pycdhit4 0.1.0__tar.gz

pycdhit4-0.1.0/.github/workflows/package.yml

@@ -0,0 +1,266 @@
+name: Package
+
+on:
+  push:
+    tags:
+      - v*
+
+jobs:
+
+  wheel-linux-aarch64:
+    name: Build Linux wheels (Aarch64)
+    runs-on: ubuntu-22.04-arm
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+    - name: Build manylinux wheels
+      uses: pypa/cibuildwheel@v4.3.5
+      env:
+        CIBW_ARCHS: aarch64
+        CIBW_BUILD: '*-manylinux_aarch64'
+        CIBW_BUILD_VERBOSITY: 2
+      with:
+        output-dir: dist
+    - uses: actions/upload-artifact@v4
+      with:
+        name: wheels-manylinux_aarch64
+        path: dist/*
+
+  wheel-linux-x86_64:
+    name: Build Linux wheels (x86-64)
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - name: Build manylinux wheels
+      uses: pypa/cibuildwheel@v4.3.5
+      env:
+        CIBW_ARCHS: x86_64
+        CIBW_BUILD: '*-manylinux_x86_64'
+        CIBW_BUILD_VERBOSITY: 2
+      with:
+        output-dir: dist
+    - uses: actions/upload-artifact@v4
+      with:
+        name: wheels-manylinux_x86_64
+        path: dist/*
+
+  wheel-macos-x86_64:
+    name: Build MacOS wheels (x86-64)
+    runs-on: macOS-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - name: Build manylinux wheels
+      uses: pypa/cibuildwheel@v4.3.5
+      env:
+        CIBW_ARCHS: x86_64
+        CIBW_BUILD: '*-macosx_x86_64'
+        CIBW_BUILD_VERBOSITY: 2
+        MACOSX_DEPLOYMENT_TARGET: 11.0
+      with:
+        output-dir: dist
+    - uses: actions/upload-artifact@v4
+      with:
+        name: wheels-macosx_x86_64
+        path: dist/*
+
+  wheel-macos-aarch64:
+    name: Build MacOS wheels (Aarch64)
+    runs-on: macOS-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - name: Build manylinux wheels
+      uses: pypa/cibuildwheel@v4.3.5
+      env:
+        CIBW_ARCHS: arm64
+        CIBW_BUILD: '*-macosx_arm64'
+        CIBW_BUILD_VERBOSITY: 2
+      with:
+        output-dir: dist
+    - uses: actions/upload-artifact@v4
+      with:
+        name: wheels-macosx_arm64
+        path: dist/*
+
+  wheel-win32-x86_64:
+    name: Build Windows wheels (x86-64)
+    runs-on: windows-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - name: Configure build for amd64
+      uses: ilammy/msvc-dev-cmd@v1
+      with:
+        arch: amd64
+    - name: Build manylinux wheels
+      uses: pypa/cibuildwheel@v4.3.5
+      env:
+        CIBW_ARCHS: AMD64
+        CIBW_BUILD: '*-win_amd64'
+        CIBW_BUILD_VERBOSITY: 2
+        CMAKE_GENERATOR: Ninja
+      with:
+        output-dir: dist
+    - uses: actions/upload-artifact@v4
+      with:
+        name: wheels-win_amd64
+        path: dist/*
+
+  wheel-wasm:
+    name: Build WebAssembly wheel
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+    - name: Set up Python 3.13
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.13
+    - name: Install Pyodide
+      run: python -m pip install pyodide-build
+    - name: Build wheel
+      run: pyodide build .
+    - name: Create virtualenv
+      run: pyodide venv .venv-pyodide
+    - name: Install WebAssembly wheel
+      run: .venv-pyodide/bin/pip install dist/pycdhit4-*.whl
+    - name: Run tests
+      run: .venv-pyodide/bin/python -m unittest pycdhit4.tests -vv
+    - uses: actions/upload-artifact@v4
+      with:
+        name: wheels-wasm
+        path: dist/*
+
+  sdist:
+    runs-on: ubuntu-latest
+    name: Build source distribution
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.12
+    - 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 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.12
+    - name: Download built wheels
+      uses: actions/download-artifact@v4
+      with:
+          name: sdist
+          path: dist/
+    - name: Update pip to latest version
+      run: python -m pip install -U pip
+    - name: Install built wheel
+      run: python -m pip install --no-binary pycdhit4 --find-links=dist pycdhit4
+    - name: Run tests without coverage
+      run: python -m unittest pycdhit4.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
+    - wheel-wasm
+    steps:
+    - uses: actions/download-artifact@v4
+      with:
+        name: sdist
+        path: dist
+        merge-multiple: true
+    - 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: recursive
+    - uses: rasmus-saks/release-a-changelog-action@v1.2.0
+      with:
+        github-token: '${{ secrets.GITHUB_TOKEN }}'
+
+  # aur:
+  #   environment: Arch User Repository
+  #   runs-on: ubuntu-latest
+  #   if: "!contains(github.ref, 'alpha') && !contains(github.ref, 'rc') && !contains(github.ref, 'post')"
+  #   name: Update AUR package
+  #   needs:
+  #   - sdist
+  #   - test-sdist
+  #   - upload
+  #   steps:
+  #   - uses: actions/checkout@v3
+  #     with:
+  #       submodules: recursive
+  #   - name: Set up Python 3.13
+  #     uses: actions/setup-python@v5
+  #     with:
+  #       python-version: '3.13'
+  #   - name: Download source distribution
+  #     uses: actions/download-artifact@v4
+  #     with:
+  #       name: sdist
+  #       path: dist
+  #   - name: Extract package version
+  #     run: echo PKGVER=$(echo '${{ github.ref }}' | cut -d'v' -f2) >> $GITHUB_ENV
+  #   - name: Compute SHA256 of source distribution
+  #     run: echo SHA256=$(sha256sum dist/pycdhit4-${{ 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-pycdhit4
+  #       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 }}
+  #       ssh_keyscan_types: rsa,ecdsa,ed25519

pycdhit4-0.1.0/.github/workflows/requirements.txt

@@ -0,0 +1,7 @@
+# coverage ~=7.0
+cython ~=3.0
+# semantic-version ~=2.10
+scikit-build-core
+build
+importlib-resources ; python_version < '3.9'
+scoring-matrices ~=0.3.0

pycdhit4-0.1.0/.github/workflows/test.yml

@@ -0,0 +1,202 @@
+name: Test
+
+on:
+  - push
+  - pull_request
+
+jobs:
+
+  test_linux:
+    name: Test (Linux)
+    runs-on: ubuntu-latest
+    env:
+      OS: Linux
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - 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: 3.13
+          python-release: v3.13
+          python-impl: CPython
+        - python-version: 3.14
+          python-release: v3.14
+          python-impl: CPython
+        - 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: recursive
+    - 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 extension in debug mode
+      run: python -m pip install -v -e . --no-build-isolation
+    - name: Test extension
+      run: python -m unittest pycdhit.tests -vv
+    # - name: Upload to Codecov
+    #   if: matrix.python-impl == 'CPython'
+    #   uses: codecov/codecov-action@v3
+    #   with:
+    #     flags: ${{ matrix.python-impl }},${{ matrix.python-release }},${{ env.OS }}
+    #     name: test-python-${{ matrix.python-version }}
+    #     fail_ci_if_error: true
+    #     token: ${{ secrets.CODECOV_TOKEN }}
+
+  test_osx:
+    name: Test (OSX)
+    runs-on: macos-latest
+    env:
+      OS: OSX
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - 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: '3.14'
+          python-release: v3.13
+          python-impl: CPython
+        - python-version: '3.14'
+          python-release: v3.13
+          python-impl: CPython
+        - 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: recursive
+    - name: Setup Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    # - name: Setup deployment target
+    #   shell: bash
+    #   if: ${{ startsWith(matrix.python-version, 'pypy') || matrix.python-version == '3.11' || matrix.python-version == '3.12' }}
+    #   run: echo "MACOSX_DEPLOYMENT_TARGET=10.12" >> $GITHUB_ENV
+    - name: Update pip
+      run: python -m pip install -U pip wheel setuptools
+    - name: Install Python requirements
+      run: python -m pip install -r .github/workflows/requirements.txt
+
+    - name: Install LLVM
+      run: brew install llvm
+    - name: Build extension in debug mode
+      run: python -m pip install -v -e . --no-build-isolation -C cmake.define.CMAKE_C_COMPILER=$(brew --prefix llvm)/bin/clang -C cmake.define.CMAKE_CXX_COMPILER=$(brew --prefix llvm)/bin/clang++
+    - name: Test extension
+      run: python -m unittest pycdhit.tests -vv
+    # - name: Upload to Codecov
+    #   if: matrix.python-impl == 'CPython'
+    #   uses: codecov/codecov-action@v3
+    #   with:
+    #     flags: ${{ matrix.python-impl }},${{ matrix.python-release }},${{ env.OS }}
+    #     name: test-python-${{ matrix.python-version }}
+    #     fail_ci_if_error: true
+    #     token: ${{ secrets.CODECOV_TOKEN }}
+
+  test_windows:
+    name: Test (Windows)
+    runs-on: windows-latest
+    env:
+      OS: Windows
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - python-version: 3.8
+          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: '3.13'
+          python-release: v3.13
+          python-impl: CPython
+        - python-version: '3.14'
+          python-release: v3.14
+          python-impl: CPython
+        - 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: recursive
+    - 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 extension in debug mode
+      run: python -m pip install -v . --no-build-isolation
+    - name: Test extension
+      run: python -m unittest pycdhit.tests -vv

pycdhit4-0.1.0/.gitignore

@@ -0,0 +1,171 @@
+
+### Cython ###
+
+# 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

pycdhit4-0.1.0/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "vendor/cdhit"]
+	path = vendor/cdhit
+	url = https://github.com/weizhongli/cdhit

pycdhit4-0.1.0/CHANGELOG.md

@@ -0,0 +1,15 @@
+# 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/pycdhit4/compare/v0.1.0...HEAD
+
+
+## [v0.1.0] - 2026-11-08
+[v0.1.0]: https://github.com/althonos/pycdhit4/compare/ee06510...v0.1.0
+
+Initial release.

pycdhit4-0.1.0/CMakeLists.txt

@@ -0,0 +1,24 @@
+cmake_minimum_required(VERSION 3.20)
+project(${SKBUILD_PROJECT_NAME} VERSION ${SKBUILD_PROJECT_VERSION} LANGUAGES C CXX)
+
+set(BUILD_SHARED_LIBS OFF)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+set(CMAKE_CXX_STANDARD 20)
+set(CMAKE_CXX_STANDARD_REQUIRED TRUE)
+
+message(STATUS "Building ${SKBUILD_PROJECT_NAME} for ${CMAKE_SYSTEM_PROCESSOR}")
+
+# --- Setup include folders ----------------------------------------------------
+
+set_property(GLOBAL PROPERTY PYTHON_EXTENSIONS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
+set(CYTHON_HEADERS_DIR ${CMAKE_CURRENT_LIST_DIR}/include)
+
+# --- Add scripts for Cython ---------------------------------------------------
+
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/src/scripts/cmake")
+include(CythonExtension)
+
+# --- Compile code -------------------------------------------------------------
+
+add_subdirectory("src")