macenko-pca 0.1.0__tar.gz

macenko_pca-0.1.0/.editorconfig

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+# EditorConfig — https://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[*.py]
+indent_size = 4
+max_line_length = 88
+
+[*.{yml,yaml}]
+indent_size = 2
+
+[*.{json,jsonc}]
+indent_size = 2
+
+[*.{toml,cfg,ini}]
+indent_size = 4
+
+[*.md]
+trim_trailing_whitespace = false
+
+[*.{sh,bash,zsh}]
+indent_size = 2
+
+[Makefile]
+indent_style = tab
+
+[Dockerfile*]
+indent_size = 4

macenko_pca-0.1.0/.github/dependabot.yml

@@ -0,0 +1,21 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+
+  - package-ecosystem: "docker"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+
+  - package-ecosystem: "cargo"
+    directory: "/"
+    schedule:
+      interval: "weekly"

macenko_pca-0.1.0/.github/workflows/build.yml

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+name: Build Wheels (CI)
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  build-wheels:
+    name: Build wheels — ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-14]
+        # macos-14 = arm64
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install Rust toolchain
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Build wheels (Linux — manylinux)
+        if: runner.os == 'Linux'
+        uses: PyO3/maturin-action@v1
+        with:
+          target: x86_64
+          manylinux: auto
+          args: --release --out dist
+          sccache: "true"
+          before-script-linux: |
+            # Try yum (CentOS-based manylinux) first, then fall back to apt (Debian/Ubuntu).
+            # Install OpenBLAS and OpenSSL development headers + pkg-config so native crates can link.
+            yum install -y openblas-devel openssl-devel pkgconfig || \
+            (apt-get update && apt-get install -y libopenblas-dev libssl-dev pkg-config) || true
+
+      - name: Install macOS system deps
+        if: runner.os == 'macOS'
+        run: brew install openblas pkg-config openssl
+
+      - name: Build wheels (macOS)
+        if: runner.os == 'macOS'
+        uses: PyO3/maturin-action@v1
+        env:
+          # Help pkg-config find Homebrew's openblas and openssl on both Intel and ARM runners
+          PKG_CONFIG_PATH: /opt/homebrew/opt/openblas/lib/pkgconfig:/usr/local/opt/openblas/lib/pkgconfig:/opt/homebrew/opt/openssl/lib/pkgconfig:/usr/local/opt/openssl/lib/pkgconfig
+        with:
+          args: --release --out dist
+          sccache: "true"
+
+      # Windows-specific vcpkg / OpenBLAS install removed — Windows is not supported.
+      # See README for platform support and rationale (we only build and test on Linux/macOS).
+
+      # Windows build step removed — we only build wheels on Linux and macOS.
+
+      - name: Upload wheel artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}
+          path: dist/*.whl
+          if-no-files-found: error
+
+  build-sdist:
+    name: Build sdist
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist
+
+      - name: Upload sdist artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist/*.tar.gz
+          if-no-files-found: error

macenko_pca-0.1.0/.github/workflows/lint.yml

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+name: Lint and Format with Ruff
+
+on:
+  push:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  lint-and-format:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install Ruff
+        run: pip install ruff
+
+      - name: Check formatting with Ruff
+        run: ruff format src tests --check
+
+      - name: Run Ruff linter
+        run: ruff check src tests

macenko_pca-0.1.0/.github/workflows/publish.yml

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+# Publish to PyPI using trusted publishing (OIDC)
+#
+# Triggered when a GitHub Release is created (which should be done after
+# tagging a version, e.g. `git tag v0.2.0 && git push --tags`).
+#
+# Prerequisites — one-time PyPI setup:
+#   1. Go to https://pypi.org/manage/account/publishing/
+#      (or the org-level page for the "lavlab" org).
+#   2. Add a new "pending publisher" with:
+#        • PyPI project name:  macenko-pca
+#        • Owner:              lavlab  (GitHub org)
+#        • Repository:         macenko-pca
+#        • Workflow name:      publish.yml
+#        • Environment name:   pypi
+#   3. (Optional) Repeat for TestPyPI at https://test.pypi.org/manage/account/publishing/
+#      using environment name "testpypi".
+#
+# No API tokens or secrets are needed — GitHub's OIDC identity token is
+# exchanged directly with PyPI via trusted publishing.
+
+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+  # Allow manual dispatch for testing the workflow without creating a release.
+  workflow_dispatch:
+    inputs:
+      target:
+        description: "Publish target"
+        required: true
+        default: "testpypi"
+        type: choice
+        options:
+          - testpypi
+          - pypi
+
+# Only one publish job should run at a time for the same ref.
+concurrency:
+  group: publish-${{ github.ref }}
+  cancel-in-progress: false
+
+jobs:
+  # ---------------------------------------------------------------------------
+  # Build wheels for every platform
+  # ---------------------------------------------------------------------------
+  build-wheels:
+    name: Build wheels — ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: true
+      matrix:
+        os: [ubuntu-latest, macos-14]
+        # macos-14 = arm64
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install Rust toolchain
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Build wheels (Linux — manylinux)
+        if: runner.os == 'Linux'
+        uses: PyO3/maturin-action@v1
+        with:
+          target: x86_64
+          manylinux: auto
+          args: --release --out dist
+          sccache: "true"
+          before-script-linux: |
+            # Try yum (CentOS-based manylinux) first, then fall back to apt (Debian/Ubuntu).
+            # Install OpenBLAS, OpenSSL development headers and pkg-config so native crates can link.
+            yum install -y openblas-devel openssl-devel pkgconfig || \
+            (apt-get update && apt-get install -y libopenblas-dev libssl-dev pkg-config) || true
+
+      - name: Install macOS system deps
+        if: runner.os == 'macOS'
+        run: brew install openblas pkg-config openssl
+
+      - name: Build wheels (macOS)
+        if: runner.os == 'macOS'
+        uses: PyO3/maturin-action@v1
+        env:
+          # Help pkg-config find Homebrew's openblas and openssl on both Intel and ARM runners
+          PKG_CONFIG_PATH: /opt/homebrew/opt/openblas/lib/pkgconfig:/usr/local/opt/openblas/lib/pkgconfig:/opt/homebrew/opt/openssl/lib/pkgconfig:/usr/local/opt/openssl/lib/pkgconfig
+        with:
+          args: --release --out dist
+          sccache: "true"
+
+      - name: Upload wheel artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}
+          path: dist/*.whl
+          if-no-files-found: error
+
+  # ---------------------------------------------------------------------------
+  # Build source distribution
+  # ---------------------------------------------------------------------------
+  build-sdist:
+    name: Build sdist
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist
+
+      - name: Upload sdist artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist/*.tar.gz
+          if-no-files-found: error
+
+  # ---------------------------------------------------------------------------
+  # Publish to PyPI (production) — runs on GitHub Release
+  # ---------------------------------------------------------------------------
+  publish-pypi:
+    name: Publish to PyPI
+    needs: [build-wheels, build-sdist]
+    runs-on: ubuntu-latest
+    # Only publish on release events (not manual dispatch to testpypi)
+    if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && inputs.target == 'pypi')
+    environment:
+      name: pypi
+      url: https://pypi.org/p/macenko-pca
+    permissions:
+      id-token: write # Required for trusted publishing OIDC exchange
+    steps:
+      - name: Download all artifacts
+        uses: actions/download-artifact@v4
+        with:
+          path: dist
+          merge-multiple: true
+
+      - name: List artifacts
+        run: ls -lhR dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          # No password needed — trusted publishing uses the OIDC token.
+          print-hash: true
+
+  # ---------------------------------------------------------------------------
+  # Publish to TestPyPI — manual dispatch only
+  # ---------------------------------------------------------------------------
+  publish-testpypi:
+    name: Publish to TestPyPI
+    needs: [build-wheels, build-sdist]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'workflow_dispatch' && inputs.target == 'testpypi'
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/macenko-pca
+    permissions:
+      id-token: write
+    steps:
+      - name: Download all artifacts
+        uses: actions/download-artifact@v4
+        with:
+          path: dist
+          merge-multiple: true
+
+      - name: List artifacts
+        run: ls -lhR dist/
+
+      - name: Publish to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          print-hash: true

macenko_pca-0.1.0/.github/workflows/pytest.yml

@@ -0,0 +1,86 @@
+name: Run Pytest with Maturin
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  test:
+    name: Test on Python ${{ matrix.python-version }} / ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+
+    env:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Rust toolchain
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Install system dependencies (Linux)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libopenblas-dev pkg-config
+
+      - name: Install system dependencies (macOS)
+        if: runner.os == 'macOS'
+        run: brew install openblas pkg-config
+
+      - name: Create virtualenv
+        run: python -m venv .venv
+
+      - name: Install Python dependencies into virtualenv
+        run: |
+          # Activate the venv and install dependencies into it. Using explicit
+          # `python -m pip` ensures we use the venv's pip regardless of shell.
+          . .venv/bin/activate
+          python -m pip install --upgrade pip
+          python -m pip install maturin pytest pytest-cov coverage
+
+      - name: Build and install extension (inside virtualenv)
+        run: |
+          . .venv/bin/activate
+          # Run maturin via `python -m` so it uses the venv's site-packages entrypoint.
+          python -m maturin develop --release
+
+      - name: Run pytest and generate coverage report (inside virtualenv)
+        run: |
+          . .venv/bin/activate
+          python -m pytest --cov=src --cov-report=term-missing --cov-report=xml tests/
+
+      - name: Upload coverage artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-xml-${{ matrix.os }}-py${{ matrix.python-version }}
+          path: coverage.xml
+
+      - name: Upload coverage report to Codecov
+        if: ${{ env.CODECOV_TOKEN != '' }}
+        uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: true
+          files: coverage.xml
+        env:
+          CODECOV_TOKEN: ${{ env.CODECOV_TOKEN }}
+
+      - name: Skip Codecov upload (no token)
+        if: ${{ env.CODECOV_TOKEN == '' }}
+        run: |
+          echo "CODECOV_TOKEN not found. Skipping Codecov upload."
+          echo ""
+          echo "If you want coverage uploaded to Codecov for protected branches, set a"
+          echo "repository or organization secret named CODECOV_TOKEN with your Codecov token."
+          echo ""
+          echo "Alternatively, you can rely on the uploaded coverage artifact to inspect coverage locally."

macenko_pca-0.1.0/.gitignore

@@ -0,0 +1,84 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Distribution / packaging
+dist/
+build/
+*.egg-info/
+*.egg
+*.whl
+sdist/
+
+# Virtual environments
+.venv/
+venv/
+ENV/
+env/
+
+# Hatch
+.hatch/
+
+# IDE / Editor
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+.project
+.settings/
+
+# OS files
+.DS_Store
+Thumbs.db
+
+# Testing / Coverage
+htmlcov/
+.coverage
+.coverage.*
+coverage.xml
+*.cover
+.pytest_cache/
+.mypy_cache/
+
+# Documentation builds
+site/
+
+# Jupyter Notebooks
+.ipynb_checkpoints/
+
+# Ruff
+.ruff_cache/
+
+# Environment variables
+.env
+.env.*
+!.env.example
+
+# Secrets — never commit these
+*.pem
+*.key
+
+# Logs
+*.log
+
+# Type stubs
+.pytype/
+dmypy.json
+
+# Pre-commit
+.pre-commit-cache/
+
+# Rust / Cargo / Maturin
+target/
+**/*.rs.bk
+Cargo.lock
+*.so
+*.dylib
+*.dll
+*.pyd
+
+# Misc
+*.bak
+*.tmp

macenko_pca-0.1.0/.pre-commit-config.yaml

@@ -0,0 +1,27 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+      - id: check-added-large-files
+      - id: check-merge-conflict
+      - id: debug-statements
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.8
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.10.0
+    hooks:
+      - id: mypy
+        additional_dependencies: [numpy>=1.22]
+        args: [--ignore-missing-imports]