Remove fusion retrieval to circumvent failures with nested config imports #234
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: nf-aggregate linting | |
| # This workflow is triggered on pushes and PRs to the repository. | |
| # It runs markdown lint tests to ensure | |
| # that the code meets the nf-core guidelines. | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| pull_request: | |
| release: | |
| types: [published] | |
| jobs: | |
| EditorConfig: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-node@v3 | |
| - name: Install editorconfig-checker | |
| run: npm install -g editorconfig-checker | |
| - name: Run ECLint check | |
| run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile') | |
| Prettier: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-node@v3 | |
| - name: Install Prettier | |
| run: npm install -g prettier | |
| - name: Run Prettier --check | |
| run: prettier --check ${GITHUB_WORKSPACE} | |
| PythonBlack: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Check code lints with Black | |
| uses: psf/black@stable | |
| # If the above check failed, post a comment on the PR explaining the failure | |
| - name: Post PR comment | |
| if: failure() | |
| uses: mshick/add-pr-comment@v1 | |
| with: | |
| message: | | |
| ## Python linting (`black`) is failing | |
| To keep the code consistent with lots of contributors, we run automated code consistency checks. | |
| To fix this CI test, please run: | |
| * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black` | |
| * Fix formatting errors in your pipeline: `black .` | |
| Once you push these changes the test should pass, and you can hide this comment :+1: | |
| We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help! | |
| Thanks again for your contribution! | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| allow-repeats: false | |
| nf-core: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 | |
| with: | |
| python-version: "3.11" | |
| architecture: "x64" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install nf-core | |
| - name: Run nf-core lint | |
| env: | |
| GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} | |
| run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md | |
| - name: Save PR number | |
| if: ${{ always() }} | |
| run: echo ${{ github.event.pull_request.number }} > PR_number.txt | |
| - name: Upload linting log file artifact | |
| if: ${{ always() }} | |
| uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 | |
| with: | |
| name: linting-logs | |
| path: | | |
| lint_log.txt | |
| lint_results.md | |
| PR_number.txt |