feat(executor): upgrade to Snakemake v8 #358
Workflow file for this run
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| # This file is part of REANA. | |
| # Copyright (C) 2021, 2022, 2024 CERN. | |
| # | |
| # REANA is free software; you can redistribute it and/or modify it | |
| # under the terms of the MIT License; see LICENSE file for more details. | |
| name: CI | |
| on: [push, pull_request] | |
| jobs: | |
| lint-commitlint: | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Setup Node | |
| uses: actions/setup-node@v4 | |
| - name: Install commitlint | |
| run: | | |
| npm install conventional-changelog-conventionalcommits | |
| npm install commitlint@latest | |
| - name: Check commit message compliance of the recently pushed commit | |
| if: github.event_name == 'push' | |
| run: | | |
| ./run-tests.sh --check-commitlint HEAD~1 HEAD | |
| - name: Check commit message compliance of the pull request | |
| if: github.event_name == 'pull_request' | |
| run: | | |
| ./run-tests.sh --check-commitlint ${{ github.event.pull_request.base.sha }} ${{ github.event.pull_request.head.sha }} ${{ github.event.pull_request.number }} | |
| lint-shellcheck: | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Runs shell script static analysis | |
| run: | | |
| sudo apt-get install shellcheck | |
| ./run-tests.sh --check-shellcheck | |
| lint-black: | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Check Python code formatting | |
| run: | | |
| pip install --upgrade pip | |
| pip install black | |
| ./run-tests.sh --check-black | |
| lint-flake8: | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Check compliance with pep8, pyflakes and circular complexity | |
| run: | | |
| pip install --upgrade pip | |
| pip install flake8 | |
| ./run-tests.sh --check-flake8 | |
| lint-pydocstyle: | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Check compliance with Python docstring conventions | |
| run: | | |
| pip install --upgrade pip | |
| pip install pydocstyle | |
| ./run-tests.sh --check-pydocstyle | |
| lint-check-manifest: | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Check Python manifest completeness | |
| run: | | |
| pip install --upgrade pip | |
| pip install check-manifest | |
| ./run-tests.sh --check-manifest | |
| docs-sphinx: | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update -y | |
| sudo apt install libcurl4-openssl-dev libssl-dev | |
| sudo apt-get install libgnutls28-dev | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update -y | |
| sudo apt-get install python3.12-dev graphviz libgraphviz-dev pkg-config uuid-dev | |
| - name: Install Python dependencies | |
| run: | | |
| pip install --upgrade pip 'setuptools' py wheel | |
| pip install -e .[all] | |
| - name: Run Sphinx documentation with doctests | |
| run: ./run-tests.sh --check-sphinx | |
| python-tests: | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update -y | |
| sudo apt-get install python3.12-dev graphviz libgraphviz-dev pkg-config uuid-dev | |
| - name: Install Python dependencies | |
| run: | | |
| pip install --upgrade pip 'setuptools' py | |
| pip install twine wheel | |
| pip install -e .[all] | |
| - name: Run pytest | |
| run: ./run-tests.sh --check-pytest | |
| - name: Codecov Coverage | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| files: coverage.xml | |
| lint-dockerfile: | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Check Dockerfile compliance | |
| run: ./run-tests.sh --check-dockerfile | |
| docker-build: | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Build Docker image | |
| run: ./run-tests.sh --check-docker-build | |
| release-docker: | |
| runs-on: ubuntu-24.04 | |
| if: > | |
| vars.RELEASE_DOCKER == 'true' && | |
| github.event_name == 'push' && | |
| startsWith(github.ref, 'refs/tags/') | |
| needs: | |
| - docs-sphinx | |
| - lint-black | |
| - lint-check-manifest | |
| - lint-commitlint | |
| - lint-dockerfile | |
| - lint-flake8 | |
| - lint-pydocstyle | |
| - lint-shellcheck | |
| - python-tests | |
| steps: | |
| - name: Release Docker image | |
| uses: reanahub/reana-github-actions/release-docker@v1 | |
| with: | |
| username: ${{ secrets.DOCKER_USER }} | |
| token: ${{ secrets.DOCKER_TOKEN }} | |
| organisation: ${{ vars.DOCKER_ORGANISATION }} | |
| registry: ${{ vars.DOCKER_REGISTRY }} | |
| platform: | | |
| linux/amd64 |