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FROM scilus/scilus:1.6.0 | ||
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RUN apt update && apt install -y \ | ||
git \ | ||
python3-venv \ | ||
wget \ | ||
&& rm -rf /var/lib/apt/lists/* | ||
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RUN python3 -m pip install pipx && \ | ||
python3 -m pipx ensurepath && \ | ||
pipx install poetry | ||
FROM scilus/scilus:1.6.0 | ||
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RUN apt update && apt install -y \ | ||
git \ | ||
python3-venv \ | ||
wget \ | ||
&& rm -rf /var/lib/apt/lists/* | ||
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RUN python3 -m pip install pipx && \ | ||
python3 -m pipx ensurepath && \ | ||
pipx install poetry |
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{ | ||
"name": "NF-SCIL development container", | ||
"build": { "dockerfile": "Dockerfile" }, | ||
"forwardPorts": [3000], | ||
"onCreateCommand": "bash .devcontainer/setup_container.sh", | ||
"features": { | ||
"ghcr.io/devcontainers/features/git:1": {}, | ||
"ghcr.io/devcontainers/features/git-lfs:1": {}, | ||
"ghcr.io/devcontainers/features/github-cli:1": {}, | ||
"ghcr.io/devcontainers/features/docker-in-docker:2": {}, | ||
"ghcr.io/devcontainers-contrib/features/apt-get-packages:1": {}, | ||
"ghcr.io/robsyme/features/nextflow:1": {}, | ||
"ghcr.io/devcontainers-contrib/features/curl-apt-get:1": {}, | ||
"ghcr.io/devcontainers-contrib/features/tmux-apt-get:1": {}, | ||
"ghcr.io/devcontainers-contrib/features/wget-apt-get:1": {} | ||
}, | ||
"customizations": { | ||
"vscode": { | ||
"extensions": [ | ||
"AlexVCaron.nf-scil-extensions" | ||
] | ||
} | ||
}, | ||
"init": true, | ||
"privileged": true | ||
} | ||
{ | ||
"name": "NF-SCIL development container", | ||
"build": { "dockerfile": "Dockerfile" }, | ||
"forwardPorts": [3000], | ||
"onCreateCommand": "bash .devcontainer/setup_container.sh", | ||
"features": { | ||
"ghcr.io/devcontainers/features/git:1": {}, | ||
"ghcr.io/devcontainers/features/git-lfs:1": {}, | ||
"ghcr.io/devcontainers/features/github-cli:1": {}, | ||
"ghcr.io/devcontainers/features/docker-in-docker:2": {}, | ||
"ghcr.io/devcontainers-contrib/features/apt-get-packages:1": {}, | ||
"ghcr.io/robsyme/features/nextflow:1": {}, | ||
"ghcr.io/devcontainers-contrib/features/curl-apt-get:1": {}, | ||
"ghcr.io/devcontainers-contrib/features/tmux-apt-get:1": {}, | ||
"ghcr.io/devcontainers-contrib/features/wget-apt-get:1": {} | ||
}, | ||
"mounts": [ | ||
{ | ||
"source": "nf-scil-venv", | ||
"target": "/workspaces/nf-scil/.venv", | ||
"type": "volume" | ||
}, | ||
{ | ||
"source": "nf-scil-tmp", | ||
"target": "/tmp", | ||
"type": "volume" | ||
} | ||
], | ||
"customizations": { | ||
"vscode": { | ||
"settings": { | ||
"pythonIndent.keepHangingBracketOnLine": true, | ||
"pythonIndent.trimLinesWithOnlyWhitespace": true, | ||
"python.createEnvironment.trigger": "off", | ||
"python.terminal.activateEnvironment": true, | ||
"python.poetryPath": "/root/.local/bin/poetry", | ||
"python.defaultInterpreterPath": "${workspaceFolder}/.venv", | ||
"python.analysis.exclude": [ | ||
"${workspaceFolder}/.dvc", | ||
"${workspaceFolder}/.pytest_cache", | ||
"${workspaceFolder}/.test_data", | ||
"${workspaceFolder}/.vscode", | ||
"${workspaceFolder}/nf-scil-extensions", | ||
"**/__pycache__", | ||
"${workspaceFolder}/.git" | ||
], | ||
"python.analysis.ignore": [ | ||
"${workspaceFolder}/.dvc", | ||
"${workspaceFolder}/.pytest_cache", | ||
"${workspaceFolder}/.test_data", | ||
"${workspaceFolder}/.vscode", | ||
"${workspaceFolder}/nf-scil-extensions", | ||
"**/__pycache__", | ||
"${workspaceFolder}/.git" | ||
] | ||
}, | ||
"extensions": [ | ||
"AlexVCaron.nf-scil-extensions", | ||
"ms-python.autopep8" | ||
] | ||
} | ||
}, | ||
"init": true, | ||
"privileged": true | ||
} |
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#!/usr/bin/env bash | ||
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poetry install | ||
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echo "poetry shell" >> ~/.bashrc | ||
poetry install --no-root | ||
echo "export PROFILE=docker" >> ~/.bashrc | ||
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root = true | ||
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[*] | ||
charset = utf-8 | ||
end_of_line = lf | ||
insert_final_newline = true | ||
trim_trailing_whitespace = true | ||
indent_size = 4 | ||
indent_style = space | ||
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[*.{md,yml,yaml,html,css,scss,js,cff}] | ||
indent_size = 2 | ||
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[LICENSE] | ||
indent_size = 1 |
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name: Code Linting | ||
run-name: Code Linting (automated) | ||
on: | ||
issue_comment: | ||
types: [created] | ||
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jobs: | ||
fix-linting: | ||
# 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-scil-bot fix linting') && | ||
github.repository == 'scilus/nf-scil' | ||
runs-on: ubuntu-latest | ||
steps: | ||
# Use the @nf-scil-bot token to check out so we can push later | ||
- uses: actions/checkout@v4 | ||
with: | ||
token: ${{ secrets.GITHUB_TOKEN }} | ||
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# indication that the linting is being fixed | ||
- name: React on comment | ||
uses: peter-evans/create-or-update-comment@v3 | ||
with: | ||
comment-id: ${{ github.event.comment.id }} | ||
reactions: eyes | ||
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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.GITHUB_TOKEN }} | ||
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- uses: actions/setup-node@v4 | ||
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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 "::set-output name=result::pass" | ||
else | ||
echo "::set-output name=result::fail" | ||
fi | ||
- name: Run 'prettier --write' | ||
if: steps.prettier_status.outputs.result == 'fail' | ||
run: prettier --write ${GITHUB_WORKSPACE} | ||
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- name: Post nothing-to-do comment | ||
if: steps.prettier_status.outputs.result == 'pass' | ||
uses: peter-evans/create-or-update-comment@v3 | ||
with: | ||
issue-number: ${{ github.event.issue.number }} | ||
body: | | ||
Nothing for me to do here! :shrug: | ||
This is probably because the linting errors come from `nf-core lint` and have to be fixed manually (or with `nf-core lint --fix`). | ||
- name: Commit & push changes | ||
if: steps.prettier_status.outputs.result == 'fail' | ||
run: | | ||
git config user.email "[email protected]" | ||
git config user.name "nf-scil-bot" | ||
git config push.default upstream | ||
git add . | ||
git status | ||
git commit -m "[automated] Fix linting with Prettier" | ||
git push |
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