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109 lines
3.2 KiB
YAML
109 lines
3.2 KiB
YAML
name: nf-core linting
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# This workflow is triggered on pushes and PRs to the repository.
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# It runs the `nf-core lint` and markdown lint tests to ensure
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# that the code meets the nf-core guidelines.
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on:
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push:
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branches:
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- dev
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pull_request:
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release:
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types: [published]
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jobs:
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EditorConfig:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-node@v3
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- name: Install editorconfig-checker
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run: npm install -g editorconfig-checker
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- name: Run ECLint check
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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')
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Prettier:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-node@v3
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- name: Install Prettier
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run: npm install -g prettier
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- name: Run Prettier --check
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run: prettier --check ${GITHUB_WORKSPACE}
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PythonBlack:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Check code lints with Black
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uses: psf/black@stable
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# If the above check failed, post a comment on the PR explaining the failure
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- name: Post PR comment
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if: failure()
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uses: mshick/add-pr-comment@v1
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with:
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message: |
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## Python linting (`black`) is failing
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To keep the code consistent with lots of contributors, we run automated code consistency checks.
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To fix this CI test, please run:
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* Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
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* Fix formatting errors in your pipeline: `black .`
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Once you push these changes the test should pass, and you can hide this comment :+1:
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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!
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Thanks again for your contribution!
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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allow-repeats: false
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nf-core:
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runs-on: ubuntu-latest
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v3
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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v1
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- uses: actions/setup-python@v4
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with:
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python-version: "3.8"
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architecture: "x64"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install nf-core
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- name: Run nf-core lint
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env:
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GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
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run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
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- name: Save PR number
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if: ${{ always() }}
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run: echo ${{ github.event.pull_request.number }} > PR_number.txt
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- name: Upload linting log file artifact
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if: ${{ always() }}
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uses: actions/upload-artifact@v3
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with:
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name: linting-logs
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path: |
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lint_log.txt
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lint_results.md
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PR_number.txt
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