Pre tag #636
Workflow file for this run
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name: nf-core linting | |
# This workflow is triggered on pushes and PRs to the repository. | |
# It runs the `nf-core lint` and 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@v3 | |
- name: Install Nextflow | |
uses: nf-core/setup-nextflow@v1 | |
- uses: actions/setup-python@v4 | |
with: | |
python-version: "3.8" | |
architecture: "x64" | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip | |
pip install nf-core==2.8.0 | |
- 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@v3 | |
with: | |
name: linting-logs | |
path: | | |
lint_log.txt | |
lint_results.md | |
PR_number.txt |