build(deps): bump snakemake from 7.32.3 to 8.4.12 #20

Workflow file for this run

	name: test

	on:
	push:
	branches:
	- main
	pull_request:
	merge_group:

	concurrency:
	group: ${{ github.workflow }}-${{ github.head_ref \|\| github.run_id }}
	cancel-in-progress: true

	permissions:
	contents: read

	env:
	MINIMUM_PYTHON_VERSION: "3.9"

	jobs:

	coverage:
	name: "${{ matrix.os }} / ${{ matrix.python-version }} / coverage"
	strategy:
	max-parallel: 4
	fail-fast: false
	matrix:
	os: [ubuntu]
	python-version:
	# remove the unused versions
	- "3.9"
	- "3.10"
	- "3.11"
	# - "3.12" TODO support this

	runs-on: ${{ matrix.os }}-latest
	steps:
	- uses: actions/checkout@v4

	- name: Set up the environment
	uses: pdm-project/setup-pdm@v4
	id: setup-python
	with:
	python-version: ${{ matrix.python-version }}

	- name: Load cached venv
	id: cached-venv
	uses: actions/cache@v4
	with:
	path: .venv
	key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/pyproject.toml') }}-${{ hashFiles('.github/workflows/test.yml') }}

	- name: Install dependencies
	if: steps.cached-venv.outputs.cache-hit != 'true'
	run: make install-dev

	- name: Run tests for coverage
	run: make test-w-coverage

	- name: Upload coverage artifact
	uses: actions/upload-artifact@v4
	with:
	name: .coverage-${{ matrix.os }}-${{ matrix.python-version }}
	path: .coverage

	upload-coverage:
	name: ubuntu / 3.9 / upload-coverage
	needs:
	- coverage
	runs-on: ubuntu-latest
	permissions:
	statuses: write
	steps:
	- uses: actions/checkout@v4
	- name: Set up python ${{ env.MINIMUM_PYTHON_VERSION }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ env.MINIMUM_PYTHON_VERSION }}

	- name: Install dependencies
	run: pip install coverage

	- name: Download coverage artifacts
	uses: actions/download-artifact@v4
	with:
	pattern: .coverage-*

	- name: convert coverage to xml
	run: \|
	ls -aR
	coverage combine .coverage*/.coverage
	coverage xml -i
	ls -a

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	# directory: ./coverage
	# env_vars: OS,PYTHON
	fail_ci_if_error: false
	# files: ./coverage/coverage.xml
	# flags: unittests
	# name: codecov-umbrella
	verbose: true

	minimal:
	# This action chooses the oldest version of the dependencies permitted by Cargo.toml to ensure
	# that this crate is compatible with the minimal version that this crate and its dependencies
	# require. This will pickup issues where this create relies on functionality that was introduced
	# later than the actual version specified (e.g., when we choose just a major version, but a
	# method was added after this version).
	#

	runs-on: ubuntu-latest
	name: ubuntu / 3.9 / minimal-versions
	steps:
	- uses: actions/checkout@v4
	- name: Set up the environment
	uses: pdm-project/setup-pdm@v4
	id: setup-python
	with:
	python-version: ${{ env.MINIMUM_PYTHON_VERSION }}

	- name: pdm lock --strategy direct_minimal_versions
	run: pdm lock --strategy direct_minimal_versions
	- name: pdm sync --dev
	run: pdm sync --dev
	- name: make test
	run: make test
	# https://github.com/marketplace/actions/alls-green#why used for branch protection checks
	test-check:
	if: always()
	needs:
	- coverage
	- minimal
	- upload-coverage
	runs-on: ubuntu-latest
	permissions: {}
	steps:
	- name: Decide whether the needed jobs succeeded or failed
	uses: re-actors/alls-green@release/v1
	with:
	jobs: ${{ toJSON(needs) }}
	allowed-failures: upload-coverage

	build:
	name: ubuntu / 3.9 / build package
	# only run on push to main and on release
	if: success() && (startsWith(github.ref, 'refs/tags/v') \|\| github.ref == 'refs/heads/main')
	runs-on: ubuntu-latest
	steps:
	#----------------------------------------------
	# check-out repo and set-up python
	#----------------------------------------------
	- name: Check out repository
	uses: actions/checkout@v4

	#----------------------------------------------
	# ----- setup python -----
	#----------------------------------------------
	- name: Set up the environment
	uses: pdm-project/setup-pdm@v4
	id: setup-python
	with:
	python-version: ${{ env.MINIMUM_PYTHON_VERSION }}

	#----------------------------------------------
	# ----- build distribution -----
	#----------------------------------------------
	- name: Build distribution
	run: make build

	#----------------------------------------------
	# ----- upload artifacts -----
	#----------------------------------------------
	- uses: actions/upload-artifact@v4
	with:
	name: pypi_files
	path: dist

	test-build:
	needs: [build]

	strategy:
	fail-fast: false
	matrix:
	os: [ubuntu]
	name: ${{ matrix.os }} / 3.9 / test built package

	runs-on: ${{ matrix.os }}-latest
	steps:
	- uses: actions/checkout@v4

	- name: set up python
	uses: actions/setup-python@v5
	with:
	python-version: ${{ env.MINIMUM_PYTHON_VERSION }}

	- name: get dist artifacts
	uses: actions/download-artifact@v4
	with:
	name: pypi_files
	path: dist

	- run: rm -r src/ocr_suggestion
	- run: pip install typing-extensions
	- run: pip install -r tests/requirements-testing.txt
	- run: pip install sparv-ocr-suggestion-plugin --no-index --no-deps --find-links dist --force-reinstall
	- run: pytest

	publish:
	needs:
	- test-check
	- test-build
	if: success() && startsWith(github.ref, 'refs/tags/v')
	runs-on: ubuntu-latest
	environment: release
	permissions:
	# IMPORTANT: this permission is mandatory for trusted publishing
	id-token: write
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 0
	- name: Set up Python ${{ env.MINIMUM_PYTHON_VERSION }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ env.MINIMUM_PYTHON_VERSION }}
	- name: get dist artifacts
	uses: actions/download-artifact@v4
	with:
	name: pypi_files
	path: dist

	- name: Publish package to PyPI
	uses: pypa/gh-action-pypi-publish@release/v1

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

build(deps): bump snakemake from 7.32.3 to 8.4.12 #20

Workflow file

build(deps): bump snakemake from 7.32.3 to 8.4.12 #20

Jobs

Run details

Workflow file for this run