feat: upgrade snakemake to version 8.14.0 #100
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| # This is a basic workflow to help you get started with Actions | |
| name: dev build CI | |
| # Controls when the action will run. | |
| on: | |
| # Triggers the workflow on push or pull request events | |
| push: | |
| branches: | |
| - 'main' | |
| pull_request: | |
| branches: | |
| - 'main' | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
| jobs: | |
| # This workflow contains a single job called "build" | |
| test: | |
| # The type of runner that the job will run on | |
| strategy: | |
| matrix: | |
| python-versions: ['3.11'] | |
| # github action doesn't goes well with windows due to docker support | |
| # github action doesn't goes well with macos due to `no docker command` | |
| #os: [ubuntu-20.04, windows-latest, macos-latest] | |
| os: [ubuntu-latest] | |
| runs-on: ${{ matrix.os }} | |
| # map step outputs to job outputs so they can be share among jobs | |
| outputs: | |
| package_version: ${{ steps.variables_step.outputs.package_version }} | |
| package_name: ${{ steps.variables_step.outputs.package_name }} | |
| repo_name: ${{ steps.variables_step.outputs.repo_name }} | |
| repo_owner: ${{ steps.variables_step.outputs.repo_owner }} | |
| # uncomment the following to pickup services | |
| # services: | |
| # redis: | |
| # image: redis | |
| # options: >- | |
| # --health-cmd "redis-cli ping" | |
| # --health-interval 10s | |
| # --health-timeout 5s | |
| # --health-retries 5 | |
| # ports: | |
| # - 6379:6379 | |
| # Steps represent a sequence of tasks that will be executed as part of the job | |
| steps: | |
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-versions }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install tox tox-gh-actions poetry | |
| # declare package_version, repo_owner, repo_name, package_name so you may use it in web hooks. | |
| - name: Declare variables for convenient use | |
| id: variables_step | |
| run: | | |
| echo "::set-output name=repo_owner::${GITHUB_REPOSITORY%/*}" | |
| echo "::set-output name=repo_name::${GITHUB_REPOSITORY#*/}" | |
| echo "::set-output name=package_name::`poetry version | awk '{print $1}'`" | |
| echo "::set-output name=package_version::`poetry version --short`" | |
| shell: bash | |
| - name: test with tox | |
| run: tox | |
| - uses: codecov/codecov-action@v4 | |
| with: | |
| version: "v0.1.15" | |
| fail_ci_if_error: false | |
| publish_dev_build: | |
| # if test failed, we should not publish | |
| needs: test | |
| # you may need to change os below | |
| 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 | |
| pip install poetry tox tox-gh-actions setuptools | |
| - name: build documentation | |
| run: | | |
| poetry install -E doc | |
| poetry run mkdocs build | |
| git config --global user.name Docs deploy | |
| git config --global user.email docs@dummy.bot.com | |
| poetry run mike deploy -p -f --ignore "`poetry version --short`.dev" | |
| poetry run mike set-default -p "`poetry version --short`.dev" | |
| - name: Build wheels and source tarball | |
| run: | | |
| poetry version $(poetry version --short)-dev.$GITHUB_RUN_NUMBER | |
| poetry lock | |
| poetry build | |
| #- name: publish to Test PyPI | |
| # uses: pypa/gh-action-pypi-publish@release/v1 | |
| # with: | |
| # user: __token__ | |
| # password: ${{ secrets.TEST_PYPI_API_TOKEN}} | |
| # repository_url: https://test.pypi.org/legacy/ | |
| # skip_existing: true | |
| # notification: | |
| # needs: [test,publish_dev_build] | |
| # if: always() | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - uses: martialonline/workflow-status@v2 | |
| # id: check | |
| # - name: build success notification via email | |
| # if: ${{ steps.check.outputs.status == 'success' }} | |
| # uses: dawidd6/action-send-mail@v3 | |
| # with: | |
| # server_address: ${{ secrets.BUILD_NOTIFY_MAIL_SERVER }} | |
| # server_port: ${{ secrets.BUILD_NOTIFY_MAIL_PORT }} | |
| # username: ${{ secrets.BUILD_NOTIFY_MAIL_FROM }} | |
| # password: ${{ secrets.BUILD_NOTIFY_MAIL_PASSWORD }} | |
| # from: build-bot | |
| # to: ${{ secrets.BUILD_NOTIFY_MAIL_RCPT }} | |
| # subject: ${{ needs.test.outputs.package_name }}.${{ needs.test.outputs.package_version}} build successfully | |
| # convert_markdown: true | |
| # html_body: | | |
| # ## Build Success | |
| # ${{ needs.test.outputs.package_name }}.${{ needs.test.outputs.package_version }} is built and published to test pypi | |
| # ## Change Details | |
| # ${{ github.event.head_commit.message }} | |
| # For more information, please check change history at https://${{ needs.test.outputs.repo_owner }}.github.io/${{ needs.test.outputs.repo_name }}/${{ needs.test.outputs.package_version }}/history | |
| # ## Package Download | |
| # The pacakge is available at: https://test.pypi.org/project/${{ needs.test.outputs.package_name }}/ | |
| # - name: build failure notification via email | |
| # if: ${{ steps.check.outputs.status == 'failure' }} | |
| # uses: dawidd6/action-send-mail@v3 | |
| # with: | |
| # server_address: ${{ secrets.BUILD_NOTIFY_MAIL_SERVER }} | |
| # server_port: ${{ secrets.BUILD_NOTIFY_MAIL_PORT }} | |
| # username: ${{ secrets.BUILD_NOTIFY_MAIL_FROM }} | |
| # password: ${{ secrets.BUILD_NOTIFY_MAIL_PASSWORD }} | |
| # from: build-bot | |
| # to: ${{ secrets.BUILD_NOTIFY_MAIL_RCPT }} | |
| # subject: ${{ needs.test.outputs.package_name }}.${{ needs.test.outputs.package_version}} build failure | |
| # convert_markdown: true | |
| # html_body: | | |
| # ## Change Details | |
| # ${{ github.event.head_commit.message }} | |
| # ## View Log | |
| # https://github.com/${{ needs.test.outputs.repo_owner }}/${{ needs.test.outputs.repo_name }}/actions | |
| # - name: Dingtalk Robot Notify | |
| # if: always() | |
| # uses: leafney/dingtalk-action@v1.0.0 | |
| # env: | |
| # DINGTALK_ACCESS_TOKEN: ${{ secrets.DINGTALK_ACCESS_TOKEN }} | |
| # DINGTALK_SECRET: ${{ secrets.DINGTALK_SECRET }} | |
| # with: | |
| # msgtype: markdown | |
| # title: CI Notification | Success | |
| # text: | | |
| # ### Build Success | |
| # ${{ needs.test.outputs.package_version_full }} is built and published to test pypi | |
| # ### Change History | |
| # Please check change history at https://${{ needs.test.outputs.repo_owner }}.github.io/${{ needs.test.outputs.repo_name }}/history | |
| # ### Package Download | |
| # Please download the pacakge at: https://test.pypi.org/project/${{ needs.test.outputs.repo_name }}/ |