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Add CI/CD tooling and developer documentation
Merge unique additions from refactor branch into dev: - Add pre-commit configuration (ruff, prettier, standard hooks) - Add lint workflow using pre-commit action - Add PyPI publish workflow with trusted publishing - Add report validation to test workflow - Add dev dependencies to pyproject.toml - Add CLAUDE.md with updated architecture documentation 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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‎.github/workflows/lint.yaml‎

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name: "Lint"
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on:
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push:
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branches: [main, master]
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pull_request:
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jobs:
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pre-commit:
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name: Pre-commit
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runs-on: ubuntu-latest
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timeout-minutes: 5
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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- name: Run pre-commit
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uses: pre-commit/action@v3.0.1

‎.github/workflows/linux.yaml‎

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name: "Build - Linux"
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on: [push, pull_request]
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on:
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push:
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branches: [main, master, dev]
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pull_request:
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jobs:
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run_multiqc:
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name: Linux - Python ${{ matrix.python-version }}
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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python-version: [3.11, 3.12, 3.13]
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python-version: ["3.11", "3.12", "3.13"]
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timeout-minutes: 10
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steps:
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# Check out MultiQC code
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- uses: actions/checkout@v2
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- name: Checkout code
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uses: actions/checkout@v4
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# Set up Python
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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# Update pip and install beautifulsoup4 for CI tests (CSP checking)
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- name: Install dependencies for CI tests
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip setuptools beautifulsoup4 multiqc
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python -m pip install --upgrade pip setuptools wheel
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pip install multiqc
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# Install MultiQC
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- name: Install MultiQC_SAV
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run: pip install .
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# Run all of the tests!
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- name: MiSeq
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run: multiqc -m SAV test_data/MiSeq
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- name: Test MiSeq
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run: |
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multiqc --strict -v --no-version-check -m SAV test_data/MiSeq -o test_output/MiSeq
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test -f test_output/MiSeq/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1)
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grep -q "SAV" test_output/MiSeq/multiqc_data/multiqc.log || (echo "ERROR: SAV module not found in log" && exit 1)
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- name: MiSeqI100
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run: multiqc --strict -v --no-version-check -m SAV test_data/MiSeqI100
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- name: Test MiSeqI100
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run: |
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multiqc --strict -v --no-version-check -m SAV test_data/MiSeqI100 -o test_output/MiSeqI100
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test -f test_output/MiSeqI100/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1)
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grep -q "SAV" test_output/MiSeqI100/multiqc_data/multiqc.log || (echo "ERROR: SAV module not found in log" && exit 1)
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- name: HiSeq3000
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run: multiqc --strict -v --no-version-check -m SAV test_data/HiSeq3000
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- name: Test HiSeq3000
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run: |
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multiqc --strict -v --no-version-check -m SAV test_data/HiSeq3000 -o test_output/HiSeq3000
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test -f test_output/HiSeq3000/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1)
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grep -q "SAV" test_output/HiSeq3000/multiqc_data/multiqc.log || (echo "ERROR: SAV module not found in log" && exit 1)
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- name: NextSeq500
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run: multiqc --strict -v --no-version-check -m SAV test_data/NextSeq500
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- name: Test NextSeq500
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run: |
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multiqc --strict -v --no-version-check -m SAV test_data/NextSeq500 -o test_output/NextSeq500
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test -f test_output/NextSeq500/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1)
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grep -q "SAV" test_output/NextSeq500/multiqc_data/multiqc.log || (echo "ERROR: SAV module not found in log" && exit 1)
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- name: NextSeq2000
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run: multiqc --strict -v --no-version-check -m SAV test_data/NextSeq2000
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- name: Test NextSeq2000
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run: |
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multiqc --strict -v --no-version-check -m SAV test_data/NextSeq2000 -o test_output/NextSeq2000
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test -f test_output/NextSeq2000/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1)
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grep -q "SAV" test_output/NextSeq2000/multiqc_data/multiqc.log || (echo "ERROR: SAV module not found in log" && exit 1)
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- name: NovaSeq6000
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run: multiqc --strict -v --no-version-check -m SAV test_data/NovaSeq6000
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- name: Test NovaSeq6000
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run: |
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multiqc --strict -v --no-version-check -m SAV test_data/NovaSeq6000 -o test_output/NovaSeq6000
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test -f test_output/NovaSeq6000/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1)
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grep -q "SAV" test_output/NovaSeq6000/multiqc_data/multiqc.log || (echo "ERROR: SAV module not found in log" && exit 1)
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- name: NovaSeqX
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run: multiqc --strict -v --no-version-check -m SAV test_data/NovaSeqX
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- name: Test NovaSeqX
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run: |
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multiqc --strict -v --no-version-check -m SAV test_data/NovaSeqX -o test_output/NovaSeqX
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test -f test_output/NovaSeqX/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1)
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grep -q "SAV" test_output/NovaSeqX/multiqc_data/multiqc.log || (echo "ERROR: SAV module not found in log" && exit 1)

‎.github/workflows/publish.yaml‎

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name: "Publish to PyPI"
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on:
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release:
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types: [published]
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jobs:
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publish:
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name: Publish to PyPI
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runs-on: ubuntu-latest
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environment: pypi
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permissions:
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id-token: write
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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- name: Install build dependencies
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run: pip install build
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- name: Build package
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run: python -m build
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1

‎.pre-commit-config.yaml‎

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minimum_pre_commit_version: "2.9.2"
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repos:
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# Meta hooks for verification
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- repo: meta
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hooks:
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- id: identity
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- id: check-hooks-apply
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# Standard pre-commit hooks
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: "v5.0.0"
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hooks:
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- id: check-added-large-files
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args: ["--maxkb=1000"]
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- id: check-merge-conflict
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- id: check-yaml
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- id: check-toml
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- id: debug-statements
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- id: end-of-file-fixer
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exclude: ^(test_data|docs/example)/
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- id: trailing-whitespace
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exclude: ^(test_data|docs/example)/
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- id: mixed-line-ending
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args: ["--fix=lf"]
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exclude: ^(test_data|docs/example)/
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# Line ending normalization
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- repo: https://github.com/Lucas-C/pre-commit-hooks
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rev: "v1.5.5"
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hooks:
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- id: remove-crlf
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exclude: ^(test_data|docs/example)/
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# Prettier for markdown, yaml, json formatting
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- repo: https://github.com/pre-commit/mirrors-prettier
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rev: "v3.1.0"
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hooks:
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- id: prettier
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types_or: [markdown, yaml, json]
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additional_dependencies:
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- "prettier@3.1.0"
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# Ruff formatting
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: "v0.8.3"
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hooks:
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- id: ruff-format
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# Ruff linting with auto-fix
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: "v0.8.3"
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hooks:
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- id: ruff
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args: [--fix, --exit-non-zero-on-fix]

‎.prettierignore‎

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# Build artifacts
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dist/
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build/
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*.egg-info/
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# Python cache
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__pycache__/
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*.pyc
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# Test data
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test_data/
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# Virtual environments
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venv/
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.venv/
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env/
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# Coverage
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htmlcov/
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.coverage
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# IDE
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.idea/
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.vscode/
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# Example reports
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docs/example/
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# Lock files
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*.lock

‎.prettierrc.js‎

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module.exports = {
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printWidth: 120,
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tabWidth: 2,
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useTabs: false,
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semi: true,
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singleQuote: false,
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trailingComma: "all",
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bracketSpacing: true,
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proseWrap: "preserve",
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};

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