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Feat/remove ignore errors in mypy settings (#78)
* feat: Add competing risks models and enhance data visualization * feat: Add competing risks models and enhance data visualization * chore: fixes * chore: fixes unit test * chore: solve issues with formatting * Add files via upload * docs: update fix reference (#37) * Add missing dependencies and configure quality tools (#39) * feat: add dataset export utility (#41) * Fix black formatting (#43) * Add extensive summary tests (#45) * Add visualization CLI tests (#47) * Expand validate tests (#49) * docs: rewrite README (#51) * Increase test coverage (#52) * Fix docs build and sort imports (#54) * Add scikit-survival integration (#56) * chore: finalize 1.0.9 release metadata (#58) * refactor: unify error handling (#60) * Feat/consolidate and optimize (#63) * chore: tighten tooling and fix visualization * docs: document Python 3.10 requirement * ci: align workflow with review template * feat: expose dev extras (#65) * test: broaden competing risks coverage (#67) * fix: ensure doc links and tag workflow (#69) * ci: streamline coverage and install flags (#71) * feat: share covariate utilities (#73) * ci: separate manual pypi publish (#76) * fix: tighten sequence checks and streamline competing-risk helpers
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‎.flake8‎

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[flake8]
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max-line-length = 120
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extend-ignore = E501,W291,W293,W391,E402,E302,E305

‎.github/workflows/bump-version.yml‎

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# .github/workflows/bump-version.yml
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name: Bump Version on Merge to Main
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name: Tag Version on Merge to Main
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on:
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push:
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branches:
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- main
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jobs:
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bump-version:
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tag-version:
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runs-on: ubuntu-latest
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permissions:
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contents: write
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id-token: write
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0 # Fetch all history for all branches and tags
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fetch-depth: 0
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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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- run: pip install python-semantic-release
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- name: Configure Git
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run: |
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git config user.name "github-actions[bot]"
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git config user.email "github-actions[bot]@users.noreply.github.com"
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- name: Run Semantic Release
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env:
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GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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run: semantic-release version
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- name: Tag repository from pyproject
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run: python scripts/check_version_match.py --fix
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- name: Push changes
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run: |
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git push --follow-tags
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- name: "Install Poetry"
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run: pip install poetry
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- name: "Determine version bump type"
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run: |
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git fetch --tags
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# This defaults to a patch type, unless a feature commit was pushed, then set type to minor
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LAST_TAG=$(git describe --tags $(git rev-list --tags --max-count=1))
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LAST_COMMIT=$(git log -1 --format='%H')
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echo "Last git tag: $LAST_TAG"
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echo "Last git commit: $LAST_COMMIT"
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echo "Commits:"
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git log --no-merges --pretty=oneline $LAST_TAG...$LAST_COMMIT
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git log --no-merges --pretty=format:"%s" $LAST_TAG...$LAST_COMMIT | grep -q ^feat: && BUMP_TYPE="minor" || BUMP_TYPE="patch"
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echo "Version bump type: $BUMP_TYPE"
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echo "BUMP_TYPE=$BUMP_TYPE" >> $GITHUB_ENV
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- name: "Version bump"
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run: |
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poetry version $BUMP_TYPE
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- name: "Push new version"
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run: |
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git add pyproject.toml
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git commit -m "Update version to $(poetry version -s)"
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git pull --ff-only origin main
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git push origin main --follow-tags
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎.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:
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- main
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tags:
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- 'v*'
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pull_request:
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branches:
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- main
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jobs:
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test:
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name: Test with Python ${{ matrix.python-version }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.10", "3.11", "3.12"]
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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 ${{ matrix.python-version }}
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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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- name: Cache Poetry dependencies
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uses: actions/cache@v4
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with:
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path: ~/.cache/pypoetry
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key: ${{ runner.os }}-poetry-${{ matrix.python-version }}-${{ hashFiles('**/poetry.lock') }}
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- name: Install Poetry
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run: |
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curl -sSL https://install.python-poetry.org | python3 -
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echo "$HOME/.local/bin" >> $GITHUB_PATH
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- name: Install dependencies
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run: poetry install --with dev --no-interaction --no-root
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- name: Check runtime dependencies
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run: |
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poetry run python - <<'PY'
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import importlib, sys
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missing = [m for m in ("pandas",) if importlib.util.find_spec(m) is None]
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if missing:
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print("Missing dependencies:", ", ".join(missing))
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sys.exit(1)
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PY
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- name: Verify version matches tag
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if: startsWith(github.ref, 'refs/tags/')
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run: python scripts/check_version_match.py
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- name: Run tests with coverage
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run: poetry run pytest --cov=gen_surv --cov-report=xml --cov-report=term
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- name: Upload coverage to Codecov
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if: matrix.python-version == '3.11'
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uses: codecov/codecov-action@v5
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with:
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files: coverage.xml
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token: ${{ secrets.CODECOV_TOKEN }}
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lint:
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name: Code Quality
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runs-on: ubuntu-latest
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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: Cache Poetry dependencies
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uses: actions/cache@v4
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with:
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path: ~/.cache/pypoetry
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key: ${{ runner.os }}-poetry-3.11-${{ hashFiles('**/poetry.lock') }}
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- name: Install Poetry
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run: |
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curl -sSL https://install.python-poetry.org | python3 -
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echo "$HOME/.local/bin" >> $GITHUB_PATH
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- name: Install dependencies
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run: poetry install --with dev --no-interaction --no-root
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- name: Run pre-commit checks
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run: poetry run pre-commit run --all-files

‎.github/workflows/docs.yml‎

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name: Documentation Build
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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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jobs:
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docs:
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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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- uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Cache Poetry dependencies
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uses: actions/cache@v4
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with:
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path: ~/.cache/pypoetry
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key: ${{ runner.os }}-poetry-3.11-${{ hashFiles('**/poetry.lock') }}
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- name: Install Poetry
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run: |
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curl -sSL https://install.python-poetry.org | python3 -
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echo "$HOME/.local/bin" >> $GITHUB_PATH
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- name: Install dependencies
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run: poetry install --with docs
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- name: Build documentation
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run: poetry run sphinx-build -W -b html docs/source docs/build
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- name: Upload artifacts
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uses: actions/upload-artifact@v4
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with:
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name: documentation
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path: docs/build/

‎.github/workflows/publish.yml‎

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name: Publish to PyPI
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on:
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workflow_dispatch:
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jobs:
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publish:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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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: Verify version matches tag
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run: python scripts/check_version_match.py
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- name: Install Poetry
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run: |
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curl -sSL https://install.python-poetry.org | python3 -
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echo "$HOME/.local/bin" >> $GITHUB_PATH
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- name: Publish
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env:
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POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
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run: poetry publish --build --no-interaction

‎.github/workflows/test.yml‎

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‎.gitignore‎

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# Temporary
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*.log
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*.tmp
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.hypothesis/

‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/psf/black
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rev: 24.1.0
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hooks:
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- id: black
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- repo: https://github.com/pycqa/isort
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rev: 5.13.2
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hooks:
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- id: isort
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- repo: https://github.com/pycqa/flake8
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rev: 6.1.0
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hooks:
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- id: flake8
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- repo: https://github.com/pre-commit/mirrors-mypy
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rev: v1.15.0
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hooks:
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- id: mypy
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pass_filenames: false
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args: [--config-file=pyproject.toml, gen_surv]

‎.readthedocs.yml‎

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os: ubuntu-22.04
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tools:
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python: "3.11"
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jobs:
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post_create_environment:
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- pip install poetry
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post_install:
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- poetry config virtualenvs.create false
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- poetry install --with docs
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python:
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install:
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- requirements: docs/requirements.txt
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- method: pip
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path: .
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sphinx:
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configuration: docs/source/conf.py
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fail_on_warning: false
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formats:
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- pdf
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- epub

‎CHANGELOG.md‎

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# CHANGELOG
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## v1.0.9 (2025-08-02)
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### Features
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- export datasets to RDS files
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- test workflow runs on a Python version matrix
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- scikit-learn compatible data generator
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- compatibility helpers for lifelines and scikit-survival
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### Documentation
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- updated usage examples and tutorials
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- document optional scikit-survival dependency throughout the docs
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### Continuous Integration
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- auto-tag releases using the version check script
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### Misc
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- README quick example uses `covariate_range`
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## v1.0.8 (2025-07-30)
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### Documentation
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- ensure absolute path resolution in `conf.py`
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- drop unsupported theme option
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- define bibliography anchors and headings
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- fix tutorial links to non-existing docs
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- add additional references to the bibliography
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### Testing
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- add CLI integration test
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- expand piecewise generator test coverage
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### Misc
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- remove fix_recommendations.md
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## v1.0.0 (2025-06-06)
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