${{ matrix.path }}
	with:
	flags: lambda
	name: ${{ github.job }}
	env_vars: LAMBDA

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.github/workflows/py-ci.yml #9903

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