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Merge pull request #48 from nf-core/dev
[Release] 1.1
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{ | ||
"name": "nfcore", | ||
"image": "nfcore/gitpod:latest", | ||
"remoteUser": "gitpod", | ||
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// Configure tool-specific properties. | ||
"customizations": { | ||
// Configure properties specific to VS Code. | ||
"vscode": { | ||
// Set *default* container specific settings.json values on container create. | ||
"settings": { | ||
"python.defaultInterpreterPath": "/opt/conda/bin/python", | ||
"python.linting.enabled": true, | ||
"python.linting.pylintEnabled": true, | ||
"python.formatting.autopep8Path": "/opt/conda/bin/autopep8", | ||
"python.formatting.yapfPath": "/opt/conda/bin/yapf", | ||
"python.linting.flake8Path": "/opt/conda/bin/flake8", | ||
"python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", | ||
"python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", | ||
"python.linting.pylintPath": "/opt/conda/bin/pylint" | ||
}, | ||
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// Add the IDs of extensions you want installed when the container is created. | ||
"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"] | ||
} | ||
} | ||
} |
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*.config linguist-language=nextflow | ||
*.nf.test linguist-language=nextflow | ||
modules/nf-core/** linguist-generated | ||
subworkflows/nf-core/** linguist-generated |
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name: Fix linting from a comment | ||
on: | ||
issue_comment: | ||
types: [created] | ||
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jobs: | ||
deploy: | ||
# Only run if comment is on a PR with the main repo, and if it contains the magic keywords | ||
if: > | ||
contains(github.event.comment.html_url, '/pull/') && | ||
contains(github.event.comment.body, '@nf-core-bot fix linting') && | ||
github.repository == 'nf-core/quantms' | ||
runs-on: ubuntu-latest | ||
steps: | ||
# Use the @nf-core-bot token to check out so we can push later | ||
- uses: actions/checkout@v3 | ||
with: | ||
token: ${{ secrets.nf_core_bot_auth_token }} | ||
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# Action runs on the issue comment, so we don't get the PR by default | ||
# Use the gh cli to check out the PR | ||
- name: Checkout Pull Request | ||
run: gh pr checkout ${{ github.event.issue.number }} | ||
env: | ||
GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} | ||
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- uses: actions/setup-node@v3 | ||
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- name: Install Prettier | ||
run: npm install -g prettier @prettier/plugin-php | ||
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# Check that we actually need to fix something | ||
- name: Run 'prettier --check' | ||
id: prettier_status | ||
run: | | ||
if prettier --check ${GITHUB_WORKSPACE}; then | ||
echo "result=pass" >> $GITHUB_OUTPUT | ||
else | ||
echo "result=fail" >> $GITHUB_OUTPUT | ||
fi | ||
- name: Run 'prettier --write' | ||
if: steps.prettier_status.outputs.result == 'fail' | ||
run: prettier --write ${GITHUB_WORKSPACE} | ||
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- name: Commit & push changes | ||
if: steps.prettier_status.outputs.result == 'fail' | ||
run: | | ||
git config user.email "core@nf-co.re" | ||
git config user.name "nf-core-bot" | ||
git config push.default upstream | ||
git add . | ||
git status | ||
git commit -m "[automated] Fix linting with Prettier" | ||
git push |
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