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build(deps): bump snakemake from 7.32.3 to 8.4.0 #37

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build(deps): bump snakemake from 7.32.3 to 8.4.0

build(deps): bump snakemake from 7.32.3 to 8.4.0 #37

Workflow file for this run

.github/workflows/ci.yml at 3629bd4
name: CI
on:
push:
branches:
- main
pull_request:
merge_group:
permissions:
contents: read
env:
MINIMUM_PYTHON_VERSION: "3.9"
CI: "github-actions"
jobs:
lint:
name: ${{ matrix.task.name }} (${{ matrix.os }})
strategy:
max-parallel: 4
fail-fast: false
matrix:
# Only run checks for ubuntu
os: [ubuntu]
task:
- name: Type check
run: make type-check
- name: Check formatting
run: make check-fmt
- name: Lint code
run: make lint
runs-on: ${{ matrix.os }}-latest
steps:
#----------------------------------------------
# check-out repo
#----------------------------------------------
- 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: ${{ env.MINIMUM_PYTHON_VERSION }}
- name: Load cached venv
id: cached-venv
uses: actions/cache@v3
with:
path: .venv
key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/pyproject.toml') }}-${{ hashFiles('.github/workflows/ci.yml') }}
- name: Install dependencies
if: steps.cached-venv.outputs.cache-hit != 'true'
run: make install-dev
- run: make info
#----------------------------------------------
# Run matrix task
#----------------------------------------------
- name: ${{ matrix.task.name }}
run: ${{ matrix.task.run }}
coverage:
name: "Test py-${{ matrix.python-version }} (${{ matrix.os }})"
strategy:
max-parallel: 4
fail-fast: false
matrix:
os: [ubuntu]
python-version:
- "3.9"
- "3.10"
- "3.11"
# - "3.12" not supported
runs-on: ${{ matrix.os }}-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: ${{ matrix.python-version }}
- name: Load cached venv
id: cached-venv
uses: actions/cache@v3
with:
path: .venv
key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/pyproject.toml') }}-${{ hashFiles('.github/workflows/ci.yml') }}
- name: Install dependencies
if: steps.cached-venv.outputs.cache-hit != 'true'
run: make install-dev
#----------------------------------------------
# Run tests and upload coverage
#----------------------------------------------
- name: Run tests for coverage
run: make test-w-coverage
- name: Upload coverage artifact
uses: actions/upload-artifact@v4
with:
name: .coverage-${{ matrix.os }}-${{ matrix.python-version }}
path: .coverage
upload-coverage:
name: Upload test coverage to CodeCov
needs: [coverage]
runs-on: ubuntu-latest
permissions:
statuses: write
steps:
#----------------------------------------------
# check-out repo and set-up python
#----------------------------------------------
- name: Check out repository
uses: actions/checkout@v4
- name: Set up python ${{ env.MINIMUM_PYTHON_VERSION }}
id: setup-python
uses: actions/setup-python@v5
with:
python-version: ${{ env.MINIMUM_PYTHON_VERSION }}
#----------------------------------------------
# install dependencies if cache does not exist
#----------------------------------------------
- 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@v3
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
# https://github.com/marketplace/actions/alls-green#why used for branch protection checks
check:
if: always()
needs: [lint, 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: coverage
build:
name: 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:
name: test build on ${{ matrix.os }}
needs: [build]
strategy:
fail-fast: false
matrix:
os: [ubuntu]
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: [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