survival 0.0.6__tar.gz → 1.1.16__tar.gz

survival-1.1.16/.cargo/config.toml

@@ -0,0 +1,6 @@
+[build]
+rustflags = ["-Dwarnings"]
+
+# For builds with AVX2
+# [target.x86_64-unknown-linux-gnu]
+# rustflags = ["-C", "target-feature=+avx2,+fma", "-Dwarnings"]

survival-1.1.16/.github/dependabot.yml

@@ -0,0 +1,16 @@
+  version: 2
+  updates:
+    - package-ecosystem: "cargo"
+      directory: "/"
+      schedule:
+        interval: "weekly"
+
+    - package-ecosystem: "pip"
+      directory: "/"
+      schedule:
+        interval: "weekly"
+
+    - package-ecosystem: "github-actions"
+      directory: "/"
+      schedule:
+        interval: "weekly"

survival-1.1.16/.github/workflows/lint.yml

@@ -0,0 +1,103 @@
+name: Lint
+
+on:
+  pull_request:
+    branches: [main]
+
+env:
+  CARGO_TERM_COLOR: always
+
+jobs:
+  rust-lint:
+    name: Rust Lint & Format
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6
+
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@stable
+        with:
+          components: rustfmt, clippy
+
+      - name: Cache Rust dependencies
+        uses: actions/cache@v5
+        with:
+          path: |
+            ~/.cargo/bin/
+            ~/.cargo/registry/index/
+            ~/.cargo/registry/cache/
+            ~/.cargo/git/db/
+            target/
+          key: ${{ runner.os }}-cargo-lint-${{ hashFiles('**/Cargo.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-cargo-
+
+      - name: Check formatting
+        run: cargo fmt --all -- --check
+
+      - name: Run clippy
+        run: cargo clippy --all-targets --all-features -- -D warnings
+
+      - name: Check for unused dependencies
+        run: |
+          cargo install cargo-machete || true
+          cargo machete || true
+
+  python-lint:
+    name: Python Lint & Format
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.14'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+
+      - name: Install linters
+        run: uv pip install --system ruff mypy
+
+      - name: Check formatting
+        run: ruff format test/ --check
+
+      - name: Lint code
+        run: ruff check test/
+
+      - name: Type check stubs
+        run: |
+          uv pip install --system numpy
+          mypy survival.pyi --ignore-missing-imports || true
+
+  typos:
+    name: Spell Check
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6
+
+      - name: Check for typos
+        uses: crate-ci/typos@master
+        with:
+          config: .typos.toml
+        continue-on-error: true
+
+  veto:
+    name: Veto
+    runs-on: ubuntu-latest
+    needs: [rust-lint, python-lint, typos]
+    if: always()
+    steps:
+      - name: Check all lint jobs passed
+        run: |
+          if [[ "${{ needs.rust-lint.result }}" != "success" ]] || \
+             [[ "${{ needs.python-lint.result }}" != "success" ]] || \
+             [[ "${{ needs.typos.result }}" != "success" ]]; then
+            echo "One or more lint jobs failed"
+            exit 1
+          fi
+          echo "All lint jobs passed"

survival-1.1.16/.github/workflows/publish.yml

@@ -0,0 +1,234 @@
+name: Publish
+
+on:
+  push:
+    branches: [main]
+  release:
+    types: [published]
+  workflow_dispatch:
+    inputs:
+      target:
+        description: 'Publish target'
+        required: true
+        default: 'testpypi'
+        type: choice
+        options:
+          - testpypi
+          - pypi
+
+permissions:
+  contents: write
+
+env:
+  CARGO_TERM_COLOR: always
+
+jobs:
+  linux-x86:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          ref: ${{ github.event_name == 'push' && 'main' || github.ref }}
+
+      - uses: actions/setup-python@v6
+        with:
+          python-version: '3.14'
+
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          args: --release --out dist
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v6
+        with:
+          name: wheels-linux-x86_64
+          path: dist
+
+  linux-arm:
+    runs-on: ubuntu-24.04-arm
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          ref: ${{ github.event_name == 'push' && 'main' || github.ref }}
+
+      - uses: actions/setup-python@v6
+        with:
+          python-version: '3.14'
+
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          args: --release --out dist
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v6
+        with:
+          name: wheels-linux-aarch64
+          path: dist
+
+  macos:
+    runs-on: macos-14
+    strategy:
+      matrix:
+        target: [x86_64-apple-darwin, aarch64-apple-darwin]
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          ref: ${{ github.event_name == 'push' && 'main' || github.ref }}
+
+      - uses: actions/setup-python@v6
+        with:
+          python-version: '3.14'
+
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v6
+        with:
+          name: wheels-macos-${{ matrix.target }}
+          path: dist
+
+  windows:
+    runs-on: windows-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          ref: ${{ github.event_name == 'push' && 'main' || github.ref }}
+
+      - uses: actions/setup-python@v6
+        with:
+          python-version: '3.14'
+
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: x86_64-pc-windows-msvc
+          args: --release --out dist
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v6
+        with:
+          name: wheels-windows-x64
+          path: dist
+
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          ref: ${{ github.event_name == 'push' && 'main' || github.ref }}
+
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist
+
+      - name: Upload sdist
+        uses: actions/upload-artifact@v6
+        with:
+          name: wheels-sdist
+          path: dist
+
+  publish-testpypi:
+    name: Publish to TestPyPI
+    runs-on: ubuntu-latest
+    if: github.event_name == 'workflow_dispatch' && github.event.inputs.target == 'testpypi'
+    needs: [linux-x86, linux-arm, macos, windows, sdist]
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/project/survival
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v7
+        with:
+          path: dist
+          merge-multiple: true
+
+      - name: Publish to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  publish-pypi:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' || github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && github.event.inputs.target == 'pypi')
+    needs: [linux-x86, linux-arm, macos, windows, sdist]
+    environment:
+      name: pypi
+      url: https://pypi.org/project/survival
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          ref: ${{ github.event_name == 'push' && 'main' || github.ref }}
+
+      - name: Get version from Cargo.toml
+        id: version
+        run: |
+          VERSION=$(grep '^version' Cargo.toml | head -1 | sed 's/.*"\(.*\)".*/\1/')
+          echo "version=$VERSION" >> $GITHUB_OUTPUT
+
+      - name: Check if version exists on PyPI
+        id: check
+        run: |
+          if curl -s "https://pypi.org/pypi/survival/${{ steps.version.outputs.version }}/json" | grep -q '"version"'; then
+            echo "exists=true" >> $GITHUB_OUTPUT
+            echo "Version ${{ steps.version.outputs.version }} already exists on PyPI, skipping publish"
+          else
+            echo "exists=false" >> $GITHUB_OUTPUT
+            echo "Version ${{ steps.version.outputs.version }} not found on PyPI, will publish"
+          fi
+
+      - uses: actions/download-artifact@v7
+        if: steps.check.outputs.exists == 'false'
+        with:
+          path: dist
+          merge-multiple: true
+
+      - name: Publish to PyPI
+        if: steps.check.outputs.exists == 'false'
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
+
+  publish-crates:
+    name: Publish to crates.io
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' || github.event_name == 'release'
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          ref: ${{ github.event_name == 'push' && 'main' || github.ref }}
+
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Get version from Cargo.toml
+        id: version
+        run: |
+          VERSION=$(grep '^version' Cargo.toml | head -1 | sed 's/.*"\(.*\)".*/\1/')
+          echo "version=$VERSION" >> $GITHUB_OUTPUT
+
+      - name: Check if version exists on crates.io
+        id: check
+        run: |
+          if curl -s "https://crates.io/api/v1/crates/survival/${{ steps.version.outputs.version }}" | grep -q '"version"'; then
+            echo "exists=true" >> $GITHUB_OUTPUT
+            echo "Version ${{ steps.version.outputs.version }} already exists on crates.io, skipping publish"
+          else
+            echo "exists=false" >> $GITHUB_OUTPUT
+            echo "Version ${{ steps.version.outputs.version }} not found on crates.io, will publish"
+          fi
+
+      - name: Publish to crates.io
+        if: steps.check.outputs.exists == 'false'
+        run: cargo publish --no-verify --allow-dirty
+        env:
+          CARGO_REGISTRY_TOKEN: ${{ secrets.CARGO_REGISTRY_TOKEN }}

survival-1.1.16/.github/workflows/release.yml

@@ -0,0 +1,45 @@
+name: Release
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+jobs:
+  release:
+    name: Create GitHub Release
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Get version from Cargo.toml
+        id: version
+        run: |
+          VERSION=$(grep '^version' Cargo.toml | head -1 | sed 's/.*"\(.*\)".*/\1/')
+          echo "version=$VERSION" >> $GITHUB_OUTPUT
+          echo "tag=v$VERSION" >> $GITHUB_OUTPUT
+
+      - name: Check if tag exists
+        id: check
+        run: |
+          if git rev-parse "v${{ steps.version.outputs.version }}" >/dev/null 2>&1; then
+            echo "exists=true" >> $GITHUB_OUTPUT
+            echo "Tag v${{ steps.version.outputs.version }} already exists"
+          else
+            echo "exists=false" >> $GITHUB_OUTPUT
+            echo "Tag v${{ steps.version.outputs.version }} does not exist, will create release"
+          fi
+
+      - name: Create GitHub Release
+        if: steps.check.outputs.exists == 'false'
+        run: |
+          gh release create "${{ steps.version.outputs.tag }}" \
+            --title "${{ steps.version.outputs.tag }}" \
+            --generate-notes
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

survival-1.1.16/.github/workflows/rust.yml

@@ -0,0 +1,185 @@
+name: CI
+
+on:
+  pull_request:
+    branches: [main]
+
+env:
+  CARGO_TERM_COLOR: always
+  RUST_BACKTRACE: 1
+
+jobs:
+  build-and-test:
+    name: Build & Test (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.14'
+
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Cache Rust dependencies
+        uses: actions/cache@v5
+        with:
+          path: |
+            ~/.cargo/bin/
+            ~/.cargo/registry/index/
+            ~/.cargo/registry/cache/
+            ~/.cargo/git/db/
+            target/
+          key: ${{ runner.os }}-cargo-py3.14-${{ hashFiles('**/Cargo.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-cargo-py3.14-
+
+      - name: Install maturin and test dependencies
+        run: pip install maturin numpy pandas polars
+
+      - name: Clean old wheels
+        run: rm -rf target/wheels || true
+        shell: bash
+
+      - name: Build with maturin
+        run: maturin build --release --interpreter python --features extension-module
+
+      - name: Run Rust tests
+        if: matrix.os == 'ubuntu-latest'
+        run: cargo test --release
+
+      - name: Install wheel (Unix)
+        if: matrix.os != 'windows-latest'
+        run: pip install target/wheels/survival-*.whl
+
+      - name: Install wheel (Windows)
+        if: matrix.os == 'windows-latest'
+        run: |
+          $wheel = Get-ChildItem -Path target/wheels -Filter "survival-*.whl" | Select-Object -First 1
+          pip install $wheel.FullName
+
+      - name: Run Python tests
+        run: python test/test_all.py
+
+  python-matrix:
+    name: Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.14']
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Cache Rust dependencies
+        uses: actions/cache@v5
+        with:
+          path: |
+            ~/.cargo/bin/
+            ~/.cargo/registry/index/
+            ~/.cargo/registry/cache/
+            ~/.cargo/git/db/
+            target/
+          key: ${{ runner.os }}-cargo-py${{ matrix.python-version }}-${{ hashFiles('**/Cargo.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-cargo-py${{ matrix.python-version }}-
+
+      - name: Install maturin and test dependencies
+        run: pip install maturin numpy pandas polars
+
+      - name: Clean old wheels
+        run: rm -rf target/wheels || true
+
+      - name: Build and install
+        run: |
+          maturin build --release --interpreter python --features extension-module
+          pip install target/wheels/survival-*.whl
+
+      - name: Run Rust tests
+        run: cargo test --release
+
+      - name: Run Python tests
+        run: python test/test_all.py
+
+  r-validation:
+    name: R Survival Package Validation
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6
+
+      - name: Install R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: '4.5.2'
+
+      - name: Install R dependencies
+        run: |
+          install.packages(c("survival", "jsonlite"), repos = "https://cloud.r-project.org")
+        shell: Rscript {0}
+
+      - name: Regenerate expected values
+        run: |
+          cd test
+          Rscript generate_r_expected_values.R
+
+      - name: Check for differences
+        run: |
+          if git diff --exit-code test/r_expected_values.json; then
+            echo "✓ R expected values are up to date"
+          else
+            echo "✗ R expected values have changed!"
+            echo "Please run 'Rscript test/generate_r_expected_values.R' and commit the changes"
+            exit 1
+          fi
+
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.14'
+
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Cache Rust dependencies
+        uses: actions/cache@v5
+        with:
+          path: |
+            ~/.cargo/bin/
+            ~/.cargo/registry/index/
+            ~/.cargo/registry/cache/
+            ~/.cargo/git/db/
+            target/
+          key: ${{ runner.os }}-cargo-docs-${{ hashFiles('**/Cargo.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-cargo-
+
+      - name: Build documentation
+        run: cargo doc --no-deps
+        env:
+          RUSTDOCFLAGS: -D warnings

survival-1.1.16/.github/workflows/security.yml

@@ -0,0 +1,38 @@
+name: Security Audit
+
+on:
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  audit:
+    name: Security Audit
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6
+
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Install cargo-audit
+        run: cargo install cargo-audit
+
+      - name: Run security audit
+        run: cargo audit
+
+  dependency-review:
+    name: Dependency Review
+    runs-on: ubuntu-latest
+    if: github.event_name == 'pull_request'
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6
+
+      - name: Dependency Review
+        uses: actions/dependency-review-action@v4
+        with:
+          fail-on-severity: high

survival-1.1.16/.github/workflows/version-bump.yml

@@ -0,0 +1,43 @@
+name: Version Bump
+
+on:
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: write
+
+jobs:
+  bump-version:
+    name: Bump Version
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          token: ${{ secrets.PAT_TOKEN || secrets.GITHUB_TOKEN }}
+          ref: ${{ github.head_ref }}
+
+      - name: Check and bump version if needed
+        run: |
+          CURRENT=$(grep '^version' Cargo.toml | head -1 | sed 's/.*"\(.*\)".*/\1/')
+          echo "Current version: $CURRENT"
+
+          if curl -s "https://pypi.org/pypi/survival/$CURRENT/json" | grep -q '"version"'; then
+            echo "Version $CURRENT exists on PyPI, bumping patch version"
+
+            IFS='.' read -r major minor patch <<< "$CURRENT"
+            NEW_VERSION="$major.$minor.$((patch + 1))"
+            echo "New version: $NEW_VERSION"
+
+            sed -i "s/^version = \"$CURRENT\"/version = \"$NEW_VERSION\"/" Cargo.toml
+
+            sed -i "s/^version = \"$CURRENT\"/version = \"$NEW_VERSION\"/" pyproject.toml
+
+            git config user.name "github-actions[bot]"
+            git config user.email "github-actions[bot]@users.noreply.github.com"
+            git add Cargo.toml pyproject.toml
+            git commit -m "Bump version to $NEW_VERSION"
+            git push
+          else
+            echo "Version $CURRENT is new, no bump needed"
+          fi

survival-1.1.16/.gitignore

@@ -0,0 +1,25 @@
+# Virtualenv
+.venv/
+venv/
+ENV/
+
+# Test extraction directory
+.test_wheel_extract/
+
+# Python cache
+__pycache__/
+*.pyc
+*.pyo
+*.pyd
+.Python
+
+# Rust build artifacts
+target/
+Cargo.lock
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+*~