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‎.editorconfig‎

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root = true
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[*]
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end_of_line = lf
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insert_final_newline = true
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trim_trailing_whitespace = true
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charset = utf-8
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[*.py]
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indent_style = space
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indent_size = 4
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max_line_length = 100
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[*.{yml,yaml}]
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indent_style = space
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indent_size = 2
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[*.{toml,json}]
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indent_style = space
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indent_size = 2
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[*.md]
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trim_trailing_whitespace = false
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[Makefile]
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indent_style = tab

‎.gitattributes‎

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*.pdf filter=lfs diff=lfs merge=lfs -text

‎.github/pull_request_template.md‎

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## Summary
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<!-- Brief description of what this PR does -->
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## Changes
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-
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## Type of Change
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- [ ] Bug fix
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- [ ] New feature
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- [ ] Refactoring
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- [ ] Documentation
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- [ ] Tests
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- [ ] CI/CD
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## Checklist
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- [ ] Tests pass (`uv run pytest`)
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- [ ] Linting passes (`uv run ruff check src/`)
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- [ ] Type checking passes (`uv run pyright src/`)
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- [ ] Pre-commit hooks pass (`uv run pre-commit run --all-files`)
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- [ ] Coverage >= 80% on new code

‎.github/workflows/build-verification.yml‎

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name: Build Verification
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on:
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push:
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branches: [main]
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pull_request:
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branches: [main]
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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build:
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name: Build (${{ matrix.os }}, Python ${{ matrix.python-version }})
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-14]
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python-version: ["3.11", "3.12"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up uv
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uses: astral-sh/setup-uv@v4
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with:
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enable-cache: true
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- name: Set up Python
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run: uv python install ${{ matrix.python-version }}
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- name: Create virtual environment
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run: uv venv
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- name: Build wheel
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run: uv build
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- name: Check distribution
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run: |
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uv pip install twine
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uv run twine check dist/*
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- name: Pyright
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run: |
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uv pip install -e ".[dev]"
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uv run pyright --warnings src/
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- name: Install in clean venv and verify import
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run: |
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uv venv /tmp/test-env
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VIRTUAL_ENV=/tmp/test-env uv pip install dist/*.whl
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/tmp/test-env/bin/python -c "import calibrax; print(calibrax.__version__)"

‎.github/workflows/ci.yml‎

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name: CI
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on:
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push:
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branches: [main]
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pull_request:
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branches: [main]
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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lint:
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name: Lint
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up uv
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uses: astral-sh/setup-uv@v4
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with:
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enable-cache: true
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- name: Set up Python
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run: uv python install 3.11
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- name: Create virtual environment
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run: uv venv
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- name: Install dependencies
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run: uv pip install -e ".[dev]"
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- name: Ruff check
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run: uv run ruff check src/ tests/
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- name: Ruff format check
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run: uv run ruff format --check src/ tests/
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- name: Pyright
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run: uv run pyright --warnings src/
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test:
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name: Test (Python ${{ matrix.python-version }}, ${{ matrix.os }})
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runs-on: ${{ matrix.os }}
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needs: lint
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-14]
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python-version: ["3.11"]
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env:
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JAX_PLATFORMS: cpu
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WANDB_DIR: /tmp/calibrax-test-wandb
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WANDB_MODE: offline
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XLA_PYTHON_CLIENT_PREALLOCATE: "false"
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TF_CPP_MIN_LOG_LEVEL: "1"
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steps:
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- uses: actions/checkout@v4
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- name: Set up uv
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uses: astral-sh/setup-uv@v4
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with:
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enable-cache: true
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- name: Set up Python
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run: uv python install ${{ matrix.python-version }}
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- name: Create virtual environment
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run: uv venv
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- name: Install dependencies
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run: uv pip install -e ".[dev,test,stats,changepoint,mlflow]"
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- name: Create temp directory
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run: mkdir -p temp
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- name: Run tests
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run: |
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uv run pytest tests/ \
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--cov=calibrax \
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--cov-report=term-missing \
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--cov-report=xml:coverage.xml \
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--cov-fail-under=80 \
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--timeout=300 \
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-v
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- name: Upload coverage
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if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
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uses: codecov/codecov-action@v4
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with:
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file: coverage.xml
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fail_ci_if_error: false
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build:
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name: Build
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runs-on: ubuntu-latest
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needs: test
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steps:
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- uses: actions/checkout@v4
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- name: Set up uv
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uses: astral-sh/setup-uv@v4
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with:
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enable-cache: true
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- name: Set up Python
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run: uv python install 3.11
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- name: Create virtual environment
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run: uv venv
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- name: Build package
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run: uv build
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- name: Check distribution
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run: |
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uv pip install twine
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uv run twine check dist/*

‎.github/workflows/docs.yml‎

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name: Documentation
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on:
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push:
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branches: [main]
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paths:
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- "docs/**"
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- "mkdocs.yml"
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- "src/calibrax/**"
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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deploy:
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name: Deploy Docs
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runs-on: ubuntu-latest
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v4
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- name: Set up uv
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uses: astral-sh/setup-uv@v4
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with:
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enable-cache: true
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- name: Set up Python
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run: uv python install 3.11
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- name: Create virtual environment
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run: uv venv
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- name: Install dependencies
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run: uv pip install -e ".[docs]"
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- name: Build docs
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run: uv run mkdocs build --clean
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- name: Deploy to GitHub Pages
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uses: peaceiris/actions-gh-pages@v3
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./site
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destination_dir: deploy/calibrax
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cname: docs.avitai.bio

‎.github/workflows/quality-checks.yml‎

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name: Quality Checks
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on:
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push:
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branches: [main]
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pull_request:
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branches: [main]
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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quality:
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name: Quality (${{ 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"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up uv
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uses: astral-sh/setup-uv@v4
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with:
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enable-cache: true
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- name: Set up Python
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run: uv python install ${{ matrix.python-version }}
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- name: Create virtual environment
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run: uv venv
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- name: Install dependencies
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run: uv pip install -e ".[dev]"
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- name: Pre-commit
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run: uv run pre-commit run --all-files
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- name: Pyright
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run: uv run pyright --warnings src/
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- name: Ruff check
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run: uv run ruff check src/ tests/
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- name: Ruff format check
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run: uv run ruff format --check src/ tests/
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- name: Ruff isort check
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run: uv run ruff check --select I --diff src/ tests/
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- name: Pip audit
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run: |
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uv pip install pip-audit
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uv run pip-audit --ignore-vuln PYSEC-2022-42969

‎.github/workflows/security.yml‎

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name: Security
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on:
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push:
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branches: [main]
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pull_request:
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branches: [main]
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schedule:
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- cron: "0 0 * * 1"
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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security:
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name: Security Scan
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up uv
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uses: astral-sh/setup-uv@v4
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with:
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enable-cache: true
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- name: Set up Python
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run: uv python install 3.11
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- name: Create virtual environment
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run: uv venv
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- name: Install dependencies
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run: |
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uv pip install -e ".[dev]"
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uv pip install pip-audit bandit
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- name: Pip audit
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run: uv run pip-audit --ignore-vuln PYSEC-2022-42969
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- name: Bandit
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run: uv run bandit -r src/calibrax/ -c pyproject.toml -f json -o bandit-report.json
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- name: Upload Bandit report
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if: always()
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uses: actions/upload-artifact@v4
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with:
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name: bandit-report
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path: bandit-report.json

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