scoring-matrices - npm Package Compare versions

Comparing version 0.2.2 to 0.3.0rc1

.github/workflows/package.yml

+name: Package 
+
+on:
+  push:
+    tags:
+      - v*
+
+jobs:
+
+  wheel-linux-aarch64:
+    name: Build Linux wheels (Aarch64)
+    runs-on: ubuntu-22.04
+    strategy:
+      matrix:
+        python-tag:
+        - cp37-manylinux_aarch64
+        - cp38-manylinux_aarch64
+        - cp39-manylinux_aarch64
+        - cp310-manylinux_aarch64
+        - cp311-manylinux_aarch64
+        - cp312-manylinux_aarch64
+        - pp37-manylinux_aarch64
+        - pp38-manylinux_aarch64
+        - pp39-manylinux_aarch64
+        - pp310-manylinux_aarch64
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+    - name: Set up QEMU
+      id: qemu
+      uses: docker/setup-qemu-action@v2
+      with:
+        platforms: all
+    - name: Build manylinux wheels
+      uses: pypa/cibuildwheel@v2.16.5
+      env:
+        CIBW_ARCHS: aarch64
+        CIBW_BUILD: ${{ matrix.python-tag }}
+        CIBW_BUILD_VERBOSITY: 2
+        CIBW_BEFORE_BUILD: pip install cython
+        CIBW_TEST_COMMAND: python -m unittest scoring_matrices.tests -vv
+        CIBW_TEST_REQUIRES: importlib-resources
+      with:
+        output-dir: dist
+    - uses: actions/upload-artifact@v4
+      with:
+        name: wheels-${{ matrix.python-tag }}
+        path: dist/*
+
+  wheel-linux-x86_64:
+    name: Build Linux wheels (x86-64)
+    runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        python-tag:
+        - cp37-manylinux_x86_64
+        - cp38-manylinux_x86_64
+        - cp39-manylinux_x86_64
+        - cp310-manylinux_x86_64
+        - cp311-manylinux_x86_64
+        - cp312-manylinux_x86_64
+        - pp37-manylinux_x86_64
+        - pp38-manylinux_x86_64
+        - pp39-manylinux_x86_64
+        - pp310-manylinux_x86_64
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+    - uses: actions-rs/toolchain@v1
+      with:
+        toolchain: stable
+        override: true
+    - name: Build manylinux wheels
+      uses: pypa/cibuildwheel@v2.16.5
+      env:
+        CIBW_ARCHS: x86_64
+        CIBW_BUILD: ${{ matrix.python-tag }}
+        CIBW_BEFORE_BUILD: pip install cython
+        CIBW_BUILD_VERBOSITY: 2
+        CIBW_TEST_COMMAND: python -m unittest scoring_matrices.tests -vv
+        CIBW_TEST_REQUIRES: importlib-resources
+      with:
+        output-dir: dist
+    - uses: actions/upload-artifact@v4
+      with:
+        name: wheels-${{ matrix.python-tag }}
+        path: dist/*
+
+  wheel-macos-x86_64:
+    name: Build MacOS wheels (x86-64)
+    runs-on: macOS-12
+    strategy:
+      matrix:
+        python-tag:
+        - cp37-macosx_x86_64
+        - cp38-macosx_x86_64
+        - cp39-macosx_x86_64
+        - cp310-macosx_x86_64
+        - cp311-macosx_x86_64
+        - cp312-macosx_x86_64
+        - pp37-macosx_x86_64
+        - pp38-macosx_x86_64
+        - pp39-macosx_x86_64
+        - pp310-macosx_x86_64
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+    - uses: actions-rs/toolchain@v1
+      with:
+        toolchain: stable
+        override: true
+    - name: Build manylinux wheels
+      uses: pypa/cibuildwheel@v2.16.5
+      env:
+        CIBW_ARCHS: x86_64
+        CIBW_BUILD: ${{ matrix.python-tag }}
+        CIBW_BEFORE_BUILD: pip install cython
+        CIBW_BUILD_VERBOSITY: 2
+        CIBW_TEST_COMMAND: python -m unittest scoring_matrices.tests -vv
+        CIBW_TEST_REQUIRES: importlib-resources
+        CIBW_ENVIRONMENT_MACOS: MACOSX_DEPLOYMENT_TARGET=10.12
+      with:
+        output-dir: dist
+    - uses: actions/upload-artifact@v4
+      with:
+        name: wheels-${{ matrix.python-tag }}
+        path: dist/*
+
+  wheel-macos-aarch64:
+    name: Build MacOS wheels (Aarch64)
+    runs-on: macOS-12
+    strategy:
+      matrix:
+        python-tag:
+        - cp38-macosx_arm64
+        - cp39-macosx_arm64
+        - cp310-macosx_arm64
+        - cp311-macosx_arm64
+        - cp312-macosx_arm64
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+    - uses: actions-rs/toolchain@v1
+      with:
+        toolchain: stable
+        override: true
+        target: aarch64-apple-darwin
+    - name: Build manylinux wheels
+      uses: pypa/cibuildwheel@v2.16.5
+      env:
+        CIBW_ARCHS: arm64
+        CIBW_BUILD: ${{ matrix.python-tag }}
+        CIBW_BEFORE_BUILD: pip install cython
+        CIBW_BUILD_VERBOSITY: 2
+        CIBW_TEST_COMMAND: python -m unittest scoring_matrices.tests -vv
+        CIBW_TEST_REQUIRES: importlib-resources
+      with:
+        output-dir: dist
+    - uses: actions/upload-artifact@v4
+      with:
+        name: wheels-${{ matrix.python-tag }}
+        path: dist/*
+
+  wheel-win32-x86_64:
+    name: Build Windows wheels (x86-64)
+    runs-on: windows-2019
+    strategy:
+      matrix:
+        python-tag:
+        - cp37-win_amd64
+        - cp38-win_amd64
+        - cp39-win_amd64
+        - cp310-win_amd64
+        - cp311-win_amd64
+        - cp312-win_amd64
+        - pp37-win_amd64
+        - pp38-win_amd64
+        - pp39-win_amd64
+        - pp310-win_amd64
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+    - uses: actions-rs/toolchain@v1
+      with:
+        toolchain: stable
+        override: true
+    - name: Build manylinux wheels
+      uses: pypa/cibuildwheel@v2.16.5
+      env:
+        CIBW_ARCHS: AMD64
+        CIBW_BUILD: ${{ matrix.python-tag }}
+        CIBW_BEFORE_BUILD: pip install cython
+        CIBW_BUILD_VERBOSITY: 2
+        CIBW_TEST_COMMAND: python -m unittest scoring_matrices.tests -vv
+        CIBW_TEST_REQUIRES: importlib-resources
+      with:
+        output-dir: dist
+    - uses: actions/upload-artifact@v4
+      with:
+        name: wheels-${{ matrix.python-tag }}
+        path: dist/*
+
+  sdist:
+    runs-on: ubuntu-latest
+    name: Build source distribution
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.11
+    - name: Install build requirements
+      run: python -m pip install -r .github/workflows/requirements.txt
+    - name: Build source distribution
+      run: python -m build -s
+    - name: Store built source distribution
+      uses: actions/upload-artifact@v4
+      with:
+        name: sdist
+        path: dist/*
+
+  test-sdist:
+    runs-on: ubuntu-latest
+    name: Test source distribution
+    needs:
+    - sdist
+    steps:
+    - name: Setup Python 3.11
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.11'
+    - name: Download source distribution
+      uses: actions/download-artifact@v4
+      with:
+        name: sdist
+        path: dist/
+    - name: Update pip to latest version
+      run: python -m pip install -U pip setuptools wheel
+    - name: Install built wheel
+      run: python -m pip install --no-binary scoring-matrices --find-links=dist scoring-matrices
+    - name: Run tests without coverage
+      run: python -m unittest scoring_matrices.tests -vv
+
+  upload:
+    environment: PyPI
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    name: Upload
+    needs:
+    - sdist
+    - test-sdist
+    - wheel-linux-aarch64
+    - wheel-linux-x86_64
+    - wheel-macos-aarch64
+    - wheel-macos-x86_64
+    - wheel-win32-x86_64
+    steps:
+    - name: Download source distribution
+      uses: actions/download-artifact@v4
+      with:
+        name: sdist
+        path: dist/
+        merge-multiple: true
+    - name: Download wheel distributions
+      uses: actions/download-artifact@v4
+      with:
+        pattern: wheels-*
+        path: dist/
+        merge-multiple: true
+    - uses: pypa/gh-action-pypi-publish@release/v1
+      if: startsWith(github.ref, 'refs/tags')
+
+  release:
+    environment: GitHub Releases
+    runs-on: ubuntu-latest
+    if: "!contains(github.ref, 'rc')"
+    name: Release
+    needs: upload
+    permissions: write-all
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+    - uses: rasmus-saks/release-a-changelog-action@v1.2.0
+      with:
+        github-token: '${{ secrets.GITHUB_TOKEN }}'
+
+  aur:
+    environment: Arch User Repository
+    runs-on: ubuntu-latest
+    if: "!contains(github.ref, 'rc')"
+    name: Update AUR package
+    needs:
+    - sdist
+    - upload
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.11'
+    - name: Download built wheels
+      uses: actions/download-artifact@v2
+      with:
+          name: sdist
+          path: dist
+    - name: Extract package version
+      run: echo PKGVER=${{ github.ref }} >> $GITHUB_ENV
+    - name: Compute SHA256 of source distribution
+      run: echo SHA256=$(sha256sum dist/scoring-matrices-${{ env.PKGVER }}.tar.gz | cut -f1 -d' ') >> $GITHUB_ENV
+    - name: Generate PKGBUILD
+      run: sed -e "s/%pkgver/${{ env.PKGVER }}/g" -e "s/%sha256sum/${{ env.SHA256 }}/g" pkg/aur/PKGBUILD.in > pkg/aur/PKGBUILD
+    - name: Update package
+      uses: KSXGitHub/github-actions-deploy-aur@v2.7.2
+      with:
+        pkgname: python-scoring-matrices
+        pkgbuild: pkg/aur/PKGBUILD
+        commit_username: ${{ secrets.AUR_USER }}
+        commit_email: ${{ secrets.AUR_EMAIL }}
+        ssh_private_key: ${{ secrets.AUR_SSH_PRIVATE_KEY }}
+        commit_message: ${{ github.event.head_commit.message }}

.github/workflows/requirements.txt

+coverage ~=7.0
+cython ~=3.0
+importlib-resources ; python_version < '3.7'
+scikit-build-core
+build

.github/workflows/test.yml

+name: Test
+
+on:
+  - push
+  - pull_request
+
+jobs:
+
+  test_linux:
+    name: Test (Linux)
+    runs-on: ubuntu-22.04
+    env:
+      OS: Linux
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - python-version: 3.7
+          python-release: v3.7
+          python-impl: CPython
+        - python-version: 3.8
+          python-release: v3.8
+          python-impl: CPython
+        - python-version: 3.9
+          python-release: v3.9
+          python-impl: CPython
+        - python-version: '3.10'
+          python-release: v3.10
+          python-impl: CPython
+        - python-version: 3.11
+          python-release: v3.11
+          python-impl: CPython
+        - python-version: 3.12
+          python-release: v3.12
+          python-impl: CPython
+        - python-version: pypy-3.7
+          python-release: v3.7
+          python-impl: PyPy
+        - python-version: pypy-3.8
+          python-release: v3.8
+          python-impl: PyPy
+        - python-version: pypy-3.9
+          python-release: v3.9
+          python-impl: PyPy
+        - python-version: pypy-3.10
+          python-release: v3.10
+          python-impl: PyPy
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+      with:
+        submodules: true
+    - name: Setup Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Update pip
+      run: python -m pip install -U pip wheel setuptools
+    - name: Install Python requirements
+      run: python -m pip install -r .github/workflows/requirements.txt
+    - name: Build C extension in debug mode
+      run: python -m pip install -v --no-build-isolation -e .
+    - name: Test with coverage
+      run: python -m coverage run -m unittest scoring_matrices.tests -vv
+    - name: Upload to Codecov
+      if: matrix.python-impl == 'CPython'
+      uses: codecov/codecov-action@v4
+      with:
+        flags: ${{ matrix.python-impl }},${{ matrix.python-release }},${{ env.OS }}
+        name: test-python-${{ matrix.python-version }}
+        fail_ci_if_error: false
+        token: ${{ secrets.CODECOV_TOKEN }}
+
+  test_osx:
+    name: Test (OSX)
+    runs-on: macOS-12
+    env:
+      OS: OSX
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - python-version: 3.7
+          python-release: v3.7
+          python-impl: CPython
+        - python-version: 3.8
+          python-release: v3.8
+          python-impl: CPython
+        - python-version: 3.9
+          python-release: v3.9
+          python-impl: CPython
+        - python-version: '3.10'
+          python-release: v3.10
+          python-impl: CPython
+        - python-version: '3.11'
+          python-release: v3.11
+          python-impl: CPython
+        - python-version: '3.12'
+          python-release: v3.12
+          python-impl: CPython
+        - python-version: pypy-3.7
+          python-release: v3.7
+          python-impl: PyPy
+        - python-version: pypy-3.8
+          python-release: v3.8
+          python-impl: PyPy
+        - python-version: pypy-3.9
+          python-release: v3.9
+          python-impl: PyPy
+        - python-version: pypy-3.10
+          python-release: v3.10
+          python-impl: PyPy
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+      with:
+        submodules: true
+    - name: Setup Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Update pip
+      run: python -m pip install -U pip wheel setuptools
+    - name: Install Python requirements
+      run: python -m pip install -r .github/workflows/requirements.txt
+    - name: Build C extension in debug mode
+      run: python -m pip install -v -e . --no-build-isolation
+    - name: Test with coverage
+      run: python -m coverage run -m unittest scoring_matrices.tests -vv
+    - name: Upload to Codecov
+      if: matrix.python-impl == 'CPython'
+      uses: codecov/codecov-action@v4
+      with:
+        flags: ${{ matrix.python-impl }},${{ matrix.python-release }},${{ env.OS }}
+        name: test-python-${{ matrix.python-version }}
+        fail_ci_if_error: false
+        token: ${{ secrets.CODECOV_TOKEN }}
+
+  test_windows:
+    name: Test (Windows)
+    runs-on: windows-latest
+    env:
+      OS: Windows
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - python-version: 3.7
+          python-release: v3.7
+          python-impl: CPython
+        - python-version: 3.8
+          python-release: v3.8
+          python-impl: CPython
+        - python-version: 3.9
+          python-release: v3.9
+          python-impl: CPython
+        - python-version: '3.10'
+          python-release: v3.10
+          python-impl: CPython
+        - python-version: '3.11'
+          python-release: v3.11
+          python-impl: CPython
+        - python-version: '3.12'
+          python-release: v3.12
+          python-impl: CPython
+        - python-version: pypy-3.7
+          python-release: v3.7
+          python-impl: PyPy
+        - python-version: pypy-3.8
+          python-release: v3.8
+          python-impl: PyPy
+        - python-version: pypy-3.9
+          python-release: v3.9
+          python-impl: PyPy
+        - python-version: pypy-3.10
+          python-release: v3.10
+          python-impl: PyPy
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+      with:
+        submodules: true
+    - name: Setup Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        architecture: x64
+    - name: Update pip
+      run: python -m pip install -U pip wheel setuptools
+    - name: Install Python requirements
+      run: python -m pip install -r .github/workflows/requirements.txt
+    - name: Build C extension
+      run: python -m pip install -v . --no-build-isolation
+    - name: Test without coverage
+      run: python -m unittest scoring_matrices.tests -vv

.gitignore

+
+# Created by https://www.gitignore.io/api/python,c
+# Edit at https://www.gitignore.io/?templates=python,c
+
+### C ###
+# Prerequisites
+*.d
+
+# Object files
+*.o
+*.ko
+*.obj
+*.elf
+
+# Linker output
+*.ilk
+*.map
+*.exp
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Libraries
+*.lib
+*.a
+*.la
+*.lo
+
+# Shared objects (inc. Windows DLLs)
+*.dll
+*.so
+*.so.*
+*.dylib
+
+# Executables
+*.exe
+*.out
+*.app
+*.i*86
+*.x86_64
+*.hex
+
+# Debug files
+*.dSYM/
+*.su
+*.idb
+*.pdb
+
+# Kernel Module Compile Results
+*.mod*
+*.cmd
+.tmp_versions/
+modules.order
+Module.symvers
+Mkfile.old
+dkms.conf
+
+# Valgrind files
+callgrind.out.*
+
+# Memprofile
+mprofile_*.dat
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# End of https://www.gitignore.io/api/python,c

.readthedocs.yaml

+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+# VCS submodules configuration.
+submodules:
+  include: all
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+   install:
+     - requirements: docs/requirements.txt
+     - method: pip
+       path: .

CHANGELOG.md

+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+
+
+## [Unreleased]
+[Unreleased]: https://github.com/althonos/scoring-matrices/compare/v0.3.0...HEAD
+
+
+## [v0.3.0] - 2024-10-20
+[v0.3.0]: https://github.com/althonos/scoring-matrices/compare/v0.2.2...v0.3.0
+
+### Changed
+- Rewrite package build using `scikit-build-core`.
+- Use the PyData theme in documentation.
+
+### Removed
+- Support for Python 3.6.
+
+
+## [v0.2.2] - 2024-06-24
+[v0.2.2]: https://github.com/althonos/scoring-matrices/compare/v0.2.1...v0.2.2
+
+### Fixed
+- Segmentation fault due to out-of-bounds access in `ScoringMatrix.is_symmetric` ([#2](https://github.com/althonos/scoring-matrices/issues/2)).
+
+
+## [v0.2.1] - 2024-06-06
+[v0.2.1]: https://github.com/althonos/scoring-matrices/compare/v0.2.0...v0.2.1
+
+### Fixed
+- Missing type hints of `name` and `alphabet` attributes of `ScoringMatrix` ([#1](https://github.com/althonos/scoring-matrices/pull/1), by [@RayHackett](https://github.com/RayHackett)).
+
+
+## [v0.2.0] - 2024-05-06
+[v0.2.0]: https://github.com/althonos/scoring-matrices/compare/v0.1.1...v0.2.0
+
+### Added
+- `ScoringMatrix.is_symmetric` method to check whether the matrix is symmetric.
+- `ScoringMatrix.from_match_mismatch` and `ScoringMatrix.from_diagonal` constructors.
+
+### Fixed
+- Rounding of constants in generated `matrices.h` header.
+
+
+## [v0.1.1] - 2024-05-03
+[v0.1.1]: https://github.com/althonos/scoring-matrices/compare/v0.1.0...v0.1.1
+
+### Fixed
+- Compilation of Python Limited API wheels.
+
+
+## [v0.1.0] - 2024-05-03
+[v0.1.0]: https://github.com/althonos/scoring-matrices/compare/de079cc0...v0.1.0
+
+Initial release.

CMakeLists.txt

+cmake_minimum_required(VERSION 3.20)
+project(${SKBUILD_PROJECT_NAME} VERSION ${SKBUILD_PROJECT_VERSION} LANGUAGES C)
+
+set(BUILD_SHARED_LIBS OFF)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+# --- Prepare Cython extensions ------------------------------------------------
+
+set_property(GLOBAL PROPERTY PYTHON_EXTENSIONS_SOURCE_DIR ${CMAKE_CURRENT_LIST_DIR}/src)
+include("src/scripts/cmake/CythonExtension.cmake")
+
+# --- Setup include folders ----------------------------------------------------
+
+# set(CYTHON_HEADERS_DIR ${CMAKE_CURRENT_LIST_DIR}/src/scoring_matrices)
+
+# --- Compile source code ------------------------------------------------------
+
+add_subdirectory(data)
+add_subdirectory(src)

CONTRIBUTING.md

+# Contributing to `scoring-matrices`
+
+For bug fixes or new features, please file an issue before submitting a
+pull request. If the change isn't trivial, it may be best to wait for
+feedback.
+
+## Setting up a local repository
+
+You can just clone the GitHub repository to a local folder and start working
+from there:
+
+```console
+$ git clone https://github.com/althonos/scoring-matrices
+```
+
+## Running tests
+
+Tests are written as usual Python unit tests with the `unittest` module of
+the standard library. Running them requires the extension to be built
+locally:
+
+```console
+$ python -m pip install -v -e . --no-build-isolation
+$ python -m unittest scoring_matrices.tests -vv
+```
+
+## Coding guidelines
+
+This project targets Python 3.7 or later.
+
+Python objects should be typed; since it is not supported by Cython,
+you must manually declare types in type stubs (`.pyi` files). In Python
+files, you can add type annotations to function signatures (supported in
+Python 3.5) and in variable assignments (supported only from Python
+3.6 onward). 
+
+### Interfacing with C/C++
+
+When interfacing with C or C++, and in particular with pointers, use
+assertions everywhere you assume the pointer to be non-NULL. Also consider
+using assertions when accessing raw C arrays, if applicable. 

data/CMakeLists.txt

+file(GLOB MATRICES CONFIGURE_DEPENDS "*.mat")
+set(GLOBAL PROPERTY MATRICES ${MATRICES})
+
+add_custom_command(OUTPUT matrices.h
+    COMMAND ${Python_EXECUTABLE} ${PROJECT_SOURCE_DIR}/src/scripts/generate_matrices.py --output matrices.h ${MATRICES}
+    DEPENDS ${MATRICES}
+)
+
+file(CONFIGURE OUTPUT stub.c CONTENT "")
+
+add_library(matrices matrices.h ${CMAKE_CURRENT_BINARY_DIR}/stub.c)
+set_target_properties(matrices PROPERTIES LINKER_LANGUAGE C)
+target_include_directories(matrices INTERFACE ${CMAKE_CURRENT_BINARY_DIR})
+
+# install(FILES ${CMAKE_CURRENT_BINARY_DIR}/matrices.h DESTINATION ${SKBUILD_PLATLIB_DIR}/scoring_matrices)

docs/_static/js/custom-icon.js

+/*******************************************************************************
+ * Set a custom icon for pypi as it's not available in the fa built-in brands
+ */
+FontAwesome.library.add(
+  (faListOldStyle = {
+    prefix: "fa-custom",
+    iconName: "pypi",
+    icon: [
+      17.313, // viewBox width
+      19.807, // viewBox height
+      [], // ligature
+      "e001", // unicode codepoint - private use area
+      "m10.383 0.2-3.239 1.1769 3.1883 1.1614 3.239-1.1798zm-3.4152 1.2411-3.2362 1.1769 3.1855 1.1614 3.2369-1.1769zm6.7177 0.00281-3.2947 1.2009v3.8254l3.2947-1.1988zm-3.4145 1.2439-3.2926 1.1981v3.8254l0.17548-0.064132 3.1171-1.1347zm-6.6564 0.018325v3.8247l3.244 1.1805v-3.8254zm10.191 0.20931v2.3137l3.1777-1.1558zm3.2947 1.2425-3.2947 1.1988v3.8254l3.2947-1.1988zm-8.7058 0.45739c0.00929-1.931e-4 0.018327-2.977e-4 0.027485 0 0.25633 0.00851 0.4263 0.20713 0.42638 0.49826 1.953e-4 0.38532-0.29327 0.80469-0.65542 0.93662-0.36226 0.13215-0.65608-0.073306-0.65613-0.4588-6.28e-5 -0.38556 0.2938-0.80504 0.65613-0.93662 0.068422-0.024919 0.13655-0.038114 0.20156-0.039466zm5.2913 0.78369-3.2947 1.1988v3.8247l3.2947-1.1981zm-10.132 1.239-3.2362 1.1769 3.1883 1.1614 3.2362-1.1769zm6.7177 0.00213-3.2926 1.2016v3.8247l3.2926-1.2009zm-3.4124 1.2439-3.2947 1.1988v3.8254l3.2947-1.1988zm-6.6585 0.016195v3.8275l3.244 1.1805v-3.8254zm16.9 0.21143-3.2947 1.1988v3.8247l3.2947-1.1981zm-3.4145 1.2411-3.2926 1.2016v3.8247l3.2926-1.2009zm-3.4145 1.2411-3.2926 1.2016v3.8247l3.2926-1.2009zm-3.4124 1.2432-3.2947 1.1988v3.8254l3.2947-1.1988zm-6.6585 0.019027v3.8247l3.244 1.1805v-3.8254zm13.485 1.4497-3.2947 1.1988v3.8247l3.2947-1.1981zm-3.4145 1.2411-3.2926 1.2016v3.8247l3.2926-1.2009zm2.4018 0.38127c0.0093-1.83e-4 0.01833-3.16e-4 0.02749 0 0.25633 0.0085 0.4263 0.20713 0.42638 0.49826 1.97e-4 0.38532-0.29327 0.80469-0.65542 0.93662-0.36188 0.1316-0.65525-0.07375-0.65542-0.4588-1.95e-4 -0.38532 0.29328-0.80469 0.65542-0.93662 0.06842-0.02494 0.13655-0.03819 0.20156-0.03947zm-5.8142 0.86403-3.244 1.1805v1.4201l3.244 1.1805z", // svg path (https://simpleicons.org/icons/pypi.svg)
+    ],
+  }),
+);
+
+FontAwesome.library.add(
+  (faListOldStyle = {
+    prefix: "fa-custom",
+    iconName: "sword",
+    icon: [
+      256, // viewBox width
+      256, // viewBox height
+      [], // ligature
+      "e002", // unicode codepoint - private use area
+      "M221.65723,34.34326A8.00246,8.00246,0,0,0,216,32h-.02539l-63.79883.20117A8.00073,8.00073,0,0,0,146.0332,35.106L75.637,120.32275,67.31348,111.999A16.02162,16.02162,0,0,0,44.68555,112L32.001,124.68555A15.99888,15.99888,0,0,0,32,147.31348l20.88672,20.88769L22.94531,198.14258a16.01777,16.01777,0,0,0,.001,22.62695l12.28418,12.28418a16.00007,16.00007,0,0,0,22.62793,0L87.79883,203.1123,108.68652,224.001A16.02251,16.02251,0,0,0,131.31445,224L143.999,211.31445A15.99888,15.99888,0,0,0,144,188.68652l-8.32324-8.32324,85.21679-70.39648a8.00125,8.00125,0,0,0,2.90528-6.14258L224,40.02539A8.001,8.001,0,0,0,221.65723,34.34326Zm-13.84668,65.67822-83.49829,68.97706L111.314,156l54.34327-54.34277a8.00053,8.00053,0,0,0-11.31446-11.31446L100,144.686,87.00195,131.6875,155.97852,48.189l51.99609-.16357Z", // svg path (https://simpleicons.org/icons/pypi.svg)
+    ],
+  }),
+);
+
+FontAwesome.library.add(
+  (faListOldStyle = {
+    prefix: "fa-custom",
+    iconName: "knife",
+    icon: [
+      256, // viewBox width
+      256, // viewBox height
+      [], // ligature
+      "e003", // unicode codepoint - private use area
+      "M231.79883,32.2002a28.05536,28.05536,0,0,0-39.667.06933L18.27441,210.41211a8,8,0,0,0,3.92676,13.38281,155.06019,155.06019,0,0,0,34.957,4.00293c33.4209-.001,66.877-10.86914,98.32813-32.1748,31.74512-21.50391,50.14551-45.79981,50.91406-46.82325a8.00114,8.00114,0,0,0-.74316-10.457L186.919,119.60547l44.97753-47.90332A28.03445,28.03445,0,0,0,231.79883,32.2002ZM189.207,144.52148a225.51045,225.51045,0,0,1-43.10351,38.13184c-34.46973,23.23145-69.999,32.665-105.83887,28.13477l106.29492-108.915,23.30176,23.30175q.208.22852.43847.44434l.082.07617Z", // svg path (https://simpleicons.org/icons/pypi.svg)
+    ],
+  }),
+);

docs/_static/json/switcher.json

+[
+    {
+        "name": "v0.3 (latest)",
+        "version": "0.3.0",
+        "url": "https://pytantan.readthedocs.io/en/v0.3.0/"
+    },
+    {
+        "name": "v0.2",
+        "version": "0.2.2",
+        "url": "https://pytantan.readthedocs.io/en/v0.2.2/"
+    },
+    {
+        "name": "v0.1",
+        "version": "0.1.1",
+        "url": "https://pytantan.readthedocs.io/en/v0.1.1/"
+    }
+]

docs/api/index.rst

+API Reference
+=============
+
+.. currentmodule:: scoring_matrices
+
+.. automodule:: scoring_matrices
+
+Classes
+-------
+
+.. toctree::
+   :hidden:
+
+   ScoringMatrix <scoring_matrix>
+
+
+.. only:: html
+
+    .. autosummary::
+        :nosignatures:
+
+        scoring_matrices.ScoringMatrix

docs/api/scoring_matrix.rst

+``ScoringMatrix``
+=================
+
+.. currentmodule:: scoring_matrices
+
+
+.. autoclass:: ScoringMatrix
+   :members:
+
+   .. c:function:: const float* data_ptr()
+
+      Get a pointer to the scoring matrix as a C-contiguous array.
+
+   .. c:function:: const float** matrix_ptr()
+
+      Get a pointer to the scoring matrix as an array of pointers to matrix rows.
+
+   .. c:function:: const char* alphabet_ptr()
+
+      Get a pointer to the scoring matrix alphabet as a C-string.
+
+   .. c:function:: size_t size()
+
+      Get the size of the scoring matrix.
+
+   .. automethod:: __init__
+
+   .. automethod:: __len__
+
+   .. automethod:: __getitem__
+
+   .. automethod:: __copy__
+
+   .. automethod:: __eq__
+
+   .. automethod:: __reduce_ex__
+   

docs/conf.py

+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Imports -----------------------------------------------------------------
+
+import datetime
+import os
+import re
+import semantic_version
+import shutil
+import sys
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+
+docssrc_dir = os.path.dirname(os.path.abspath(__file__))
+project_dir = os.path.dirname(docssrc_dir)
+
+# When building on ReadTheDocs, we can't provide a local version of the Cython
+# extensions, so we have to install the latest public version, and avoid
+# patching the PYTHONPATH with the local development folder
+if os.getenv("READTHEDOCS", "False") != "True":
+    sys.path.insert(0, project_dir)
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+import scoring_matrices
+
+# extract the project metadata from the module itself
+project = scoring_matrices.__name__
+author = re.match("(.*) <.*>", scoring_matrices.__author__).group(1)
+year = datetime.date.today().year
+copyright = "{}, {}".format("2024" if year == 2024 else "2024-{}".format(year), author)
+
+# extract the semantic version
+semver = semantic_version.Version.coerce(scoring_matrices.__version__)
+version = str(semver.truncate(level="patch"))
+release = str(semver)
+
+# patch the docstring so that we don't show the link to redirect
+# to the docs (we don't want to see it when reading the docs already, duh!)
+doc_lines = scoring_matrices.__doc__.splitlines()
+if "See Also:" in doc_lines:
+    see_also = doc_lines.index("See Also:")
+    scoring_matrices.__doc__ = "\n".join(doc_lines[:see_also])
+
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.todo",
+    "sphinx.ext.extlinks",
+    "sphinx_design",
+    "sphinxcontrib.jquery",
+    "recommonmark",
+    "nbsphinx",
+    "IPython.sphinxext.ipython_console_highlighting",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = [
+    "_build",
+    "Thumbs.db",
+    ".DS_Store",
+    "**.ipynb_checkpoints",
+    "requirements.txt",
+]
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "monokailight"
+
+# The name of the default role for inline references
+default_role = "py:obj"
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "pydata_sphinx_theme"
+
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static/js', '_static/bibtex', '_static/css', '_static/json']
+html_js_files = ["custom-icon.js"]
+html_css_files = ["custom.css"]
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+html_theme_options = {
+    "external_links": [],
+    "show_toc_level": 2,
+    "use_edit_page_button": True,
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/althonos/scoring-matrices",
+            "icon": "fa-brands fa-github",
+        },
+        {
+            "name": "PyPI",
+            "url": "https://pypi.org/project/scoring-matrices",
+            "icon": "fa-custom fa-pypi",
+        },
+    ],
+    "logo": {
+        "text": "PyJess",
+        # "image_light": "_images/logo.png",
+        # "image_dark": "_images/logo.png",
+    },
+    "navbar_start": ["navbar-logo", "version-switcher"],
+    "navbar_align": "left",
+    "footer_start": ["copyright"],
+    "footer_center": ["sphinx-version"],
+    "switcher": {
+        "json_url": "https://scoring-matrices.readthedocs.io/en/latest/_static/switcher.json",
+        "version_match": version,
+    }
+}
+
+html_context = {
+    "github_user": "althonos",
+    "github_repo": "scoring-matrices",
+    "github_version": "main",
+    "doc_path": "docs",
+}
+
+html_favicon = '_images/favicon.ico'
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = project
+
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for imgmath extension -------------------------------------------
+
+imgmath_image_format = "svg"
+
+# -- Options for napoleon extension ------------------------------------------
+
+napoleon_include_init_with_doc = True
+napoleon_include_special_with_doc = True
+napoleon_include_private_with_doc = True
+napoleon_use_admonition_for_examples = True
+napoleon_use_admonition_for_notes = True
+napoleon_use_admonition_for_references = True
+napoleon_use_rtype = False
+
+# -- Options for autodoc extension -------------------------------------------
+
+autoclass_content = "class"
+autodoc_member_order = "bysource"
+autosummary_generate = []
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3/", None),
+}
+
+# -- Options for recommonmark extension --------------------------------------
+
+source_suffix = {
+    ".rst": "restructuredtext",
+    ".txt": "markdown",
+    ".md": "markdown",
+}
+
+# -- Options for nbsphinx extension ------------------------------------------
+
+nbsphinx_execute = "auto"
+nbsphinx_execute_arguments = [
+    "--InlineBackend.figure_formats={'svg', 'pdf'}",
+    "--InlineBackend.rc={'figure.dpi': 96}",
+]
+
+# -- Options for extlinks extension ------------------------------------------
+
+extlinks = {
+    "doi": ("https://doi.org/%s", "doi:%s"),
+    "pmid": ("https://pubmed.ncbi.nlm.nih.gov/%s", "PMID:%s"),
+    "pmc": ("https://www.ncbi.nlm.nih.gov/pmc/articles/PMC%s", "PMC%s"),
+    "isbn": ("https://www.worldcat.org/isbn/%s", "ISBN:%s"),
+    "wiki": ("https://en.wikipedia.org/wiki/%s", "Wikipedia:%s"),
+}

docs/guide/copyright.rst

+Copyright Notice
+================
+
+This library is provided under the MIT license:
+
+.. literalinclude:: ../../COPYING 

docs/guide/index.rst

+User Guide
+==========
+
+This section contains guides and documents about ``scoring-matrices`` usage.
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Getting Started
+
+    Installation <install>
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Resources
+
+   Contribution Guide <contributing>
+   Changelog <changes>
+   Copyright Notice <copyright>

docs/guide/install.rst

+Installation
+============
+
+.. note::
+
+    Wheels are provided for x86-64 Linux, MacOS, and Windows, as well
+    as Aarch64 Linux and MacOS, but other machines will have to build the 
+    wheel from the source distribution. Building ``scoring-matrices`` involves 
+    compiling some Cython code, which requires a C compiler to be available on 
+    the local machine.
+
+
+PyPi
+^^^^
+
+``scoring-matrices`` is hosted on GitHub, but the easiest way to install it is to download
+the latest release from its `PyPi repository <https://pypi.python.org/pypi/scoring-matrices>`_.
+It will install all build dependencies then install ``scoring-matrices`` 
+either from a wheel if one is available, or from source after compiling the 
+Cython code :
+
+.. code:: console
+
+   $ pip install --user scoring-matrices
+
+
+Conda
+^^^^^
+
+`scoring-matrices` is also available as a `recipe <https://anaconda.org/bioconda/scoring-matrices>`_
+in the `bioconda <https://bioconda.github.io/>`_ channel. To install, simply
+use the ``conda`` installer:
+
+.. code:: console
+
+   $ conda install bioconda::scoring-matrices
+
+
+Arch User Repository
+^^^^^^^^^^^^^^^^^^^^
+
+A package recipe for Arch Linux can be found in the Arch User Repository
+under the name `python-scoring-matrices <https://aur.archlinux.org/packages/python-scoring-matrices>`_.
+It will always match the latest release from PyPI.
+
+Steps to install on ArchLinux depend on your `AUR helper <https://wiki.archlinux.org/title/AUR_helpers>`_
+(``yaourt``, ``aura``, ``yay``, etc.). For ``aura``, you'll need to run:
+
+.. code:: console
+
+    $ aura -A python-scoring-matrices
+
+
+Piwheels
+^^^^^^^^
+
+``scoring-matrices`` is compatible with Raspberry Pi computers, and pre-built 
+wheels are compiled for `armv7l` platforms on `piwheels <https://www.piwheels.org>`_. 
+Run the following command to install these instead of compiling from source:
+
+.. code:: console
+
+   $ pip3 install scoring-matrices --extra-index-url https://www.piwheels.org/simple
+
+Check the `piwheels documentation <https://www.piwheels.org/faq.html>`_ for
+more information.
+
+
+GitHub + ``pip``
+^^^^^^^^^^^^^^^^
+
+If, for any reason, you prefer to download the library from GitHub, you can clone
+the repository and install the repository by running (with the admin rights):
+
+.. code:: console
+
+   $ git clone --recursive https://github.com/althonos/scoring-matrices
+   $ pip install --user ./scoring-matrices
+
+.. caution::
+
+    Keep in mind this will install always try to install the latest commit,
+    which may not even build, so consider using a versioned release instead.
+
+

docs/index.rst

+``scoring-matrices`` |Stars|
+============================
+
+.. |Stars| image:: https://img.shields.io/github/stars/althonos/scoring-matrices.svg?style=social&maxAge=3600&label=Star
+   :target: https://github.com/althonos/scoring-matrices/stargazers
+
+*Dependency free, Cython-compatible scoring matrices to use with biological sequences.*
+
+|Actions| |Coverage| |PyPI| |Bioconda| |AUR| |Wheel| |Versions| |Implementations| |License| |Source| |Issues| |Docs| |Changelog| |Downloads|
+
+.. |Actions| image:: https://img.shields.io/github/actions/workflow/status/althonos/scoring-matrices/test.yml?branch=main&logo=github&style=flat-square&maxAge=300
+   :target: https://github.com/althonos/scoring-matrices/actions
+
+.. |Coverage| image:: https://img.shields.io/codecov/c/gh/althonos/scoring-matrices?style=flat-square&maxAge=600
+   :target: https://codecov.io/gh/althonos/scoring-matrices/
+
+.. |PyPI| image:: https://img.shields.io/pypi/v/scoring-matrices.svg?style=flat-square&maxAge=3600
+   :target: https://pypi.python.org/pypi/scoring-matrices
+
+.. |Bioconda| image:: https://img.shields.io/conda/vn/bioconda/scoring-matrices?style=flat-square&maxAge=3600
+   :target: https://anaconda.org/bioconda/scoring-matrices
+
+.. |AUR| image:: https://img.shields.io/aur/version/python-scoring-matrices?logo=archlinux&style=flat-square&maxAge=3600
+   :target: https://aur.archlinux.org/packages/python-scoring-matrices
+
+.. |Wheel| image:: https://img.shields.io/pypi/wheel/scoring-matrices?style=flat-square&maxAge=3600
+   :target: https://pypi.org/project/scoring-matrices/#files
+
+.. |Versions| image:: https://img.shields.io/pypi/pyversions/scoring-matrices.svg?style=flat-square&maxAge=3600
+   :target: https://pypi.org/project/scoring-matrices/#files
+
+.. |Implementations| image:: https://img.shields.io/pypi/implementation/scoring-matrices.svg?style=flat-square&maxAge=3600&label=impl
+   :target: https://pypi.org/project/scoring-matrices/#files
+
+.. |License| image:: https://img.shields.io/badge/license-MIT-blue.svg?style=flat-square&maxAge=3600
+   :target: https://choosealicense.com/licenses/mit/
+
+.. |Source| image:: https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400&style=flat-square
+   :target: https://github.com/althonos/scoring-matrices/
+
+.. |Issues| image:: https://img.shields.io/github/issues/althonos/scoring-matrices.svg?style=flat-square&maxAge=600
+   :target: https://github.com/althonos/scoring-matrices/issues
+
+.. |Docs| image:: https://img.shields.io/readthedocs/scoring-matrices?style=flat-square&maxAge=3600
+   :target: http://scoring-matrices.readthedocs.io/en/stable/?badge=stable
+
+.. |Changelog| image:: https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square
+   :target: https://github.com/althonos/scoring-matrices/blob/main/CHANGELOG.md
+
+.. |Downloads| image:: https://img.shields.io/pypi/dm/scoring-matrices?style=flat-square&color=303f9f&maxAge=86400&label=downloads
+   :target: https://pepy.tech/project/scoring-matrices
+
+
+.. currentmodule:: scoring_matrices
+
+
+Overview
+--------
+
+*Scoring Matrices* are matrices used to score the matches and mismatches between
+two characters are the same position in a sequence alignment. Some of these
+matrices are derived from *substitution matrices*, which uses evolutionary 
+modeling.
+
+The ``scoring-matrices`` package is a dependency-free, batteries included 
+Cython library to handle and distribute common substitution matrices:
+
+.. grid:: 1 2 3 3
+   :gutter: 1
+
+   .. grid-item-card:: :fas:`box` Self-contained
+
+      The matrices are distributed as-is: you don't need the whole 
+      `Biopython <https://biopython.org>`_ ecosystem, or even 
+      `NumPy <https://numpy.org/>`_.
+   
+   .. grid-item-card:: :fas:`gears` Cython Support
+
+      The `ScoringMatrix` class is a Cython class that can be
+      inherited, and the matrix data can be accessed as either a raw pointer, or
+      a `typed memoryview <https://cython.readthedocs.io/en/latest/src/userguide/memoryviews.html>`_.
+
+   .. grid-item-card:: :fas:`battery-full` Batteries-included
+
+      The package distributes most common matrices, such as those used by 
+      the NCBI BLAST+ suite, including: *PAM*, *BLOSUM*, *VTML*, *BENNER*,
+      etc.
+
+   .. grid-item-card:: :fas:`file-import` I/O Support
+
+      Easily load a `ScoringMatrix` from a file, a file-like object, or by
+      name for common matrices.
+
+   .. grid-item-card:: :fas:`screwdriver-wrench` Configurable
+
+      Easily build your own scoring matrices using the Python interface,
+      including various shortcut constructors to create a `ScoringMatrix`
+      from a diagonal or a pair of match/mismatch scores.
+
+   .. grid-item-card:: :fas:`stamp` Versioned
+
+      This library follows semantic versioning to guarantee compatibility 
+      between patch versions, allowing for a safe API and ABI that can be
+      reused without recompiling on each install. 
+
+
+Setup
+-----
+
+``scoring-matrices`` is available for all modern Python versions (3.7+).
+
+Run ``pip install scoring-matrices`` in a shell to download the latest release 
+from PyPi, or have a look at the :doc:`Installation page <guide/install>` to find 
+other ways to install the package.
+
+
+Library
+-------
+
+.. toctree::
+   :maxdepth: 2
+
+   User Guide <guide/index>
+   API Reference <api/index>
+
+
+Related Projects
+----------------
+
+The following Python libraries may be of interest for bioinformaticians.
+
+.. grid:: 1 3 5 5
+   :gutter: 1
+
+   .. grid-item-card:: :fas:`diamond` PyHMMER
+      :link: https://pyhmmer.readthedocs.io
+
+      Profile Hidden Markov Models (with HMMER).
+
+   .. grid-item-card:: :fas:`fire` Pyrodigal
+      :link: https://pyrodigal.readthedocs.io
+
+      Prokaryotic Gene Finding (with Prodigal).
+
+   .. grid-item-card:: :fas:`virus-covid` Pyrodigal-gv
+      :link: https://github.com/althonos/pyrodigal-gv
+
+      Pyrodigal for Giant Viruses.
+
+   .. grid-item-card:: :fas:`align-center` PyFAMSA
+      :link: https://pyfamsa.readthedocs.io
+
+      Multiple Sequence Alignment (with FAMSA).
+
+   .. grid-item-card:: :fas:`scissors` PytrimAl
+      :link: https://pytrimal.readthedocs.io
+
+      Alignment Trimming (with trimAl).
+
+   .. grid-item-card:: :fas:`music` LightMotif
+      :link: https://lightmotif.readthedocs.io
+
+      Platform-accelerated motif scoring.
+
+   .. grid-item-card:: :fas:`knife;fa-custom` Diced
+      :link: https://diced.readthedocs.io
+
+      CRISPR Detection (with MinCED).
+
+   .. grid-item-card:: :fas:`table-cells` Scoring Matrices
+      :link: https://scoring-matrices.readthedocs.io
+
+      Scoring matrices for Cython.
+
+   .. grid-item-card:: :fas:`chain` Pyskani
+      :link: https://pyskani.readthedocs.io
+
+      Average Nucleotide Identity (with skani).
+
+   .. grid-item-card:: :fas:`forward-fast` PyFastANI
+      :link: https://pyfastani.readthedocs.io
+
+      Average Nucleotide Identity (with FastANI).
+
+   .. grid-item-card:: :fas:`magnifying-glass` PyJess
+      :link: https://pyjess.readthedocs.io
+
+      Geometric Template Matching (with Jess).
+
+   .. grid-item-card:: :fas:`repeat` PyTantan
+      :link: https://pytantan.readthedocs.io
+
+      Tandem Repeat Masking (with Tantan).
+
+   .. grid-item-card:: :fas:`gem` PyOpal
+      :link: https://pyopal.readthedocs.io
+
+      Query/Database Aligner (with Opal).
+
+   .. grid-item-card:: :fas:`sword;fa-custom` PySWRD
+      :link: https://pyswrd.readthedocs.io
+
+      Database Heuristic Filtering (with SWORD).
+
+   .. grid-item-card:: :fas:`rocket` Mini3di
+      :link: https://github.com/althonos/mini3di
+
+      Protein structure to 3di in pure Python.
+
+   .. grid-item-card:: :fas:`calculator` ``peptides.py``
+      :link: https://peptides.readthedocs.io
+
+      Peptide descriptors for Python.
+
+   .. grid-item-card:: :fas:`diagram-project` Pronto
+      :link: https://pronto.readthedocs.io
+
+      Open Biomedical Ontologies for Python.
+
+   .. grid-item-card:: :fas:`box` NAFcodec
+      :link: https://nafcodec.readthedocs.io
+
+      Nucleotide Archival Format for Python.
+
+   .. grid-item-card:: :fas:`bank` ``gb-io.py``
+      :link: https://gb-io.readthedocs.io
+
+      Fast GenBank parser for Python (with ``gb-io``).
+
+
+License
+-------
+
+This library is provided under the `MIT License <https://choosealicense.com/licenses/mit/>`_.
+Matrices were collected from the `MMseqs2 <https://github.com/soedinglab/MMseqs2>`_,
+`Biopython <https://github.com/biopython/biopython/tree/master/Bio/Align/substitution_matrices/data>`_
+and `NCBI BLAST+ <https://ftp.ncbi.nih.gov/blast/matrices/>`_ sources and are believed to
+be in the public domain.
+
+*This project was developed by* `Martin Larralde <https://github.com/althonos/>`_
+*during his PhD project at the* `Leiden University Medical Center <https://www.lumc.nl/en/>`_
+*in the* `Zeller team <https://github.com/zellerlab>`_.

docs/make.bat

+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/requirements.txt

+# build dependencies
+setuptools >=46.4
+cython ~=3.0
+
+# sphinx documentation dependencies
+semantic_version ~=2.8
+sphinx >=5.0
+recommonmark ~=0.7
+pygments-style-monokailight ~=0.4
+ipython ~=7.19
+pygments ~=2.4
+nbsphinx ~=0.8
+sphinxcontrib-jquery ~=4.1
+sphinx-design
+pydata-sphinx-theme

pkg/aur/PKGBUILD.in

+# Maintainer: Martin Larralde <[e-mail]>
+
+_name=scoring-matrices
+_module=${_name/-/_}
+pkgname=python-${_name}
+pkgver=%pkgver
+pkgrel=1
+pkgdesc="Dependency free, Cython-compatible scoring matrices to use with biological sequences."
+arch=('i686' 'pentium4' 'x86_64' 'arm' 'armv6h' 'armv7h' 'aarch64')
+url="https://github.com/althonos/scoring-matrices"
+license=("MIT")
+depends=('python')
+makedepends=('cython' 'python-build' 'python-installer' 'cmake' 'ninja' 'python-scikit-build-core')
+source=("https://files.pythonhosted.org/packages/source/${_name::1}/$_name/$_name-$pkgver.tar.gz")
+sha256sums=(%sha256sum)
+
+build() {
+    cd "${srcdir}/${_name}-${pkgver}"
+    python -m build --wheel --no-isolation --skip-dependency-check
+}
+
+check() {
+    local abitag=$(python -c 'import sys; print(*sys.version_info[:2], sep="")')
+    local machine=$(python -c 'import platform; print(platform.machine())')
+    whl="${srcdir}/${_name}-${pkgver}/dist/${_module}-${pkgver}-cp${abitag}-cp${abitag}-linux_${machine}.whl"
+
+    python -m venv --symlinks --system-site-packages "${srcdir}/env"
+    source "${srcdir}/env/bin/activate"
+    python -m installer "$whl"
+
+    python -m unittest ${_module}.tests
+}
+
+package() {
+    local abitag=$(python -c 'import sys; print(*sys.version_info[:2], sep="")')
+    local machine=$(python -c 'import platform; print(platform.machine())')
+    whl="${srcdir}/${_name}-${pkgver}/dist/${_module}-${pkgver}-cp${abitag}-cp${abitag}-linux_${machine}.whl"
+
+    python -m installer --prefix="${pkgdir}/usr" "$whl"
+    install -Dm644  ${srcdir}/${_name}-${pkgver}/COPYING "$pkgdir/usr/share/licenses/$pkgname/COPYING"
+}

src/CMakeLists.txt

+add_subdirectory(scoring_matrices)

src/scoring_matrices/__init__.pxd

+from .lib cimport ScoringMatrix

src/scoring_matrices/__init__.py

+from ._version import __version__
+
+__author__ = "Martin Larralde <[e-mail]>"
+__license__ = "MIT"
+
+from . import lib
+from .lib import ScoringMatrix
+
+__doc__ = lib.__doc__

src/scoring_matrices/_version.py

+__version__ = "0.3.0rc1"

src/scoring_matrices/.gitignore

+lib.c
+lib.html
+matrices.h

src/scoring_matrices/CMakeLists.txt

+cython_extension(lib LINKS matrices)

src/scoring_matrices/lib.pxd

+# distutils: language = c
+# cython: language_level=3, linetrace=True, binding=True
+
+cdef class ScoringMatrix:
+    cdef readonly str name
+    cdef readonly str alphabet
+
+    cdef size_t        _size
+    cdef size_t        _nitems
+    cdef Py_ssize_t[2] _shape
+
+    cdef float*  _data
+    cdef float** _matrix
+    cdef char*   _alphabet
+
+    cdef int _allocate(self, size_t length) except 1 nogil
+
+    cdef const float* data_ptr(self) except NULL nogil
+    cdef const float** matrix_ptr(self) except NULL nogil    
+    cdef const char* alphabet_ptr(self) except NULL nogil
+    cdef size_t size(self) noexcept nogil
+
+    cpdef bint is_integer(self)
+    cpdef bint is_symmetric(self)
+    cpdef float min(self)
+    cpdef float max(self)
+    cpdef ScoringMatrix copy(self)
+    cpdef ScoringMatrix shuffle(self, str alphabet)

src/scoring_matrices/lib.pyi

+import typing
+from typing import ClassVar, List, Optional, Sequence, TextIO, Tuple, Type, TypeVar
+
+S = TypeVar("S")
+
+class ScoringMatrix:
+    DEFAULT_ALPHABET: ClassVar[str]
+    @classmethod
+    def from_name(cls: Type[S], name: str = "BLOSUM62") -> S: ...
+    @classmethod
+    def from_file(cls: Type[S], file: TextIO, name: Optional[str] = None) -> S: ...
+    @classmethod
+    def from_str(cls: Type[S], text: str, name: Optional[str] = None) -> S: ...
+    @classmethod
+    def from_diagonal(
+        cls: Type[S],
+        diagonal: Iterable[float],
+        mismatch_score: float = 0.0,
+        alphabet: str = DEFAULT_ALPHABET,
+        name: Optional[str] = None,
+    ) -> S: ...
+    @classmethod
+    def from_match_mismatch(
+        cls: Type[S],
+        match_score: float = 1.0,
+        mismatch_score: float = -0.0,
+        alphabet: str = DEFAULT_ALPHABET,
+        name: Optional[str] = None,
+    ) -> S: ...
+    def __init__(
+        self,
+        matrix: Sequence[Sequence[float]],
+        alphabet: str = DEFAULT_ALPHABET,
+        name: Optional[str] = None,
+    ): ...
+    def __copy__(self: S) -> S: ...
+    def __repr__(self) -> str: ...
+    def __reduce_ex__(self, protocol: object) -> Tuple[object, ...]: ...
+    def __len__(self) -> int: ...
+    def __eq__(self, other: object) -> bool: ...
+    @property
+    def alphabet(self) -> str: ...
+    @property
+    def name(self) -> Optional[str]: ...
+    @typing.overload
+    def __getitem__(self, item: int) -> List[float]: ...
+    @typing.overload
+    def __getitem__(self, item: str) -> List[float]: ...
+    @typing.overload
+    def __getitem__(self, item: Tuple[int, int]) -> float: ...
+    @typing.overload
+    def __getitem__(self, item: Tuple[str, str]) -> float: ...
+    def copy(self: S) -> S: ...
+    def is_integer(self) -> bool: ...
+    def is_symmetric(self) -> bool: ...
+    def min(self) -> float: ...
+    def max(self) -> float: ...
+    def shuffle(self: S, alphabet: str) -> S: ...

src/scoring_matrices/lib.pyx

+# distutils: language = c
+# cython: language_level=3, linetrace=True, binding=True
+"""Dependency free, Cython-compatible scoring matrices for bioinformatics.
+"""
+
+cimport cython
+from cpython.buffer cimport PyBUF_FORMAT, PyBUF_READ, PyBUF_WRITE
+from cpython.memoryview cimport PyMemoryView_FromMemory
+
+from libc.math cimport INFINITY, lrintf
+from libc.stdlib cimport free, realloc
+from libc.string cimport memcpy, memset
+
+from .matrices cimport _ALPHABETS, _MATRICES, _NAMES, _SIZES
+
+import io
+import pickle
+
+
+cdef dict _INDICES = {
+    _NAMES[i].decode('ascii'):i
+    for i in range(sizeof(_NAMES) /sizeof(const char*) - 1)
+}
+
+cdef class ScoringMatrix:
+    """A scoring matrix to use for biological sequence alignments.
+    """
+
+    DEFAULT_ALPHABET = "ARNDCQEGHILKMFPSTWYVBZX*"
+    BUILTIN_MATRICES = frozenset(_INDICES)
+
+    # --- Constructors ---------------------------------------------------------
+
+    @classmethod
+    def from_name(cls, str name not None = "BLOSUM62"):
+        """Load a built-in scoring matrix by name.
+
+        Arguments:
+            name (`str`): The name of the scoring matrix.
+
+        Example:
+            >>> blosum62 = ScoringMatrix.from_name("BLOSUM62")
+
+        Raises:
+            `ValueError`: When no scoring matrix with the given ``name``
+                can be found in the embedded matrix data.
+
+        """
+        cdef size_t i
+        cdef size_t j
+        cdef size_t k
+        cdef list   rows
+
+        try:
+            i = _INDICES[name]
+        except KeyError as err:
+            raise ValueError(f"Unknown scoring matrix: {name!r}") from err
+        else:
+            alphabet = _ALPHABETS[i].decode('ascii')
+
+        rows = []
+        for j in range(0, _SIZES[i] * _SIZES[i], _SIZES[i]):
+            row = []
+            for k in range(_SIZES[i]):
+                row.append(_MATRICES[i][j + k])
+            rows.append(row)
+
+        return cls(rows, alphabet=alphabet, name=name)
+
+    @classmethod
+    def from_file(cls, object file, str name = None):
+        """Load a scoring matrix from a file-like object.
+        """
+        # ignore lines with comments
+        lines = filter(lambda line: not line.startswith("#"), file)
+
+        # get the header line with the alphabet
+        header = next(lines, None)
+        if header is None:
+            raise ValueError("Missing expected header line")
+        alphabet = ''.join(header.split())
+
+        # get the numerical matrix
+        matrix = []
+        for i, line in enumerate(lines):
+            row = line.split()
+            try:
+                float(row[0])
+            except ValueError:
+                if row[0] != alphabet[i]:
+                    raise ValueError(f"Matrix must be symmetric (expected row {alphabet[i]!r}, got {row[0]!r})") from None
+                row = row[1:]
+            matrix.append(list(map(float, row)))
+
+        # create the object with default constructor
+        return cls(matrix, alphabet=alphabet, name=name)
+
+    @classmethod
+    def from_str(cls, str text, str name = None):
+        """Load a scoring matrix from a string.
+        """
+        return cls.from_file(io.StringIO(text))
+
+    @classmethod
+    def from_diagonal(
+        cls, 
+        object diagonal, 
+        float mismatch_score=0.0, 
+        str alphabet not None = DEFAULT_ALPHABET, 
+        str name = None
+    ):
+        """Create a scoring matrix from a diagonal vector.
+
+        Arguments:
+            diagonal (sequence of `float`): The diagonal of the scoring
+                matrix, used to score character matches.
+            mismatch_score (`float`): The mismatch score to use for 
+                every mismatches.
+            alphabet (`str`): The alphabet to use with the scoring matrix.
+            name (`str` or `None`): A name for the scoring matrix, if any.
+
+        Example:
+            >>> matrix = ScoringMatrix.from_diagonal(
+            ...     diagonal=[2, 2, 3, 3],
+            ...     mismatch_score=-3.0,
+            ...     alphabet="ATGC",
+            ... )
+            >>> for row in matrix:
+            ...     print(row)
+            [2.0, -3.0, -3.0, -3.0]
+            [-3.0, 2.0, -3.0, -3.0]
+            [-3.0, -3.0, 3.0, -3.0]
+            [-3.0, -3.0, -3.0, 3.0]
+
+        .. versionadded:: 0.2.0
+
+        """
+        cdef list   matrix = []
+        cdef size_t length = len(alphabet)
+
+        for i, x in enumerate(diagonal):
+            row = [ x if j == i else mismatch_score for j in range(length) ]
+            matrix.append(row)
+        return cls(matrix, alphabet=alphabet, name=name)
+
+    @classmethod
+    def from_match_mismatch(
+        cls,
+        float match_score = 1.0, 
+        float mismatch_score = -1.0,
+        str alphabet not None = DEFAULT_ALPHABET,
+        str name = None,
+    ):
+        """Create a scoring matrix from two match/mismatch scores.
+
+        .. versionadded:: 0.2.0
+
+        """
+        cdef list   matrix = []
+        cdef size_t length = len(alphabet)
+
+        for i in range(length):
+            row = [ match_score if j == i else mismatch_score for j in range(length) ]
+            matrix.append(row)
+        return cls(matrix, alphabet=alphabet, name=name)
+
+    # --- Magic methods --------------------------------------------------------
+
+    def __cinit__(self):
+        self._data = NULL
+        self._matrix = NULL
+        self._size = 0
+        self._shape[0] = self._shape[1] = 0
+
+    def __init__(
+        self,
+        object matrix not None,
+        str alphabet not None = DEFAULT_ALPHABET,
+        str name = None,
+    ):
+        """__init__(self, matrix, alphabet="ARNDCQEGHILKMFPSTWYVBZX", name=None)\n--\n
+        
+        Create a new scoring matrix.
+
+        Arguments:
+            matrix (array-like of `float`): A square matrix with dimensions
+                equal to the ``alphabet`` length, storing the scores for each
+                pair of characters.
+            alphabet (`str`): The alphabet used to index the rows and columns
+                of the scoring matrix.
+            name (`str` or `None`): The name of the scoring matrix, if any.
+
+        Example:
+            >>> matrix = ScoringMatrix(
+            ...     [[91, -114,  -31, -123],
+            ...      [-114, 100, -125, -31],
+            ...      [-31, -125,  100, -114],
+            ...      [-123, -31, -114,  91]],
+            ...     alphabet="ACGT",
+            ...     name="HOXD70",
+            ... )
+
+        Raises:
+            `ValueError`: When the matrix is not a valid matrix or does not
+                match the given alphabet.
+            `MemoryError`: When memory for storing the scores could not be
+                allocated successfully.
+
+        """
+        cdef ssize_t i
+        cdef ssize_t j
+        cdef float   x
+        cdef size_t  size = len(alphabet)
+
+        if len(alphabet) != len(set(alphabet)):
+            raise ValueError(f"Duplicate letters found in alphabet: {self.alphabet!r}")
+        if len(matrix) != size:
+            raise ValueError("Matrix must contain one row per alphabet letter")
+
+        self.alphabet = alphabet
+        self.name = name
+
+        with nogil:
+            self._allocate(size)
+
+        for i, c in enumerate(self.alphabet):
+            self._alphabet[i] = ord(c)
+        for i, row in enumerate(matrix):
+            if len(row) != size:
+                raise ValueError("Matrix must contain one column per alphabet letter")
+            for j, x in enumerate(row):
+                self._matrix[i][j] = x
+
+    def __copy__(self):
+        return self.copy()
+
+    def __repr__(self):
+        cdef str ty    = type(self).__name__
+        cdef list args = [repr(list(self))]
+
+        if self.alphabet != ScoringMatrix.DEFAULT_ALPHABET:
+            args.append(f"alphabet={self.alphabet!r}")
+        if self.name is not None:
+            args.append(f"name={self.name!r}")
+        return f"{ty}({', '.join(args)})"
+
+    def __reduce_ex__(self, int protocol):
+        assert self._data != NULL
+        assert self._matrix != NULL
+
+        # use out-of-band pickling (only supported since protocol 5, see
+        # https://docs.python.org/3/library/pickle.html#out-of-band-buffers)
+        if protocol >= 5:
+            matrix = pickle.PickleBuffer(self)
+        else:
+            matrix = list(self)
+        return (type(self), (matrix, self.alphabet, self.name))
+
+    def __getbuffer__(self, Py_buffer* buffer, int flags):
+        assert self._data != NULL
+
+        if flags & PyBUF_FORMAT:
+            buffer.format = b"f"
+        else:
+            buffer.format = NULL
+        buffer.buf = self._data
+        buffer.internal = NULL
+        buffer.itemsize = sizeof(float)
+        buffer.len = self._nitems * sizeof(float)
+        buffer.ndim = 2
+        buffer.obj = self
+        buffer.readonly = 1
+        buffer.shape = <Py_ssize_t*> &self._shape
+        buffer.suboffsets = NULL
+        buffer.strides = NULL
+
+    def __len__(self):
+        return self._size
+
+    def __getitem__(self, object item):
+        cdef ssize_t index_
+        cdef list    row
+
+        if isinstance(item, str) and len(item) == 1:
+            try:
+                item = self.alphabet.index(item)
+            except ValueError:
+                raise IndexError(f"{item!r} not in matrix alphabet ({self.alphabet!r})") from None
+
+        if isinstance(item, int):
+            index_ = item
+            if index_ < 0:
+                index_ += self._size
+            if index_ < 0 or index_ >= self._size:
+                raise IndexError(item)
+            row = []
+            for i in range(self._size):
+                row.append(self._matrix[index_][i])
+            return row
+
+        elif isinstance(item, tuple):
+            if len(item) > 2:
+                raise IndexError(f"too many indices for array: array is 2-dimensional, but {len(item)!r} were indexed")
+            i, j = item
+            if isinstance(i, str) and len(i) == 1:
+                try:
+                    i = self.alphabet.index(i)
+                except ValueError:
+                    raise IndexError(f"{i!r} not in matrix alphabet ({self.alphabet!r})") from None
+            if isinstance(j, str) and len(j) == 1:
+                try:
+                    j = self.alphabet.index(j)
+                except ValueError:
+                    raise IndexError(f"{j!r} not in matrix alphabet ({self.alphabet!r})") from None
+            if isinstance(i, int) and isinstance(j, int):
+                return self._matrix[i][j]
+
+        raise TypeError(item)
+
+    def __eq__(self, object other):
+        assert self._data != NULL
+        assert self._matrix != NULL
+
+        cdef size_t        i
+        cdef ScoringMatrix other_
+
+        if not isinstance(other, ScoringMatrix):
+            return NotImplemented
+        other_ = other
+        if other_.alphabet != self.alphabet:
+            return False
+        for i in range(self._nitems):
+            if self._data[i] != other_._data[i]:
+                return False
+        return True
+
+    # --- Private methods ------------------------------------------------------
+    
+    cdef int _allocate(self, size_t size) except 1 nogil:
+        cdef size_t i
+
+        self._data = <float*> realloc(self._data, sizeof(float) * size * size)
+        self._matrix = <float**> realloc(self._matrix, sizeof(float*) * size)
+        self._alphabet = <char*> realloc(self._alphabet, sizeof(char) * (size + 1))
+        if self._data is NULL or self._matrix is NULL or self._alphabet is NULL:
+            raise MemoryError("Failed to allocate matrix")
+
+        self._size = self._shape[0] = self._shape[1] = size
+        self._nitems = self._size * self._size
+        for i in range(size):
+            self._matrix[i] = &self._data[i * self._size]
+        memset(self._alphabet, 0, sizeof(char) * (size + 1))
+
+        return 0
+
+    # --- Public methods -------------------------------------------------------
+
+    cdef size_t size(self) noexcept nogil:
+        """Get the size of the scoring matrix.
+        """
+        return self._size
+
+    cdef const char* alphabet_ptr(self) except NULL nogil:
+        """Get the alphabet of the scoring matrix as a C-string.
+        """
+        if self._alphabet == NULL:
+            with gil:
+                raise RuntimeError("uninitialized scoring matrix")
+        return <const char*> self._alphabet
+
+    cdef const float* data_ptr(self) except NULL nogil:
+        """Get the matrix scores as a dense array.
+        """
+        if self._data == NULL:
+            with gil:
+                raise RuntimeError("uninitialized scoring matrix")
+        return <const float*> self._data
+
+    cdef const float** matrix_ptr(self) except NULL nogil:
+        """Get the matrix scores as an array of pointers.
+        """
+        if self._matrix == NULL:
+            with gil:
+                raise RuntimeError("uninitialized scoring matrix")
+        return <const float**> self._matrix
+
+    cpdef ScoringMatrix copy(self):
+        """Get a copy of the matrix.
+        """
+        return type(self)(self, alphabet=self.alphabet, name=self.name)
+
+    cpdef bint is_integer(self):
+        """Test whether the scoring matrix is an integer matrix.
+
+        Returns:
+            `bool`: `True` if the matrix only contains integer scores.
+
+        Example:
+            >>> blosum62 = ScoringMatrix.from_name("BLOSUM62")
+            >>> blosum62.is_integer()
+            True
+            >>> benner6 = ScoringMatrix.from_name("BENNER6")
+            >>> benner6.is_integer()
+            False
+
+        """
+        cdef size_t       i
+        cdef float        x
+        cdef bint         integer = True
+        cdef const float* _data   = self.data_ptr()
+
+        with nogil:
+            for i in range(self._nitems):
+                x = _data[i]
+                if lrintf(x) != x:
+                    integer = False
+                    break
+        return integer
+
+    cpdef bint is_symmetric(self):
+        """Test whether the scoring matrix is symmetric.
+
+        Returns:
+            `bool`: `True` if the matrix is a symmetric matrix.
+
+        .. versionadded:: 0.2.0
+
+        """
+        cdef size_t        i
+        cdef size_t        j
+        cdef bint          symmetric = True
+        cdef const float** _matrix   = self.matrix_ptr()
+
+        with nogil:
+            for i in range(self._size):
+                for j in range(i + 1, self._size):
+                    if _matrix[i][j] != _matrix[j][i]:
+                        symmetric = False
+                        break
+        return symmetric
+
+    cpdef float min(self):
+        """Get the minimum score of the scoring matrix.
+
+        Example:
+            >>> blosum62 = ScoringMatrix.from_name("BLOSUM62")
+            >>> blosum62.min()
+            -4.0
+
+        """
+        assert self._data != NULL
+
+        cdef size_t i
+        cdef float  m = INFINITY
+
+        with nogil:
+            for i in range(self._nitems):
+                if self._data[i] < m:
+                    m = self._data[i]
+        return m
+
+    cpdef float max(self):
+        """Get the maximum score of the scoring matrix.
+
+        Example:
+            >>> blosum62 = ScoringMatrix.from_name("BLOSUM62")
+            >>> blosum62.max()
+            11.0
+
+        """
+        assert self._data != NULL
+        
+        cdef size_t i
+        cdef float  m = -INFINITY
+
+        with nogil:
+            for i in range(self._nitems):
+                if self._data[i] > m:
+                    m = self._data[i]
+        return m
+
+    cpdef ScoringMatrix shuffle(self, str alphabet):
+        """Shuffle the matrix using the new given alphabet.
+
+        The matrix name is retained only when the provided ``alphabet`` is a
+        permutation of the current alphabet, e.g. there is no loss of data.
+
+        Arguments:
+            alphabet (`str`): The new alphabet to use for the columns. It 
+                must be a subset of ``self.alphabet``.
+
+        Raises:
+            `KeyError`: When some required alphabet letters are missing from
+                the source matrix alphabet.
+
+        Example:
+            >>> m1 = ScoringMatrix.from_name("BLOSUM62")
+            >>> m1[1, 1]
+            5.0
+            >>> m1['R', 'R']
+            5.0
+            >>> m2 = m1.shuffle("ABCDEFGHIKLMNPQRSTVWXYZ*")
+            >>> m2[1, 1]
+            4.0
+            >>> m2['R', 'R']
+            5.0
+
+        """
+        cdef size_t i
+        cdef list   indices = []
+        cdef list   matrix  = []
+
+        for x in alphabet:
+            try:
+                indices.append(self.alphabet.index(x))
+            except ValueError:
+                raise KeyError(f"new alphabet contains unknown letter: {x!r}") from None
+
+        for letter in alphabet:
+            row = self[<str> letter]
+            matrix.append([row[j] for j in indices])
+
+        name = self.name if len(alphabet) == len(self.alphabet) else None
+        return type(self)(matrix, alphabet=alphabet, name=name)

src/scoring_matrices/matrices.pxd

+cdef extern from "matrices.h" nogil:
+    const char* _NAMES[]
+    const char* _ALPHABETS[]
+    const size_t _SIZES[]
+    const float* _MATRICES[]

src/scoring_matrices/py.typed

src/scoring_matrices/tests/__init__.py

+# noqa: D104
+
+from . import test_doctest, test_scoring_matrix
+
+
+def load_tests(loader, suite, pattern):
+    test_doctest.load_tests(loader, suite, pattern)
+    suite.addTests(loader.loadTestsFromModule(test_scoring_matrix))
+    return suite

src/scoring_matrices/tests/test_doctest.py

+# coding: utf-8
+"""Test doctest contained tests in every file of the module.
+"""
+
+import configparser
+import doctest
+import importlib
+import os
+import pkgutil
+import re
+import shutil
+import sys
+import types
+import warnings
+from unittest import mock
+
+import scoring_matrices
+
+
+def _load_tests_from_module(tests, module, globs, setUp=None, tearDown=None):
+    """Load tests from module, iterating through submodules."""
+    for attr in (getattr(module, x) for x in dir(module) if not x.startswith("_")):
+        if isinstance(attr, types.ModuleType):
+            suite = doctest.DocTestSuite(
+                attr,
+                globs,
+                setUp=setUp,
+                tearDown=tearDown,
+                optionflags=+doctest.ELLIPSIS,
+            )
+            tests.addTests(suite)
+    return tests
+
+
+def load_tests(loader, tests, ignore):
+    """`load_test` function used by unittest to find the doctests."""
+    _current_cwd = os.getcwd()
+    # demonstrate how to use Biopython substitution matrices without
+    # actually requiring Biopython
+    Bio = mock.Mock()
+    Bio.Align = mock.Mock()
+    Bio.Align.substitution_matrices = mock.Mock()
+    Bio.Align.substitution_matrices.load = mock.Mock()
+    Bio.Align.substitution_matrices.load.return_value = feng = mock.Mock()
+
+    data = [ [-1 for _ in range(20)] for _ in range(20) ]
+    for i in range(20):
+        data[i][i] = 1
+
+    feng.alphabet = "ARNDCQEGHILKMFPSTWYV"
+    feng.__len__ = mock.Mock(return_value=20)
+    feng.__iter__ = mock.Mock(wraps=data.__iter__)
+
+    def setUp(self):
+        warnings.simplefilter("ignore")
+        # os.chdir(os.path.realpath(os.path.join(__file__, os.path.pardir, "data")))
+
+    def tearDown(self):
+        # os.chdir(_current_cwd)
+        warnings.simplefilter(warnings.defaultaction)
+
+    # doctests are not compatible with `green`, so we may want to bail out
+    # early if `green` is running the tests
+    if sys.argv[0].endswith("green"):
+        return tests
+
+    # recursively traverse all library submodules and load tests from them
+    packages = [None, scoring_matrices.lib]
+
+    for pkg in iter(packages.pop, None):
+        globs = dict(scoring_matrices=scoring_matrices, Bio=Bio, **pkg.__dict__)
+        tests.addTests(
+            doctest.DocTestSuite(
+                pkg,
+                globs=globs,
+                setUp=setUp,
+                tearDown=tearDown,
+                optionflags=+doctest.ELLIPSIS,
+            )
+        )
+
+    return tests

src/scoring_matrices/tests/test_scoring_matrix.py

+import pickle
+import sys
+import unittest
+
+from scoring_matrices import ScoringMatrix
+
+
+class TestScoringMatrix(unittest.TestCase):
+
+    def test_from_name_blosum50(self):
+        matrix = ScoringMatrix.from_name("BLOSUM50")
+        diagonal = [ matrix[i, i] for i in range(len(matrix)) ]
+        self.assertEqual(len(diagonal), 24)
+        self.assertEqual(diagonal, [5, 7, 7, 8, 13, 7, 6, 8, 10, 5, 5, 6, 7, 8, 10, 5, 5, 15, 8, 5, 5, 5 ,-1 ,1])
+
+    def test_from_name_blosum62(self):
+        matrix = ScoringMatrix.from_name("BLOSUM62")
+        diagonal = [ matrix[i, i] for i in range(len(matrix)) ]
+        self.assertEqual(len(diagonal), 24)
+        self.assertEqual(diagonal, [4, 5, 6, 6, 9, 5, 5, 6, 8, 4, 4, 5, 5, 6, 7, 4, 5, 11, 7, 4, 4, 4, -1, 1])
+
+    def test_from_name_invalid_name(self):
+        with self.assertRaises(ValueError):
+            aa = ScoringMatrix.from_name("nonsensical")
+
+    def test_from_str(self):
+        m1 = ScoringMatrix.from_str(
+            """
+                A   T   G   C
+            A   5  -4  -4  -4
+            T  -4   5  -4  -4
+            G  -4  -4   5  -4
+            C  -4  -4  -4   5
+            """.strip()
+        )
+        self.assertEqual(m1.alphabet, "ATGC")
+        self.assertEqual(m1['T', 'A'], -4.0)
+        self.assertEqual(m1['A', 'A'], 5.0)
+
+        m2 = ScoringMatrix.from_str(
+            """
+             A   T   G   C
+             5  -4  -4  -4
+            -4   5  -4  -4
+            -4  -4   5  -4
+            -4  -4  -4   5
+            """.strip()
+        )
+        self.assertEqual(m2.alphabet, "ATGC")
+        self.assertEqual(m2['T', 'A'], -4.0)
+        self.assertEqual(m2['A', 'A'], 5.0)
+
+    def test_from_diagonal(self):
+        m = ScoringMatrix.from_diagonal([1, 2, 3, 4], 0.0, alphabet="ATGC")
+        self.assertEqual(m[0], [1.0, 0.0, 0.0, 0.0])
+        self.assertEqual(m[1], [0.0, 2.0, 0.0, 0.0])
+        self.assertEqual(m[2], [0.0, 0.0, 3.0, 0.0])
+        self.assertEqual(m[3], [0.0, 0.0, 0.0, 4.0])
+
+        m = ScoringMatrix.from_diagonal([1, 2, 3, 4], -1.0, alphabet="ATGC")
+        self.assertEqual(m[0], [ 1.0, -1.0, -1.0, -1.0])
+        self.assertEqual(m[1], [-1.0,  2.0, -1.0, -1.0])
+        self.assertEqual(m[2], [-1.0, -1.0,  3.0, -1.0])
+        self.assertEqual(m[3], [-1.0, -1.0, -1.0,  4.0])
+
+    def test_from_diagonal_invalid_length(self):
+        self.assertRaises(
+            ValueError,
+            ScoringMatrix.from_diagonal,
+            [ 3, 3, 3, 3, 3, 3 ],
+            alphabet="ATGC"
+        )
+        self.assertRaises(
+            ValueError,
+            ScoringMatrix.from_diagonal,
+            [ 3, 3, 3 ],
+            alphabet="ATGC"
+        )
+
+    def test_list(self):
+        aa = ScoringMatrix.from_name("BLOSUM50")
+        matrix = list(aa)
+        columns = aa.alphabet
+        self.assertEqual(len(columns), 24)
+        self.assertEqual(len(matrix), 24)
+        for row in matrix:
+            self.assertEqual(len(row), 24)
+
+    @unittest.skipUnless(sys.implementation.name == "cpython", "memoryview not supported")
+    @unittest.skipUnless(sys.version_info >= (3, 9), "memoryview not supported")
+    def test_memoryview(self):
+        aa = ScoringMatrix.from_name("BLOSUM50")
+        mem = memoryview(aa)
+        self.assertEqual(mem.shape, (24, 24))
+        self.assertEqual(mem[0, 0], 5.0) # A <-> A
+        self.assertEqual(mem[6, 6], 6.0) # E <-> E
+
+    def test_init_empty(self):
+        m = ScoringMatrix([], alphabet="")
+        self.assertEqual(len(m), 0)
+        self.assertFalse(bool(m))
+
+    def test_init_invalid_length(self):
+        with self.assertRaises(ValueError):
+            m = ScoringMatrix(
+                [
+                    [0, 0, 0, 0],
+                    [0, 0, 0, 0],
+                    [0, 0, 0, 0],
+                ],
+                alphabet="ATGC",
+            )
+        with self.assertRaises(ValueError):
+            m = ScoringMatrix(
+                [
+                    [0, 0, 0, 0],
+                    [0, 0, 0, 0],
+                    [0, 0, 0, 0],
+                    [0, 0, 0],
+                ],
+                alphabet="ATGC",
+            )
+
+    def test_eq(self):
+        sm1 = ScoringMatrix.from_name("BLOSUM50")
+        sm2 = ScoringMatrix.from_name("BLOSUM50")
+        sm3 = ScoringMatrix.from_name("BLOSUM62")
+        self.assertEqual(sm1, sm1)
+        self.assertEqual(sm1, sm2)
+        self.assertNotEqual(sm1, sm3)
+        self.assertNotEqual(sm1, 12)
+
+    def test_pickle(self):
+        sm1 = ScoringMatrix.from_name("BLOSUM62")
+        sm2 = pickle.loads(pickle.dumps(sm1))
+        self.assertEqual(sm1.alphabet, sm2.alphabet)
+        self.assertEqual(list(sm1), list(sm2))
+
+    def test_shuffle_invalid_alphabet(self):
+        matrix = ScoringMatrix.from_name("BLOSUM62")
+        self.assertRaises(KeyError, matrix.shuffle, "ARNJOU")
+
+    def test_shuffle_empty(self):
+        matrix = ScoringMatrix.from_name("BLOSUM62")
+        empty = matrix.shuffle("")
+        self.assertEqual(len(empty), 0)
+        self.assertFalse(bool(empty))
+
+    def test_is_symmetric(self):
+        matrix = ScoringMatrix.from_name("PAM250")
+        self.assertTrue(matrix.is_symmetric())
+        matrix = ScoringMatrix([[1, 2, 3], [4, 5, 6], [7, 8, 9]], "ABC")
+        self.assertFalse(matrix.is_symmetric())

src/scripts/cmake/CythonExtension.cmake

+find_package(Python COMPONENTS Interpreter Development.Module REQUIRED)
+get_property(PYTHON_EXTENSIONS_SOURCE_DIR GLOBAL PROPERTY PYTHON_EXTENSIONS_SOURCE_DIR)
+
+# --- Detect PyInterpreterState_GetID ------------------------------------------
+
+include(CheckSymbolExists)
+
+set(SAFE_CMAKE_REQUIRED_INCLUDES "${CMAKE_REQUIRED_INCLUDES}")
+set(CMAKE_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES} ${Python_INCLUDE_DIRS})
+check_symbol_exists(PyInterpreterState_GetID "stdint.h;stdlib.h;Python.h" HAVE_PYINTERPRETERSTATE_GETID)
+set(CMAKE_REQUIRED_INCLUDES "${SAFE_CMAKE_REQUIRED_INCLUDES}")
+
+# --- Detect implementation ----------------------------------------------------
+
+string(TOLOWER "${Python_INTERPRETER_ID}" SYS_IMPLEMENTATION_NAME)
+
+# --- Prepare Cython directives and constants ----------------------------------
+
+set(CYTHON_DIRECTIVES
+    -X cdivision=True
+    -X nonecheck=False
+    -E SYS_IMPLEMENTATION_NAME=${SYS_IMPLEMENTATION_NAME}
+    -E SYS_VERSION_INFO_MAJOR=${Python_VERSION_MAJOR}
+    -E SYS_VERSION_INFO_MINOR=${Python_VERSION_MINOR}
+    -E PROJECT_VERSION=${CMAKE_PROJECT_VERSION}
+)
+
+if(CMAKE_BUILD_TYPE STREQUAL Debug)
+  set(CYTHON_DIRECTIVES
+    ${CYTHON_DIRECTIVES}
+    -X cdivision_warnings=True
+    -X warn.undeclared=True
+    -X warn.unreachable=True
+    -X warn.maybe_uninitialized=True
+    -X warn.unused=True
+    -X warn.unused_arg=True
+    -X warn.unused_result=True
+    -X warn.multiple_declarators=True
+  )
+  if(NOT Python_INTERPRETER_ID STREQUAL PyPy)
+    set(CYTHON_DIRECTIVES
+      ${CYTHON_DIRECTIVES}
+      -X linetrace=true
+    )
+  endif()
+else()
+  set(CYTHON_DIRECTIVES
+    ${CYTHON_DIRECTIVES}
+    -X boundscheck=False
+    -X wraparound=False
+  )
+endif()
+
+# --- Declare Cython extension -------------------------------------------------
+
+macro(cython_extension _name)
+  set(multiValueArgs LINKS DIRECTIVES SOURCES OPTIONS)
+  cmake_parse_arguments(CYTHON_EXTENSION "" "" "${multiValueArgs}" ${ARGN} )
+
+  # Make sure that the source directory is known
+  if(NOT DEFINED PYTHON_EXTENSIONS_SOURCE_DIR)
+    message(FATAL_ERROR "The PYTHON_EXTENSIONS_SOURCE_DIR variable has not been set.")
+  endif()
+
+  # Generate C++ file from Cython file
+  add_custom_command(
+    OUTPUT 
+      ${_name}.c
+    COMMENT
+      "Cythonizing ${_name}.pyx to ${_name}.c"
+    COMMAND
+      Python::Interpreter -m cython
+        "${CMAKE_CURRENT_SOURCE_DIR}/${_name}.pyx"
+        --output-file ${_name}.c
+        --depfile
+        -I "${CYTHON_HEADERS_DIR}"
+        ${CYTHON_DIRECTIVES}
+        ${CYTHON_EXTENSION_DIRECTIVES}
+    MAIN_DEPENDENCY
+      ${_name}.pyx
+    DEPFILE
+      ${_name}.c.dep
+    VERBATIM)
+
+  # Build fully-qualified module name as the target name
+  string(REGEX REPLACE "^${PYTHON_EXTENSIONS_SOURCE_DIR}/?" "" _dest_folder ${CMAKE_CURRENT_SOURCE_DIR})
+  string(REPLACE "/" "." _target ${_dest_folder}.${_name})
+
+  # Add Python module
+  set(EXTENSION_SOURCES ${_name}.pyx ${_name}.c)
+  if(EXISTS ${_name}.pxd)
+    set(EXTENSION_SOURCES ${EXTENSION_SOURCES} ${_name}.pxd)
+  endif()
+  if(CYTHON_EXTENSION_SOURCES)
+    set(EXTENSION_SOURCES ${EXTENSION_SOURCES} ${CYTHON_EXTENSION_SOURCES})
+  endif()
+  python_add_library(${_target} MODULE WITH_SOABI ${EXTENSION_SOURCES})
+  set_target_properties(${_target} PROPERTIES OUTPUT_NAME ${_name})
+  set_target_properties(${_target} PROPERTIES CXX_STANDARD 17)
+  target_include_directories(${_target} AFTER PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})  
+  target_link_libraries(${_target} PUBLIC ${CYTHON_EXTENSION_LINKS})
+  if(CYTHON_EXTENSION_OPTIONS)
+    target_compile_options(${_target} PUBLIC ${CYTHON_EXTENSION_OPTIONS})
+  endif()
+  if(HAVE_PYINTERPRETERSTATE_GETID)
+    target_compile_definitions(${_target} PUBLIC HAVE_PYINTERPRETERSTATE_GETID)
+  endif()
+
+  if(CMAKE_BUILD_TYPE STREQUAL Debug)
+    if(NOT Python_INTERPRETER_ID STREQUAL PyPy)
+      target_compile_definitions(${_target} PUBLIC CYTHON_TRACE_NOGIL=1)
+    endif()
+  else()
+    target_compile_definitions(${_target} PUBLIC CYTHON_WITHOUT_ASSERTIONS=1)
+  endif()
+
+  # Preserve the relative project structure in the install directory
+  string(REGEX REPLACE "^${PYTHON_EXTENSIONS_SOURCE_DIR}/?" "" _dest_folder ${CMAKE_CURRENT_SOURCE_DIR})
+  install(TARGETS ${_target} DESTINATION ${_dest_folder} )
+  message(DEBUG "Install folder for extension ${_name}: ${_dest_folder}")
+
+  # Add the targets to the list of Cython extensions
+  get_property(_ext GLOBAL PROPERTY PYRODIGAL_CYTHON_EXTENSIONS)
+  list(APPEND _ext ${_target})
+  set_property(GLOBAL PROPERTY PYRODIGAL_CYTHON_EXTENSIONS ${_ext})
+endmacro()

src/scripts/generate_matrices.py

+import argparse
+import itertools
+import os
+
+
+def _parse_matrix_file(matrix_file):
+    with open(matrix_file) as f:
+        lines = filter(
+            lambda line: line and not line.startswith("#"),
+            map(str.strip, f),
+        )
+        letters = ''.join(next(lines).split())
+        matrix = [
+            list(map(float, line.strip().split()[1:]))
+            for line in map(str.strip, lines)
+            if line
+        ]
+    return letters, matrix
+
+def _generate_matrices(matrix_files, output_file):
+    matrices = {}
+    for matrix_file in matrix_files:
+        matrix_name = os.path.splitext(os.path.basename(matrix_file))[0].upper()
+        matrices[matrix_name] = _parse_matrix_file(matrix_file)
+
+    with open(output_file, "w") as dst:
+        dst.write("#include <stddef.h>\n")
+        names = sorted(matrices.keys())
+        ids = [ name.replace(".", "_") for name in names ]
+        
+        dst.write(f"const char* _NAMES[{len(names) + 1}] = {{")
+        for name in names:
+            dst.write(f'"{name}", ')
+        dst.write("NULL };\n")
+
+        dst.write(f"const char* _ALPHABETS[{len(names) + 1}] = {{")
+        for name in names:
+            alphabet, _ = matrices[name]
+            dst.write(f'"{alphabet}", ')
+        dst.write("NULL };\n")
+
+        dst.write(f"const size_t _SIZES[{len(names) + 1}] = {{")
+        for name in names:
+            alphabet, _ = matrices[name]
+            dst.write(f'{len(alphabet)}, ')
+        dst.write("-1 };\n")
+
+        for i, (name, id_) in enumerate(zip(names, ids)):
+            alphabet, matrix = matrices[name]
+            nitems = len(matrix) * len(matrix)
+            dst.write(f"float _MATRIX_{id_}[{nitems}] = {{")
+            for i, item in enumerate(itertools.chain.from_iterable(matrix)):
+                if i != 0:
+                    dst.write(", ")
+                dst.write(f"{item!r}F")
+            dst.write("};\n")
+
+        dst.write(f"const float* _MATRICES[{len(names) + 1}] = {{")
+        for id_ in ids:
+            dst.write(f'_MATRIX_{id_}, ')
+        dst.write("NULL };\n")
+
+
+parser = argparse.ArgumentParser()
+parser.add_argument("--output", required=True)
+parser.add_argument("inputs", nargs="+")
+args = parser.parse_args()
+
+_generate_matrices(args.inputs, args.output)

PKG-INFO

 Metadata-Version: 2.1
 Name: scoring-matrices
-Version: 0.2.2
+Version: 0.3.0rc1
 Summary: Dependency free, Cython-compatible scoring matrices to use with biological sequences.
-Home-page: https://github.com/althonos/score-matrices
-Author: Martin Larralde
-Author-email: [e-mail]
-License: MIT
-Project-URL: Bug Tracker, https://github.com/althonos/scoring-matrices/issues
-Project-URL: Changelog, https://github.com/althonos/scoring-matrices/blob/main/CHANGELOG.md
-Project-URL: Coverage, https://codecov.io/gh/althonos/scoring-matrices/
-Project-URL: Builds, https://github.com/althonos/scoring-matrices/actions
 Keywords: bioinformatics,sequence,substitution,matrix,score
-Platform: any
-Classifier: Development Status :: 3 - Alpha
+Author-Email: Martin Larralde <[e-mail]>
+License: MIT License
+        
+        Copyright (c) 2024 Martin Larralde <[e-mail]>
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Developers
@@ -22,3 +35,2 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Programming Language :: Cython
-Classifier: Programming Language :: Python :: 3.6
 Classifier: Programming Language :: Python :: 3.7
@@ -34,5 +46,10 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Typing :: Typed
-Requires-Python: >=3.5
+Project-URL: Documentation, https://scoring-matrices.readthedocs.io/en/stable/
+Project-URL: Bug tracker, https://github.com/althonos/scoring-matrices/issues
+Project-URL: Changelog, https://github.com/althonos/scoring-matrices/blob/main/CHANGELOG.md
+Project-URL: Coverage, https://codecov.io/gh/althonos/scoring-matrices/
+Project-URL: Builds, https://github.com/althonos/scoring-matrices/actions
+Project-URL: Pypi, https://pypi.org/project/scoring-matrices
+Requires-Python: >=3.7
 Description-Content-Type: text/markdown
-License-File: COPYING
 
@@ -39,0 +56,0 @@ # 🧬🔠 `scoring-matrices` [![Stars](https://img.shields.io/github/stars/althonos/scoring-matrices.svg?style=social&maxAge=3600&label=Star)](https://github.com/althonos/scoring-matrices/stargazers)

pyproject.toml

 [build-system]
-requires = ['setuptools >=46.4', 'cython ~=3.0']
-build-backend = "setuptools.build_meta"
+requires = ["scikit-build-core", "cython >=3.0"]
+build-backend = "scikit_build_core.build"
 
+[project]
+name = "scoring-matrices"
+version = "0.3.0-rc1"
+description = "Dependency free, Cython-compatible scoring matrices to use with biological sequences."
+readme = "README.md"
+requires-python = ">=3.7"
+license = { file = "COPYING" }
+authors = [
+  { name = "Martin Larralde", email = "[e-mail]" },
+]
+keywords = ["bioinformatics", "sequence", "substitution", "matrix", "score"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: C",
+    "Programming Language :: Cython",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Programming Language :: Python :: Implementation :: PyPy",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Typing :: Typed",
+]
+
+
+[project.urls]
+"Documentation" = "https://scoring-matrices.readthedocs.io/en/stable/"
+"Bug Tracker" = "https://github.com/althonos/scoring-matrices/issues"
+"Changelog" = "https://github.com/althonos/scoring-matrices/blob/main/CHANGELOG.md"
+"Coverage" = "https://codecov.io/gh/althonos/scoring-matrices/"
+"Builds" = "https://github.com/althonos/scoring-matrices/actions"
+"PyPI" = "https://pypi.org/project/scoring-matrices"
+
+[tool.scikit-build]
+build-dir = "build/{build_type}"
+editable.rebuild = true
+editable.verbose = false
+
+[[tool.scikit-build.generate]]
+path = "src/scoring_matrices/_version.py"
+template = '__version__ = "${version}"'
+location = 'source'
+
+[[tool.scikit-build.overrides]]
+if.state = "editable"
+cmake.build-type = "Debug"
+
+[[tool.scikit-build-overrides]]
+if.env.SCCACHE = true
+cmake.define.CMAKE_C_COMPILER_LAUNCHER = "sccache"
+cmake.define.CMAKE_CXX_COMPILER_LAUNCHER = "sccache"
+
+[[tool.scikit-build-overrides]]
+if.env.MOLD = true
+cmake.define.CMAKE_LINKER_TYPE = "mold"
+
+#[tool.coverage.run]
+#plugins = ["Cython.Coverage"]
+
+[tool.coverage.report]
+include = ["src/scoring_matrices/*"]
+omit = ["src/scoring_matrices/tests/*"]
+show_missing = true
+exclude_lines = [
+    "pragma: no cover",
+    "if typing.TYPE_CHECKING:",
+    "@abc.abstractmethod",
+    "@abc.abstractproperty",
+    "raise NotImplementedError",
+    "return NotImplemented",
+    "raise UnexpectedError",
+    "raise AllocationError",
+]
+
+[tool.coverage.paths]
+source = [
+    "src/scoring_matrices/",
+    "build/Debug/src/scoring_matrices/",
+]
+
+[tool.mypy]
+disallow_any_decorated = true
+disallow_any_generics = true
+disallow_any_unimported = false
+disallow_subclassing_any = false
+disallow_untyped_calls = true
+disallow_untyped_defs = true
+ignore_missing_imports = true
+warn_unused_ignores = true
+warn_return_any = true
+exclude = ["tests/.*\\.py"]
+
+["tool.mypy-scoring_matrices.tests.*"]
+ignore_errors = true
+
+[tool.isort]
+known_first_party = ["scoring_matrices"]
+known_standard_library = ["cpython", "cython", "_unicode"]
+known_third_party = ["libc", "libcpp"]
+line_length = 88
+profile = "black"
+skip_gitignore = true

scoring_matrices.egg-info/dependency_links.txt

-

scoring_matrices.egg-info/PKG-INFO

-Metadata-Version: 2.1
-Name: scoring-matrices
-Version: 0.2.2
-Summary: Dependency free, Cython-compatible scoring matrices to use with biological sequences.
-Home-page: https://github.com/althonos/score-matrices
-Author: Martin Larralde
-Author-email: [e-mail]
-License: MIT
-Project-URL: Bug Tracker, https://github.com/althonos/scoring-matrices/issues
-Project-URL: Changelog, https://github.com/althonos/scoring-matrices/blob/main/CHANGELOG.md
-Project-URL: Coverage, https://codecov.io/gh/althonos/scoring-matrices/
-Project-URL: Builds, https://github.com/althonos/scoring-matrices/actions
-Keywords: bioinformatics,sequence,substitution,matrix,score
-Platform: any
-Classifier: Development Status :: 3 - Alpha
-Classifier: Intended Audience :: Developers
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: C
-Classifier: Programming Language :: Cython
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: 3.7
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: Implementation :: CPython
-Classifier: Programming Language :: Python :: Implementation :: PyPy
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Classifier: Typing :: Typed
-Requires-Python: >=3.5
-Description-Content-Type: text/markdown
-License-File: COPYING
-
-# 🧬🔠 `scoring-matrices` [![Stars](https://img.shields.io/github/stars/althonos/scoring-matrices.svg?style=social&maxAge=3600&label=Star)](https://github.com/althonos/scoring-matrices/stargazers)
-
-*Dependency free, [Cython](https://cython.org/)-compatible scoring matrices to use with biological sequences.*
-
-[![Actions](https://img.shields.io/github/actions/workflow/status/althonos/scoring-matrices/test.yml?branch=main&logo=github&style=flat-square&maxAge=300)](https://github.com/althonos/scoring-matrices/actions)
-[![Coverage](https://img.shields.io/codecov/c/gh/althonos/scoring-matrices?style=flat-square&maxAge=3600&logo=codecov)](https://codecov.io/gh/althonos/scoring-matrices/)
-[![License](https://img.shields.io/badge/license-MIT-blue.svg?style=flat-square&maxAge=2678400)](https://choosealicense.com/licenses/mit/)
-[![PyPI](https://img.shields.io/pypi/v/scoring-matrices.svg?style=flat-square&maxAge=3600&logo=PyPI)](https://pypi.org/project/scoring-matrices)
-[![Bioconda](https://img.shields.io/conda/vn/bioconda/scoring-matrices?style=flat-square&maxAge=3600&logo=anaconda)](https://anaconda.org/bioconda/scoring-matrices)
-[![AUR](https://img.shields.io/aur/version/python-scoring-matrices?logo=archlinux&style=flat-square&maxAge=3600)](https://aur.archlinux.org/packages/python-scoring-matrices)
-[![Wheel](https://img.shields.io/pypi/wheel/scoring-matrices.svg?style=flat-square&maxAge=3600)](https://pypi.org/project/scoring-matrices/#files)
-[![Python Versions](https://img.shields.io/pypi/pyversions/scoring-matrices.svg?style=flat-square&maxAge=600&logo=python)](https://pypi.org/project/scoring-matrices/#files)
-[![Python Implementations](https://img.shields.io/pypi/implementation/scoring-matrices.svg?style=flat-square&maxAge=600&label=impl)](https://pypi.org/project/scoring-matrices/#files)
-[![Source](https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400&style=flat-square)](https://github.com/althonos/scoring-matrices/)
-[![Issues](https://img.shields.io/github/issues/althonos/scoring-matrices.svg?style=flat-square&maxAge=600)](https://github.com/althonos/scoring-matrices/issues)
-[![Docs](https://img.shields.io/readthedocs/scoring-matrices/latest?style=flat-square&maxAge=600)](https://scoring-matrices.readthedocs.io)
-[![Changelog](https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square)](https://github.com/althonos/scoring-matrices/blob/main/CHANGELOG.md)
-[![Downloads](https://img.shields.io/pypi/dm/scoring-matrices?style=flat-square&color=303f9f&maxAge=86400&label=downloads)](https://pepy.tech/project/scoring-matrices)
-
-## 🗺️ Overview
-
-*Scoring Matrices* are matrices used to score the matches and mismatches between
-two characters are the same position in a sequence alignment. Some of these
-matrices are derived from *substitution matrices*, which uses evolutionary 
-modeling.
-
-The `scoring-matrices` package is a dependency-free, batteries included library
-to handle and distribute common substitution matrices:
-
-- **no external dependencies**: The matrices are distributed as-is: you don't 
-  need the whole [Biopython](https://biopython.org) ecosystem, or even 
-  [NumPy](https://numpy.org/).
-- **Cython compatibility**: The `ScoringMatrix` is a Cython class that can be
-  inherited, and the matrix data can be accessed as either a raw pointer, or
-  a [typed memoryview](https://cython.readthedocs.io/en/latest/src/userguide/memoryviews.html).
-- **most common matrices**: The package distributes most common matrices, such as 
-  those used by the NCBI BLAST+ suite, including:
-  - [*PAM*](https://en.wikipedia.org/wiki/Point_accepted_mutation#) matrices by Dayhoff *et al.* (1978).
-  - [*BLOSUM*](https://en.wikipedia.org/wiki/BLOSUM) matrices by Henikoff & Henikoff (1992).
-  - *VTML* matrices by Muller *et al.* (2002).
-  - *BENNER* matrices by Benner *et al.* (1994).
-
-## 🔧 Installing
-
-`scoring-matrices` can be installed directly from [PyPI](https://pypi.org/project/scoring-matrices/),
-which hosts some pre-built wheels for the x86-64 architecture (Linux/OSX/Windows)
-and the Aarch64 architecture (Linux/OSX), as well as the code required to
-compile from source with Cython:
-```console
-$ pip install scoring-matrices
-```
-
-Otherwise, `scoring-matrices` is also available as a [Bioconda](https://bioconda.github.io/)
-package:
-```console
-$ conda install bioconda::scoring-matrices
-```
-
-## 💡 Usage
-
-### Python
-
-- Import the `ScoringMatrix` class from the installed module:
-  ```python
-  from scoring_matrices import ScoringMatrix
-  ```
-- Load one of the built-in matrices:
-  ```python
-  blosum62 = ScoringMatrix.from_name("BLOSUM62")
-  ```
-- Get individual matrix weights either by index or by alphabet letter:
-  ```python
-  x = blosum62[0, 0]
-  y = blosum62['A', 'A']
-  ```
-- Get a row of the matrix either by index or by alphabet letter:
-  ```python
-  row_x = blosum62[0]
-  row_y = blosum62['A']
-  ```
-
-### Cython
-
-- Access the matrix weights as raw pointers to constant data:
-  ```cython
-  from scoring_matrices cimport ScoringMatrix
-
-  cdef ScoringMatrix blosum = ScoringMatrix.from_name("BLOSUM62")
-  cdef const float*  data   = blosum.data_ptr()    # dense array
-  cdef const float** matrix = blosum.matrix_ptr()  # array of pointers
-  ```
-- Access the `ScoringMatrix` weights as a [typed memoryview](https://cython.readthedocs.io/en/latest/src/userguide/memoryviews.html) 
-  using the *buffer protocol* in more recents versions of Python:
-  ```cython
-  from scoring_matrices cimport ScoringMatrix
-
-  cdef ScoringMatrix     blosum  = ScoringMatrix.from_name("BLOSUM62")
-  cdef const float[:, :] weights = blosum
-  ```
-
-## 💭 Feedback
-
-### ⚠️ Issue Tracker
-
-Found a bug ? Have an enhancement request ? Head over to the [GitHub issue tracker](https://github.com/althonos/scoring-matrices/issues)
-if you need to report or ask something. If you are filing in on a bug,
-please include as much information as you can about the issue, and try to
-recreate the same bug in a simple, easily reproducible situation.
-
-### 🏗️ Contributing
-
-Contributions are more than welcome! See
-[`CONTRIBUTING.md`](https://github.com/althonos/scoring-matrices/blob/main/CONTRIBUTING.md)
-for more details.
-
-
-## 📋 Changelog
-
-This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html)
-and provides a [changelog](https://github.com/althonos/scoring-matrices/blob/main/CHANGELOG.md)
-in the [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) format.
-
-
-## ⚖️ License
-
-This library is provided under the [MIT License](https://choosealicense.com/licenses/mit/). 
-Matrices were collected from the [MMseqs2](https://github.com/soedinglab/MMseqs2), 
-[Biopython](https://github.com/biopython/biopython/tree/master/Bio/Align/substitution_matrices/data)
-and [NCBI BLAST+](https://ftp.ncbi.nih.gov/blast/matrices/) sources and are believed to 
-be in the public domain.
-
-*This project was developed by [Martin Larralde](https://github.com/althonos/) 
-during his PhD project at the [Leiden University Medical Center](https://www.lumc.nl/en/) in the [Zeller team](https://github.com/zellerlab).*

scoring_matrices.egg-info/SOURCES.txt

-COPYING
-README.md
-pyproject.toml
-setup.cfg
-setup.py
-scoring_matrices/__init__.pxd
-scoring_matrices/__init__.py
-scoring_matrices/lib.pxd
-scoring_matrices/lib.pyi
-scoring_matrices/lib.pyx
-scoring_matrices/matrices.h
-scoring_matrices/matrices.pxd
-scoring_matrices/py.typed
-scoring_matrices.egg-info/PKG-INFO
-scoring_matrices.egg-info/SOURCES.txt
-scoring_matrices.egg-info/dependency_links.txt
-scoring_matrices.egg-info/not-zip-safe
-scoring_matrices.egg-info/top_level.txt
-scoring_matrices/tests/__init__.py
-scoring_matrices/tests/test_doctest.py
-scoring_matrices/tests/test_scoring_matrix.py

scoring_matrices.egg-info/top_level.txt

-scoring_matrices

scoring_matrices/__init__.pxd

-from .lib cimport ScoringMatrix

scoring_matrices/__init__.py

-__version__ = "0.2.2"
-__author__ = "Martin Larralde <[e-mail]>"
-__license__ = "MIT"
-
-from . import lib
-from .lib import ScoringMatrix
-
-__doc__ = lib.__doc__

scoring_matrices/lib.pxd

-# distutils: language = c
-# cython: language_level=3, linetrace=True, binding=True
-
-cdef class ScoringMatrix:
-    cdef readonly str name
-    cdef readonly str alphabet
-
-    cdef size_t        _size
-    cdef size_t        _nitems
-    cdef Py_ssize_t[2] _shape
-
-    cdef float*  _data
-    cdef float** _matrix
-    cdef char*   _alphabet
-
-    cdef int _allocate(self, size_t length) except 1 nogil
-
-    cdef const float* data_ptr(self) except NULL nogil
-    cdef const float** matrix_ptr(self) except NULL nogil    
-    cdef const char* alphabet_ptr(self) except NULL nogil
-    cdef size_t size(self) noexcept nogil
-
-    cpdef bint is_integer(self)
-    cpdef bint is_symmetric(self)
-    cpdef float min(self)
-    cpdef float max(self)
-    cpdef ScoringMatrix copy(self)
-    cpdef ScoringMatrix shuffle(self, str alphabet)

scoring_matrices/lib.pyi

-import typing
-from typing import TypeVar, Type, Optional, TextIO, Sequence, ClassVar, Tuple, List
-
-S = TypeVar("S")
-
-class ScoringMatrix:
-    DEFAULT_ALPHABET: ClassVar[str]
-    @classmethod
-    def from_name(cls: Type[S], name: str = "BLOSUM62") -> S: ...
-    @classmethod
-    def from_file(cls: Type[S], file: TextIO, name: Optional[str] = None) -> S: ...
-    @classmethod
-    def from_str(cls: Type[S], text: str, name: Optional[str] = None) -> S: ...
-    @classmethod
-    def from_diagonal(
-        cls: Type[S],
-        diagonal: Iterable[float],
-        mismatch_score: float = 0.0,
-        alphabet: str = DEFAULT_ALPHABET,
-        name: Optional[str] = None,
-    ) -> S: ...
-    @classmethod
-    def from_match_mismatch(
-        cls: Type[S],
-        match_score: float = 1.0,
-        mismatch_score: float = -0.0,
-        alphabet: str = DEFAULT_ALPHABET,
-        name: Optional[str] = None,
-    ) -> S: ...
-    def __init__(
-        self,
-        matrix: Sequence[Sequence[float]],
-        alphabet: str = DEFAULT_ALPHABET,
-        name: Optional[str] = None,
-    ): ...
-    def __copy__(self: S) -> S: ...
-    def __repr__(self) -> str: ...
-    def __reduce_ex__(self, protocol: object) -> Tuple[object, ...]: ...
-    def __len__(self) -> int: ...
-    def __eq__(self, other: object) -> bool: ...
-    @property
-    def alphabet(self) -> str: ...
-    @property
-    def name(self) -> Optional[str]: ...
-    @typing.overload
-    def __getitem__(self, item: int) -> List[float]: ...
-    @typing.overload
-    def __getitem__(self, item: str) -> List[float]: ...
-    @typing.overload
-    def __getitem__(self, item: Tuple[int, int]) -> float: ...
-    @typing.overload
-    def __getitem__(self, item: Tuple[str, str]) -> float: ...
-    def copy(self: S) -> S: ...
-    def is_integer(self) -> bool: ...
-    def is_symmetric(self) -> bool: ...
-    def min(self) -> float: ...
-    def max(self) -> float: ...
-    def shuffle(self: S, alphabet: str) -> S: ...

scoring_matrices/lib.pyx

-# distutils: language = c
-# cython: language_level=3, linetrace=True, binding=True
-"""Dependency free, Cython-compatible scoring matrices for bioinformatics.
-"""
-
-cimport cython
-from cpython.memoryview cimport PyMemoryView_FromMemory
-from cpython.buffer cimport PyBUF_FORMAT, PyBUF_READ, PyBUF_WRITE
-
-from libc.math cimport INFINITY, lrintf
-from libc.stdlib cimport realloc, free
-from libc.string cimport memcpy, memset
-
-from .matrices cimport _NAMES, _ALPHABETS, _SIZES, _MATRICES
-
-import io
-import pickle
-
-
-cdef dict _INDICES = {
-    _NAMES[i].decode('ascii'):i
-    for i in range(sizeof(_NAMES) /sizeof(const char*) - 1)
-}
-
-cdef class ScoringMatrix:
-    """A scoring matrix to use for biological sequence alignments.
-    """
-
-    DEFAULT_ALPHABET = "ARNDCQEGHILKMFPSTWYVBZX*"
-    BUILTIN_MATRICES = frozenset(_INDICES)
-
-    # --- Constructors ---------------------------------------------------------
-
-    @classmethod
-    def from_name(cls, str name not None = "BLOSUM62"):
-        """Load a built-in scoring matrix by name.
-
-        Arguments:
-            name (`str`): The name of the scoring matrix.
-
-        Example:
-            >>> blosum62 = ScoringMatrix.from_name("BLOSUM62")
-
-        Raises:
-            `ValueError`: When no scoring matrix with the given ``name``
-                can be found in the embedded matrix data.
-
-        """
-        cdef size_t i
-        cdef size_t j
-        cdef size_t k
-        cdef list   rows
-
-        try:
-            i = _INDICES[name]
-        except KeyError as err:
-            raise ValueError(f"Unknown scoring matrix: {name!r}") from err
-        else:
-            alphabet = _ALPHABETS[i].decode('ascii')
-
-        rows = []
-        for j in range(0, _SIZES[i] * _SIZES[i], _SIZES[i]):
-            row = []
-            for k in range(_SIZES[i]):
-                row.append(_MATRICES[i][j + k])
-            rows.append(row)
-
-        return cls(rows, alphabet=alphabet, name=name)
-
-    @classmethod
-    def from_file(cls, object file, str name = None):
-        """Load a scoring matrix from a file-like object.
-        """
-        # ignore lines with comments
-        lines = filter(lambda line: not line.startswith("#"), file)
-
-        # get the header line with the alphabet
-        header = next(lines, None)
-        if header is None:
-            raise ValueError("Missing expected header line")
-        alphabet = ''.join(header.split())
-
-        # get the numerical matrix
-        matrix = []
-        for i, line in enumerate(lines):
-            row = line.split()
-            try:
-                float(row[0])
-            except ValueError:
-                if row[0] != alphabet[i]:
-                    raise ValueError(f"Matrix must be symmetric (expected row {alphabet[i]!r}, got {row[0]!r})") from None
-                row = row[1:]
-            matrix.append(list(map(float, row)))
-
-        # create the object with default constructor
-        return cls(matrix, alphabet=alphabet, name=name)
-
-    @classmethod
-    def from_str(cls, str text, str name = None):
-        """Load a scoring matrix from a string.
-        """
-        return cls.from_file(io.StringIO(text))
-
-    @classmethod
-    def from_diagonal(
-        cls, 
-        object diagonal, 
-        float mismatch_score=0.0, 
-        str alphabet not None = DEFAULT_ALPHABET, 
-        str name = None
-    ):
-        """Create a scoring matrix from a diagonal vector.
-
-        Arguments:
-            diagonal (sequence of `float`): The diagonal of the scoring
-                matrix, used to score character matches.
-            mismatch_score (`float`): The mismatch score to use for 
-                every mismatches.
-            alphabet (`str`): The alphabet to use with the scoring matrix.
-            name (`str` or `None`): A name for the scoring matrix, if any.
-
-        Example:
-            >>> matrix = ScoringMatrix.from_diagonal(
-            ...     diagonal=[2, 2, 3, 3],
-            ...     mismatch_score=-3.0,
-            ...     alphabet="ATGC",
-            ... )
-            >>> for row in matrix:
-            ...     print(row)
-            [2.0, -3.0, -3.0, -3.0]
-            [-3.0, 2.0, -3.0, -3.0]
-            [-3.0, -3.0, 3.0, -3.0]
-            [-3.0, -3.0, -3.0, 3.0]
-
-        .. versionadded:: 0.2.0
-
-        """
-        cdef list   matrix = []
-        cdef size_t length = len(alphabet)
-
-        for i, x in enumerate(diagonal):
-            row = [ x if j == i else mismatch_score for j in range(length) ]
-            matrix.append(row)
-        return cls(matrix, alphabet=alphabet, name=name)
-
-    @classmethod
-    def from_match_mismatch(
-        cls,
-        float match_score = 1.0, 
-        float mismatch_score = -1.0,
-        str alphabet not None = DEFAULT_ALPHABET,
-        str name = None,
-    ):
-        """Create a scoring matrix from two match/mismatch scores.
-
-        .. versionadded:: 0.2.0
-
-        """
-        cdef list   matrix = []
-        cdef size_t length = len(alphabet)
-
-        for i in range(length):
-            row = [ match_score if j == i else mismatch_score for j in range(length) ]
-            matrix.append(row)
-        return cls(matrix, alphabet=alphabet, name=name)
-
-    # --- Magic methods --------------------------------------------------------
-
-    def __cinit__(self):
-        self._data = NULL
-        self._matrix = NULL
-        self._size = 0
-        self._shape[0] = self._shape[1] = 0
-
-    def __init__(
-        self,
-        object matrix not None,
-        str alphabet not None = DEFAULT_ALPHABET,
-        str name = None,
-    ):
-        """Create a new scoring matrix.
-
-        Arguments:
-            matrix (array-like of `float`): A square matrix with dimensions
-                equal to the ``alphabet`` length, storing the scores for each
-                pair of characters.
-            alphabet (`str`): The alphabet used to index the rows and columns
-                of the scoring matrix.
-            name (`str` or `None`): The name of the scoring matrix, if any.
-
-        Example:
-            >>> matrix = ScoringMatrix(
-            ...     [[91, -114,  -31, -123],
-            ...      [-114, 100, -125, -31],
-            ...      [-31, -125,  100, -114],
-            ...      [-123, -31, -114,  91]],
-            ...     alphabet="ACGT",
-            ...     name="HOXD70",
-            ... )
-
-        Raises:
-            `ValueError`: When the matrix is not a valid matrix or does not
-                match the given alphabet.
-            `MemoryError`: When memory for storing the scores could not be
-                allocated successfully.
-
-        """
-        cdef ssize_t i
-        cdef ssize_t j
-        cdef float   x
-        cdef size_t  size = len(alphabet)
-
-        if len(alphabet) != len(set(alphabet)):
-            raise ValueError(f"Duplicate letters found in alphabet: {self.alphabet!r}")
-        if len(matrix) != size:
-            raise ValueError("Matrix must contain one row per alphabet letter")
-
-        self.alphabet = alphabet
-        self.name = name
-
-        with nogil:
-            self._allocate(size)
-
-        for i, c in enumerate(self.alphabet):
-            self._alphabet[i] = ord(c)
-        for i, row in enumerate(matrix):
-            if len(row) != size:
-                raise ValueError("Matrix must contain one column per alphabet letter")
-            for j, x in enumerate(row):
-                self._matrix[i][j] = x
-
-    def __copy__(self):
-        return self.copy()
-
-    def __repr__(self):
-        cdef str ty    = type(self).__name__
-        cdef list args = [repr(list(self))]
-
-        if self.alphabet != ScoringMatrix.DEFAULT_ALPHABET:
-            args.append(f"alphabet={self.alphabet!r}")
-        if self.name is not None:
-            args.append(f"name={self.name!r}")
-        return f"{ty}({', '.join(args)})"
-
-    def __reduce_ex__(self, int protocol):
-        assert self._data != NULL
-        assert self._matrix != NULL
-
-        # use out-of-band pickling (only supported since protocol 5, see
-        # https://docs.python.org/3/library/pickle.html#out-of-band-buffers)
-        if protocol >= 5:
-            matrix = pickle.PickleBuffer(self)
-        else:
-            matrix = list(self)
-        return (type(self), (matrix, self.alphabet, self.name))
-
-    def __getbuffer__(self, Py_buffer* buffer, int flags):
-        assert self._data != NULL
-
-        if flags & PyBUF_FORMAT:
-            buffer.format = b"f"
-        else:
-            buffer.format = NULL
-        buffer.buf = self._data
-        buffer.internal = NULL
-        buffer.itemsize = sizeof(float)
-        buffer.len = self._nitems * sizeof(float)
-        buffer.ndim = 2
-        buffer.obj = self
-        buffer.readonly = 1
-        buffer.shape = <Py_ssize_t*> &self._shape
-        buffer.suboffsets = NULL
-        buffer.strides = NULL
-
-    def __len__(self):
-        return self._size
-
-    def __getitem__(self, object item):
-        cdef ssize_t index_
-        cdef list    row
-
-        if isinstance(item, str) and len(item) == 1:
-            try:
-                item = self.alphabet.index(item)
-            except ValueError:
-                raise IndexError(f"{item!r} not in matrix alphabet ({self.alphabet!r})") from None
-
-        if isinstance(item, int):
-            index_ = item
-            if index_ < 0:
-                index_ += self._size
-            if index_ < 0 or index_ >= self._size:
-                raise IndexError(item)
-            row = []
-            for i in range(self._size):
-                row.append(self._matrix[index_][i])
-            return row
-
-        elif isinstance(item, tuple):
-            if len(item) > 2:
-                raise IndexError(f"too many indices for array: array is 2-dimensional, but {len(item)!r} were indexed")
-            i, j = item
-            if isinstance(i, str) and len(i) == 1:
-                try:
-                    i = self.alphabet.index(i)
-                except ValueError:
-                    raise IndexError(f"{i!r} not in matrix alphabet ({self.alphabet!r})") from None
-            if isinstance(j, str) and len(j) == 1:
-                try:
-                    j = self.alphabet.index(j)
-                except ValueError:
-                    raise IndexError(f"{j!r} not in matrix alphabet ({self.alphabet!r})") from None
-            if isinstance(i, int) and isinstance(j, int):
-                return self._matrix[i][j]
-
-        raise TypeError(item)
-
-    def __eq__(self, object other):
-        assert self._data != NULL
-        assert self._matrix != NULL
-
-        cdef size_t        i
-        cdef ScoringMatrix other_
-
-        if not isinstance(other, ScoringMatrix):
-            return NotImplemented
-        other_ = other
-        if other_.alphabet != self.alphabet:
-            return False
-        for i in range(self._nitems):
-            if self._data[i] != other_._data[i]:
-                return False
-        return True
-
-    # --- Private methods ------------------------------------------------------
-    
-    cdef int _allocate(self, size_t size) except 1 nogil:
-        cdef size_t i
-
-        self._data = <float*> realloc(self._data, sizeof(float) * size * size)
-        self._matrix = <float**> realloc(self._matrix, sizeof(float*) * size)
-        self._alphabet = <char*> realloc(self._alphabet, sizeof(char) * (size + 1))
-        if self._data is NULL or self._matrix is NULL or self._alphabet is NULL:
-            raise MemoryError("Failed to allocate matrix")
-
-        self._size = self._shape[0] = self._shape[1] = size
-        self._nitems = self._size * self._size
-        for i in range(size):
-            self._matrix[i] = &self._data[i * self._size]
-        memset(self._alphabet, 0, sizeof(char) * (size + 1))
-
-        return 0
-
-    # --- Public methods -------------------------------------------------------
-
-    cdef size_t size(self) noexcept nogil:
-        """Get the size of the scoring matrix.
-        """
-        return self._size
-
-    cdef const char* alphabet_ptr(self) except NULL nogil:
-        """Get the alphabet of the scoring matrix as a C-string.
-        """
-        if self._alphabet == NULL:
-            with gil:
-                raise RuntimeError("uninitialized scoring matrix")
-        return <const char*> self._alphabet
-
-    cdef const float* data_ptr(self) except NULL nogil:
-        """Get the matrix scores as a dense array.
-        """
-        if self._data == NULL:
-            with gil:
-                raise RuntimeError("uninitialized scoring matrix")
-        return <const float*> self._data
-
-    cdef const float** matrix_ptr(self) except NULL nogil:
-        """Get the matrix scores as an array of pointers.
-        """
-        if self._matrix == NULL:
-            with gil:
-                raise RuntimeError("uninitialized scoring matrix")
-        return <const float**> self._matrix
-
-    cpdef ScoringMatrix copy(self):
-        """Get a copy of the matrix.
-        """
-        return type(self)(self, alphabet=self.alphabet, name=self.name)
-
-    cpdef bint is_integer(self):
-        """Test whether the scoring matrix is an integer matrix.
-
-        Returns:
-            `bool`: `True` if the matrix only contains integer scores.
-
-        Example:
-            >>> blosum62 = ScoringMatrix.from_name("BLOSUM62")
-            >>> blosum62.is_integer()
-            True
-            >>> benner6 = ScoringMatrix.from_name("BENNER6")
-            >>> benner6.is_integer()
-            False
-
-        """
-        cdef size_t       i
-        cdef float        x
-        cdef bint         integer = True
-        cdef const float* _data   = self.data_ptr()
-
-        with nogil:
-            for i in range(self._nitems):
-                x = _data[i]
-                if lrintf(x) != x:
-                    integer = False
-                    break
-        return integer
-
-    cpdef bint is_symmetric(self):
-        """Test whether the scoring matrix is symmetric.
-
-        Returns:
-            `bool`: `True` if the matrix is a symmetric matrix.
-
-        .. versionadded:: 0.2.0
-
-        """
-        cdef size_t        i
-        cdef size_t        j
-        cdef bint          symmetric = True
-        cdef const float** _matrix   = self.matrix_ptr()
-
-        with nogil:
-            for i in range(self._size):
-                for j in range(i + 1, self._size):
-                    if _matrix[i][j] != _matrix[j][i]:
-                        symmetric = False
-                        break
-        return symmetric
-
-    cpdef float min(self):
-        """Get the minimum score of the scoring matrix.
-
-        Example:
-            >>> blosum62 = ScoringMatrix.from_name("BLOSUM62")
-            >>> blosum62.min()
-            -4.0
-
-        """
-        assert self._data != NULL
-
-        cdef size_t i
-        cdef float  m = INFINITY
-
-        with nogil:
-            for i in range(self._nitems):
-                if self._data[i] < m:
-                    m = self._data[i]
-        return m
-
-    cpdef float max(self):
-        """Get the maximum score of the scoring matrix.
-
-        Example:
-            >>> blosum62 = ScoringMatrix.from_name("BLOSUM62")
-            >>> blosum62.max()
-            11.0
-
-        """
-        assert self._data != NULL
-        
-        cdef size_t i
-        cdef float  m = -INFINITY
-
-        with nogil:
-            for i in range(self._nitems):
-                if self._data[i] > m:
-                    m = self._data[i]
-        return m
-
-    cpdef ScoringMatrix shuffle(self, str alphabet):
-        """Shuffle the matrix using the new given alphabet.
-
-        The matrix name is retained only when the provided ``alphabet`` is a
-        permutation of the current alphabet, e.g. there is no loss of data.
-
-        Arguments:
-            alphabet (`str`): The new alphabet to use for the columns. It 
-                must be a subset of ``self.alphabet``.
-
-        Raises:
-            `KeyError`: When some required alphabet letters are missing from
-                the source matrix alphabet.
-
-        Example:
-            >>> m1 = ScoringMatrix.from_name("BLOSUM62")
-            >>> m1[1, 1]
-            5.0
-            >>> m1['R', 'R']
-            5.0
-            >>> m2 = m1.shuffle("ABCDEFGHIKLMNPQRSTVWXYZ*")
-            >>> m2[1, 1]
-            4.0
-            >>> m2['R', 'R']
-            5.0
-
-        """
-        cdef size_t i
-        cdef list   indices = []
-        cdef list   matrix  = []
-
-        for x in alphabet:
-            try:
-                indices.append(self.alphabet.index(x))
-            except ValueError:
-                raise KeyError(f"new alphabet contains unknown letter: {x!r}") from None
-
-        for letter in alphabet:
-            row = self[<str> letter]
-            matrix.append([row[j] for j in indices])
-
-        name = self.name if len(alphabet) == len(self.alphabet) else None
-        return type(self)(matrix, alphabet=alphabet, name=name)

scoring_matrices/matrices.pxd

-cdef extern from "matrices.h" nogil:
-    const char* _NAMES[]
-    const char* _ALPHABETS[]
-    const size_t _SIZES[]
-    const float* _MATRICES[]

scoring_matrices/py.typed

scoring_matrices/tests/__init__.py

-# noqa: D104
-
-from . import (
-    test_doctest,
-    test_scoring_matrix,
-)
-
-
-def load_tests(loader, suite, pattern):
-    test_doctest.load_tests(loader, suite, pattern)
-    suite.addTests(loader.loadTestsFromModule(test_scoring_matrix))
-    return suite

scoring_matrices/tests/test_doctest.py

-# coding: utf-8
-"""Test doctest contained tests in every file of the module.
-"""
-
-import configparser
-import doctest
-import importlib
-import os
-import pkgutil
-import re
-import shutil
-import sys
-import types
-import warnings
-from unittest import mock
-
-import scoring_matrices
-
-
-def _load_tests_from_module(tests, module, globs, setUp=None, tearDown=None):
-    """Load tests from module, iterating through submodules."""
-    for attr in (getattr(module, x) for x in dir(module) if not x.startswith("_")):
-        if isinstance(attr, types.ModuleType):
-            suite = doctest.DocTestSuite(
-                attr,
-                globs,
-                setUp=setUp,
-                tearDown=tearDown,
-                optionflags=+doctest.ELLIPSIS,
-            )
-            tests.addTests(suite)
-    return tests
-
-
-def load_tests(loader, tests, ignore):
-    """`load_test` function used by unittest to find the doctests."""
-    _current_cwd = os.getcwd()
-    # demonstrate how to use Biopython substitution matrices without
-    # actually requiring Biopython
-    Bio = mock.Mock()
-    Bio.Align = mock.Mock()
-    Bio.Align.substitution_matrices = mock.Mock()
-    Bio.Align.substitution_matrices.load = mock.Mock()
-    Bio.Align.substitution_matrices.load.return_value = feng = mock.Mock()
-
-    data = [ [-1 for _ in range(20)] for _ in range(20) ]
-    for i in range(20):
-        data[i][i] = 1
-
-    feng.alphabet = "ARNDCQEGHILKMFPSTWYV"
-    feng.__len__ = mock.Mock(return_value=20)
-    feng.__iter__ = mock.Mock(wraps=data.__iter__)
-
-    def setUp(self):
-        warnings.simplefilter("ignore")
-        # os.chdir(os.path.realpath(os.path.join(__file__, os.path.pardir, "data")))
-
-    def tearDown(self):
-        # os.chdir(_current_cwd)
-        warnings.simplefilter(warnings.defaultaction)
-
-    # doctests are not compatible with `green`, so we may want to bail out
-    # early if `green` is running the tests
-    if sys.argv[0].endswith("green"):
-        return tests
-
-    # recursively traverse all library submodules and load tests from them
-    packages = [None, scoring_matrices.lib]
-
-    for pkg in iter(packages.pop, None):
-        globs = dict(scoring_matrices=scoring_matrices, Bio=Bio, **pkg.__dict__)
-        tests.addTests(
-            doctest.DocTestSuite(
-                pkg,
-                globs=globs,
-                setUp=setUp,
-                tearDown=tearDown,
-                optionflags=+doctest.ELLIPSIS,
-            )
-        )
-
-    return tests

scoring_matrices/tests/test_scoring_matrix.py

-import pickle
-import unittest
-import sys
-
-from scoring_matrices import ScoringMatrix
-
-
-class TestScoringMatrix(unittest.TestCase):
-
-    def test_from_name_blosum50(self):
-        matrix = ScoringMatrix.from_name("BLOSUM50")
-        diagonal = [ matrix[i, i] for i in range(len(matrix)) ]
-        self.assertEqual(len(diagonal), 24)
-        self.assertEqual(diagonal, [5, 7, 7, 8, 13, 7, 6, 8, 10, 5, 5, 6, 7, 8, 10, 5, 5, 15, 8, 5, 5, 5 ,-1 ,1])
-
-    def test_from_name_blosum62(self):
-        matrix = ScoringMatrix.from_name("BLOSUM62")
-        diagonal = [ matrix[i, i] for i in range(len(matrix)) ]
-        self.assertEqual(len(diagonal), 24)
-        self.assertEqual(diagonal, [4, 5, 6, 6, 9, 5, 5, 6, 8, 4, 4, 5, 5, 6, 7, 4, 5, 11, 7, 4, 4, 4, -1, 1])
-
-    def test_from_name_invalid_name(self):
-        with self.assertRaises(ValueError):
-            aa = ScoringMatrix.from_name("nonsensical")
-
-    def test_from_str(self):
-        m1 = ScoringMatrix.from_str(
-            """
-                A   T   G   C
-            A   5  -4  -4  -4
-            T  -4   5  -4  -4
-            G  -4  -4   5  -4
-            C  -4  -4  -4   5
-            """.strip()
-        )
-        self.assertEqual(m1.alphabet, "ATGC")
-        self.assertEqual(m1['T', 'A'], -4.0)
-        self.assertEqual(m1['A', 'A'], 5.0)
-
-        m2 = ScoringMatrix.from_str(
-            """
-             A   T   G   C
-             5  -4  -4  -4
-            -4   5  -4  -4
-            -4  -4   5  -4
-            -4  -4  -4   5
-            """.strip()
-        )
-        self.assertEqual(m2.alphabet, "ATGC")
-        self.assertEqual(m2['T', 'A'], -4.0)
-        self.assertEqual(m2['A', 'A'], 5.0)
-
-    def test_from_diagonal(self):
-        m = ScoringMatrix.from_diagonal([1, 2, 3, 4], 0.0, alphabet="ATGC")
-        self.assertEqual(m[0], [1.0, 0.0, 0.0, 0.0])
-        self.assertEqual(m[1], [0.0, 2.0, 0.0, 0.0])
-        self.assertEqual(m[2], [0.0, 0.0, 3.0, 0.0])
-        self.assertEqual(m[3], [0.0, 0.0, 0.0, 4.0])
-
-        m = ScoringMatrix.from_diagonal([1, 2, 3, 4], -1.0, alphabet="ATGC")
-        self.assertEqual(m[0], [ 1.0, -1.0, -1.0, -1.0])
-        self.assertEqual(m[1], [-1.0,  2.0, -1.0, -1.0])
-        self.assertEqual(m[2], [-1.0, -1.0,  3.0, -1.0])
-        self.assertEqual(m[3], [-1.0, -1.0, -1.0,  4.0])
-
-    def test_from_diagonal_invalid_length(self):
-        self.assertRaises(
-            ValueError,
-            ScoringMatrix.from_diagonal,
-            [ 3, 3, 3, 3, 3, 3 ],
-            alphabet="ATGC"
-        )
-        self.assertRaises(
-            ValueError,
-            ScoringMatrix.from_diagonal,
-            [ 3, 3, 3 ],
-            alphabet="ATGC"
-        )
-
-    def test_list(self):
-        aa = ScoringMatrix.from_name("BLOSUM50")
-        matrix = list(aa)
-        columns = aa.alphabet
-        self.assertEqual(len(columns), 24)
-        self.assertEqual(len(matrix), 24)
-        for row in matrix:
-            self.assertEqual(len(row), 24)
-
-    @unittest.skipUnless(sys.implementation.name == "cpython", "memoryview not supported")
-    @unittest.skipUnless(sys.version_info >= (3, 9), "memoryview not supported")
-    def test_memoryview(self):
-        aa = ScoringMatrix.from_name("BLOSUM50")
-        mem = memoryview(aa)
-        self.assertEqual(mem.shape, (24, 24))
-        self.assertEqual(mem[0, 0], 5.0) # A <-> A
-        self.assertEqual(mem[6, 6], 6.0) # E <-> E
-
-    def test_init_empty(self):
-        m = ScoringMatrix([], alphabet="")
-        self.assertEqual(len(m), 0)
-        self.assertFalse(bool(m))
-
-    def test_init_invalid_length(self):
-        with self.assertRaises(ValueError):
-            m = ScoringMatrix(
-                [
-                    [0, 0, 0, 0],
-                    [0, 0, 0, 0],
-                    [0, 0, 0, 0],
-                ],
-                alphabet="ATGC",
-            )
-        with self.assertRaises(ValueError):
-            m = ScoringMatrix(
-                [
-                    [0, 0, 0, 0],
-                    [0, 0, 0, 0],
-                    [0, 0, 0, 0],
-                    [0, 0, 0],
-                ],
-                alphabet="ATGC",
-            )
-
-    def test_eq(self):
-        sm1 = ScoringMatrix.from_name("BLOSUM50")
-        sm2 = ScoringMatrix.from_name("BLOSUM50")
-        sm3 = ScoringMatrix.from_name("BLOSUM62")
-        self.assertEqual(sm1, sm1)
-        self.assertEqual(sm1, sm2)
-        self.assertNotEqual(sm1, sm3)
-        self.assertNotEqual(sm1, 12)
-
-    def test_pickle(self):
-        sm1 = ScoringMatrix.from_name("BLOSUM62")
-        sm2 = pickle.loads(pickle.dumps(sm1))
-        self.assertEqual(sm1.alphabet, sm2.alphabet)
-        self.assertEqual(list(sm1), list(sm2))
-
-    def test_shuffle_invalid_alphabet(self):
-        matrix = ScoringMatrix.from_name("BLOSUM62")
-        self.assertRaises(KeyError, matrix.shuffle, "ARNJOU")
-
-    def test_shuffle_empty(self):
-        matrix = ScoringMatrix.from_name("BLOSUM62")
-        empty = matrix.shuffle("")
-        self.assertEqual(len(empty), 0)
-        self.assertFalse(bool(empty))
-
-    def test_is_symmetric(self):
-        matrix = ScoringMatrix.from_name("PAM250")
-        self.assertTrue(matrix.is_symmetric())
-        matrix = ScoringMatrix([[1, 2, 3], [4, 5, 6], [7, 8, 9]], "ABC")
-        self.assertFalse(matrix.is_symmetric())

setup.cfg

-[metadata]
-name = scoring-matrices
-version = attr: scoring_matrices.__version__
-author = Martin Larralde
-author_email = [e-mail]
-url = https://github.com/althonos/score-matrices
-description = Dependency free, Cython-compatible scoring matrices to use with biological sequences.
-long_description = file: README.md
-long_description_content_type = text/markdown
-license = MIT
-platform = any
-keywords = bioinformatics, sequence, substitution, matrix, score
-classifier = 
-	Development Status :: 3 - Alpha
-	Intended Audience :: Developers
-	Intended Audience :: Science/Research
-	License :: OSI Approved :: MIT License
-	Operating System :: OS Independent
-	Programming Language :: C
-	Programming Language :: Cython
-	Programming Language :: Python :: 3.6
-	Programming Language :: Python :: 3.7
-	Programming Language :: Python :: 3.8
-	Programming Language :: Python :: 3.9
-	Programming Language :: Python :: 3.10
-	Programming Language :: Python :: 3.11
-	Programming Language :: Python :: 3.12
-	Programming Language :: Python :: Implementation :: CPython
-	Programming Language :: Python :: Implementation :: PyPy
-	Topic :: Scientific/Engineering :: Bio-Informatics
-	Typing :: Typed
-project_urls = 
-	Bug Tracker = https://github.com/althonos/scoring-matrices/issues
-	Changelog = https://github.com/althonos/scoring-matrices/blob/main/CHANGELOG.md
-	Coverage = https://codecov.io/gh/althonos/scoring-matrices/
-	Builds = https://github.com/althonos/scoring-matrices/actions
-
-[options]
-zip_safe = false
-packages = scoring_matrices, scoring_matrices.tests
-include_package_data = true
-python_requires = >=3.5
-setup_requires = 
-	setuptools >=46.4
-	cython ~=3.0
-
-[options.package_data]
-scoring_matrices = py.typed, *.pyi, *.pxd, *.h
-
-[coverage:run]
-plugins = Cython.Coverage
-include = scoring_matrices/*.py, scoring_matrices/lib.pyx
-
-[coverage:report]
-include = scoring_matrices/*
-omit = scoring_matrices/tests/*
-show_missing = true
-exclude_lines = 
-	pragma: no cover
-	if typing.TYPE_CHECKING:
-	@abc.abstractmethod
-	@abc.abstractproperty
-	raise NotImplementedError
-	return NotImplemented
-	raise MemoryError()
-
-[pydocstyle]
-inherit = false
-ignore = D102,D105,D200,D203,D213,D406,D407
-match-dir = (?!tests)(?!docs)[^\.].*
-match = (?!test)(?!setup)[^\._].*\.py
-
-[mypy]
-disallow_any_decorated = true
-disallow_any_generics = true
-disallow_any_unimported = false
-disallow_subclassing_any = false
-disallow_untyped_calls = true
-disallow_untyped_defs = true
-ignore_missing_imports = true
-warn_unused_ignores = true
-warn_return_any = true
-exclude = scoring_matrices/tests/*
-
-[mypy-scoring_matrices.tests]
-disallow_untyped_defs = false
-
-[isort]
-known_first_party = scoring_matrices
-known_standard_library = cpython, cython, _unicode
-known_third_party = libc, libcpp
-line_length = 88
-profile = black
-skip_gitignore = true
-
-[egg_info]
-tag_build = 
-tag_date = 0
-

setup.py

-import configparser
-import functools
-import ftplib
-import glob
-import itertools
-import io
-import json
-import multiprocessing.pool
-import os
-import platform
-import re
-import setuptools
-import setuptools.extension
-import subprocess
-import string
-import sys
-import sysconfig
-from distutils.command.clean import clean as _clean
-from distutils.errors import CompileError
-from setuptools.command.build_ext import build_ext as _build_ext
-from setuptools.command.sdist import sdist as _sdist
-from setuptools.extension import Extension
-
-try:
-    from Cython.Build import cythonize
-except ImportError as err:
-    cythonize = err
-
-
-# --- Utils ------------------------------------------------------------------
-
-def _eprint(*args, **kwargs):
-    print(*args, **kwargs, file=sys.stderr)
-
-
-def _split_multiline(value):
-    value = value.strip()
-    sep = max('\n,;', key=value.count)
-    return list(filter(None, map(lambda x: x.strip(), value.split(sep))))
-
-
-# --- Commands ------------------------------------------------------------------
-
-
-class sdist(_sdist):
-    """A `sdist` that generates a `pyproject.toml` on the fly."""
-
-    def run(self):
-        # generate score matrices
-        if not self.distribution.have_run.get("build_matrices", False):
-            _build_cmd = self.get_finalized_command("build_matrices")
-            _build_cmd.force = self.force
-            _build_cmd.run()
-        # build `pyproject.toml` from `setup.cfg`
-        c = configparser.ConfigParser()
-        c.add_section("build-system")
-        c.set("build-system", "requires", str(self.distribution.setup_requires))
-        c.set("build-system", "build-backend", '"setuptools.build_meta"')
-        with open("pyproject.toml", "w") as pyproject:
-            c.write(pyproject)
-        # run the rest of the packaging
-        _sdist.run(self)
-
-
-class build_matrices(setuptools.Command):
-
-    user_options = [
-        ('force', 'f', 'force generation of files'),
-        ('output=', 'o', 'output file to write'),
-        ('matrices=', 'm', 'matrices to generate'),
-    ]
-
-    def initialize_options(self) -> None:
-        self.force = False
-        self.output = None
-        self.matrices = None
-
-    def finalize_options(self) -> None:
-        self.folder = "data"
-        self.output = os.path.join("scoring_matrices", "matrices.h")
-        if self.matrices is not None:
-            self.matrices = _split_multiline(self.matrices)
-        else:
-            self.matrices = [
-                os.path.splitext(os.path.basename(mat))[0]
-                for mat in glob.glob(os.path.join(self.folder, "*.mat"))
-            ]
-
-    def run(self):
-        matrix_files = [ os.path.join(self.folder, f"{matrix}.mat") for matrix in self.matrices ]
-        self.make_file(matrix_files, self.output, self._generate_matrices, (matrix_files, self.output))
-
-    def _parse_matrix_file(self, matrix_file):
-        with open(matrix_file) as f:
-            lines = filter(
-                lambda line: line and not line.startswith("#"),
-                map(str.strip, f),
-            )
-            letters = ''.join(next(lines).split())
-            matrix = [
-                list(map(float, line.strip().split()[1:]))
-                for line in map(str.strip, lines)
-                if line
-            ]
-        return letters, matrix
-
-    def _generate_matrices(self, matrix_files, output_file):
-        matrices = {}
-        for matrix_file in matrix_files:
-            matrix_name = os.path.splitext(os.path.basename(matrix_file))[0].upper()
-            matrices[matrix_name] = self._parse_matrix_file(matrix_file)
-
-        with open(output_file, "w") as dst:
-            dst.write("#include <stddef.h>\n")
-            names = sorted(matrices.keys())
-            ids = [ name.replace(".", "_") for name in names ]
-           
-            dst.write(f"const char* _NAMES[{len(names) + 1}] = {{")
-            for name in names:
-                dst.write(f'"{name}", ')
-            dst.write("NULL };\n")
-
-            dst.write(f"const char* _ALPHABETS[{len(names) + 1}] = {{")
-            for name in names:
-                alphabet, _ = matrices[name]
-                dst.write(f'"{alphabet}", ')
-            dst.write("NULL };\n")
-
-            dst.write(f"const size_t _SIZES[{len(names) + 1}] = {{")
-            for name in names:
-                alphabet, _ = matrices[name]
-                dst.write(f'{len(alphabet)}, ')
-            dst.write("-1 };\n")
-
-            for i, (name, id_) in enumerate(zip(names, ids)):
-                alphabet, matrix = matrices[name]
-                nitems = len(matrix) * len(matrix)
-                dst.write(f"float _MATRIX_{id_}[{nitems}] = {{")
-                for i, item in enumerate(itertools.chain.from_iterable(matrix)):
-                    if i != 0:
-                        dst.write(", ")
-                    dst.write(f"{item!r}F")
-                dst.write("};\n")
-
-            dst.write(f"const float* _MATRICES[{len(names) + 1}] = {{")
-            for id_ in ids:
-                dst.write(f'_MATRIX_{id_}, ')
-            dst.write("NULL };\n")
-
-
-class build_ext(_build_ext):
-    """A `build_ext` that adds various SIMD flags and defines."""
-
-    # --- Compatibility with `setuptools.Command`
-
-    def initialize_options(self):
-        _build_ext.initialize_options(self)
-
-    def finalize_options(self):
-        _build_ext.finalize_options(self)
-        # check platform
-        if self.plat_name is None:
-            self.plat_name = sysconfig.get_platform()
-
-    # --- Autotools-like helpers ---
-
-    def _check_getid(self):
-        _eprint('checking whether `PyInterpreterState_GetID` is available')
-
-        base = "have_getid"
-        testfile = os.path.join(self.build_temp, "{}.c".format(base))
-        objects = []
-
-        self.mkpath(self.build_temp)
-        with open(testfile, "w") as f:
-            f.write("""
-            #include <stdint.h>
-            #include <stdlib.h>
-            #include <Python.h>
-
-            int main(int argc, char *argv[]) {{
-                PyInterpreterState_GetID(NULL);
-                return 0;
-            }}
-            """)
-
-        if self.compiler.compiler_type == "msvc":
-            flags = ["/WX"]
-        else:
-            flags = ["-Werror=implicit-function-declaration"]
-
-        try:
-            self.mkpath(self.build_temp)
-            objects = self.compiler.compile([testfile], extra_postargs=flags)
-        except CompileError:
-            _eprint("no")
-            return False
-        else:
-            _eprint("yes")
-            return True
-        finally:
-            os.remove(testfile)
-            for obj in filter(os.path.isfile, objects):
-                os.remove(obj)
-
-    # --- Build code ---
-
-    def build_extension(self, ext):
-        # show the compiler being used
-        _eprint("building", ext.name, "with", self.compiler.compiler_type, "compiler for platform", self.plat_name)
-
-        # add debug symbols if we are building in debug mode
-        if self.debug:
-            if self.compiler.compiler_type in {"unix", "cygwin", "mingw32"}:
-                ext.extra_compile_args.append("-g")
-            elif self.compiler.compiler_type == "msvc":
-                ext.extra_compile_args.append("/Z7")
-            if sys.implementation.name == "cpython":
-                ext.define_macros.append(("CYTHON_TRACE_NOGIL", 1))
-        else:
-            ext.define_macros.append(("CYTHON_WITHOUT_ASSERTIONS", 1))
-
-        # add Windows flags
-        if self.compiler.compiler_type == "msvc":
-            ext.define_macros.append(("WIN32", 1))
-
-        # build the rest of the extension as normal
-        ext._needs_stub = False
-
-        # compile extension in its own folder: since we need to compile
-        # `tantan.cc` several times with different flags, we cannot use the
-        # default build folder, otherwise the built object would be cached
-        # and prevent recompilation
-        _build_temp = self.build_temp
-        self.build_temp = os.path.join(_build_temp, ext.name)
-        _build_ext.build_extension(self, ext)
-        self.build_temp = _build_temp
-
-    def build_extensions(self):
-        # check `cythonize` is available
-        if isinstance(cythonize, ImportError):
-            raise RuntimeError(
-                "Cython is required to run `build_ext` command"
-            ) from cythonize
-
-        # generate score matrices
-        if not self.distribution.have_run.get("build_matrices", False):
-            _build_cmd = self.get_finalized_command("build_matrices")
-            _build_cmd.force = self.force
-            _build_cmd.run()
-
-        # use debug directives with Cython if building in debug mode
-        cython_args = {
-            "include_path": ["include"],
-            "compiler_directives": {
-                "cdivision": True,
-                "nonecheck": False,
-            },
-            "compile_time_env": {
-                "SYS_IMPLEMENTATION_NAME": sys.implementation.name,
-                "SYS_VERSION_INFO_MAJOR": sys.version_info.major,
-                "SYS_VERSION_INFO_MINOR": sys.version_info.minor,
-                "SYS_VERSION_INFO_MICRO": sys.version_info.micro,
-                "DEFAULT_BUFFER_SIZE": io.DEFAULT_BUFFER_SIZE,
-            },
-        }
-        if self.force:
-            cython_args["force"] = True
-        if self.debug:
-            cython_args["annotate"] = True
-            cython_args["compiler_directives"]["cdivision_warnings"] = True
-            cython_args["compiler_directives"]["warn.undeclared"] = True
-            cython_args["compiler_directives"]["warn.unreachable"] = True
-            cython_args["compiler_directives"]["warn.maybe_uninitialized"] = True
-            cython_args["compiler_directives"]["warn.unused"] = True
-            cython_args["compiler_directives"]["warn.unused_arg"] = True
-            cython_args["compiler_directives"]["warn.unused_result"] = True
-            cython_args["compiler_directives"]["warn.multiple_declarators"] = True
-        else:
-            cython_args["compiler_directives"]["boundscheck"] = False
-            cython_args["compiler_directives"]["wraparound"] = False
-
-        # check if `PyInterpreterState_GetID` is defined
-        if self._check_getid():
-            self.compiler.define_macro("HAS_PYINTERPRETERSTATE_GETID", 1)
-
-        # cythonize the extensions
-        self.extensions = cythonize(self.extensions, **cython_args)
-
-        # build the extensions as normal
-        _build_ext.build_extensions(self)
-
-
-class clean(_clean):
-    """A `clean` that removes intermediate files created by Cython."""
-
-    def run(self):
-
-        source_dir = os.path.join(os.path.dirname(__file__), "pytantan")
-
-        patterns = ["*.html"]
-        if self.all:
-            patterns.extend(["*.so", "*.c", "*.cpp"])
-
-        for pattern in patterns:
-            for file in glob.glob(os.path.join(source_dir, pattern)):
-                _eprint("removing {!r}".format(file))
-                os.remove(file)
-
-        for ext in self.distribution.ext_modules:
-            for source_file in ext.sources:
-                if source_file.endswith(".pyx"):
-                    ext = ".cpp" if ext.language == "c++" else ".c"
-                    c_file = source_file.replace(".pyx", ext)
-                    if os.path.exists(c_file):
-                        _eprint("removing {!r}".format(c_file))
-                        os.remove(c_file)
-
-        _clean.run(self)
-
-
-# --- Setup ---------------------------------------------------------------------
-
-setuptools.setup(
-    ext_modules=[
-        Extension(
-            "scoring_matrices.lib",
-            language="c",
-            include_dirs=["scoring_matrices"],
-            sources=[os.path.join("scoring_matrices", "lib.pyx")],
-        ),
-    ],
-    cmdclass={
-        "sdist": sdist,
-        "build_ext": build_ext,
-        "build_matrices": build_matrices,
-        "clean": clean,
-    },
-)

Alert delta unavailable

Currently unable to show alert delta for PyPI packages.

Improved metrics

Number of package files

120

445.45%

Lines of code

564

2.55%

Worsened metrics

Total package byte prevSize

280335

-23.52%