pyinfernal 0.1.0__tar.gz

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

@@ -0,0 +1,217 @@
+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: true
+  #   - name: Build manylinux wheels
+  #     uses: pypa/cibuildwheel@v3.2.1
+  #     env:
+  #       CIBW_ARCHS: aarch64
+  #       CIBW_BUILD: 'cp*-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: true
+    - name: Build manylinux wheels
+      uses: pypa/cibuildwheel@v3.2.1
+      env:
+        CIBW_ARCHS: x86_64
+        CIBW_BUILD: 'cp*-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: true
+  #   - name: Build manylinux wheels
+  #     uses: pypa/cibuildwheel@v3.2.1
+  #     env:
+  #       CIBW_ARCHS: x86_64
+  #       CIBW_BUILD: 'cp*-macosx_x86_64'
+  #       CIBW_BUILD_VERBOSITY: 2
+  #     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: true
+  #   - name: Build manylinux wheels
+  #     uses: pypa/cibuildwheel@v3.2.1
+  #     env:
+  #       CIBW_ARCHS: arm64
+  #       CIBW_BUILD: 'cp*-macosx_arm64'
+  #       CIBW_BUILD_VERBOSITY: 2
+  #     with:
+  #       output-dir: dist
+  #   - uses: actions/upload-artifact@v4
+  #     with:
+  #       name: wheels-macosx_arm64
+  #       path: dist/*
+
+  sdist:
+    runs-on: ubuntu-latest
+    name: Build source distribution
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+      with:
+        submodules: true
+    - 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 wheel distribution
+      run: python -m build --sdist
+    - name: Store built wheels
+      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 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 pyinfernal --find-links=dist pyinfernal
+    - name: Run tests without coverage
+      run: python -m unittest pyinfernal.tests -vv
+
+  upload:
+    environment: PyPI
+    runs-on: ubuntu-latest
+    name: Upload
+    permissions:
+      id-token: write
+    needs:
+    - sdist
+    - test-sdist
+    # - wheel-linux-aarch64
+    - wheel-linux-x86_64
+    # - wheel-macos-x86_64
+    # - wheel-macos-aarch64
+    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
+      if: "!contains(github.ref, 'rc') && !contains(github.ref, 'alpha') && !contains(github.ref, 'dev')"  # don't upload wheels for alpha/dev/rc releases
+      with:
+        pattern: wheels-*
+        path: dist/
+        merge-multiple: true
+    - name: Publish distributions to PyPI
+      if: startsWith(github.ref, 'refs/tags/v')
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  release:
+    permissions: write-all
+    environment: GitHub Releases
+    runs-on: ubuntu-latest
+    if: "startsWith(github.ref, 'refs/tags/v')"
+    name: Release
+    needs: upload
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+    - name: Release a Changelog
+      uses: rasmus-saks/release-a-changelog-action@v1.2.0
+      with:
+        github-token: '${{ secrets.GITHUB_TOKEN }}'
+
+  # aur:
+  #   environment: Arch Linux User Repository
+  #   runs-on: ubuntu-latest
+  #   if: "!contains(github.ref, 'rc') && !contains(github.ref, 'alpha') && && !contains(github.ref, 'dev') && !contains(github.ref, 'post')"
+  #   name: Update AUR package
+  #   needs:
+  #   - sdist
+  #   - upload
+  #   steps:
+  #   - name: Checkout code
+  #     uses: actions/checkout@v4
+  #     with:
+  #       submodules: true
+  #   - name: Set up Python 3.12
+  #     uses: actions/setup-python@v5
+  #     with:
+  #       python-version: 3.12
+  #   - name: Download source distribution
+  #     uses: actions/download-artifact@v4
+  #     with:
+  #       name: sdist
+  #       path: dist/
+  #       merge-multiple: true
+  #   - name: Extract package version
+  #     run: echo PKGVER=$(echo '${{ github.ref }}' | cut -d'v' -f2) >> $GITHUB_ENV
+  #   - name: Compute SHA256 of source distribution
+  #     run: "echo SHA256=$(sha256sum dist/pyinfernal-${{ 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@v3.0.1
+  #     with:
+  #       pkgname: python-pyinfernal
+  #       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 }}

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

@@ -0,0 +1,20 @@
+# build dependencies
+cython ~=3.0
+scikit-build-core
+ninja
+
+# run dependencies
+pyhmmer ~=0.12.0a1
+psutil >=5.0,<8.0 ; python_version >= '3.9'
+psutil >=5.0,<7.0 ; python_version <= '3.8'
+
+# test dependencies
+importlib-resources ; python_version < '3.9'
+
+# coverage dependencies
+coverage ~=4.0 ; python_version == '3.6'
+coverage ~=7.0 ; python_version >= '3.7'
+
+# deployment dependencies
+build
+auditwheel

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

@@ -0,0 +1,173 @@
+name: Test
+
+on:
+  - push
+  - pull_request
+
+jobs:
+
+  test_linux_x86:
+    name: Test (Linux)
+    runs-on: ubuntu-latest
+    env:
+      OS: Linux
+    strategy:
+      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: true
+    - name: Setup Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Show Python build environment
+      run: python -m sysconfig
+    - 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: pip install -vv -e . --no-build-isolation
+    - name: Test without coverage
+      run: python -m unittest pyinfernal.tests -vv
+    #- name: Upload to Codecov
+    #  if: matrix.python-impl == 'CPython'
+    #  uses: codecov/codecov-action@v3
+    #  with:
+    #    flags: ${{ matrix.python-release }}
+    #    env_vars: OS
+    #    name: test-python-${{ matrix.python-version }}
+    #    fail_ci_if_error: false
+    #    token: ${{ secrets.CODECOV_TOKEN }}
+    #    verbose: true
+
+#  test_linux_arm64:
+#    name: Test (Linux, arm64)
+#    runs-on: ubuntu-22.04-arm
+#    strategy:
+#      matrix:
+#        python-tag:
+#        - cp310-manylinux_aarch64
+#        - cp311-manylinux_aarch64
+#    steps:
+#    - uses: actions/checkout@v4
+#      with:
+#        submodules: true
+#    - 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 pyinfernal.tests -vv
+#        CIBW_TEST_REQUIRES: importlib-resources
+#      with:
+#        output-dir: dist
+#    - uses: actions/upload-artifact@v3
+#      with:
+#        name: wheels
+#        path: dist/*
+
+  test_osx_x86:
+    name: Test (OSX)
+    runs-on: macos-latest
+    env:
+      OS: OSX
+    strategy:
+      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: true
+    - name: Setup Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Show Python build environment
+      run: python -m sysconfig
+    - 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: pip install -vv -e . --no-build-isolation
+    - name: Test without coverage
+      run: python -m unittest pyinfernal.tests -vv
+    # - name: Upload to Codecov
+    #   uses: codecov/codecov-action@v4
+    #   if: matrix.python-impl == 'CPython'
+    #   with:
+    #     flags: ${{ matrix.python-release }}
+    #     env_vars: OS
+    #     name: test-python-${{ matrix.python-version }}
+    #     fail_ci_if_error: false
+    #     token: ${{ secrets.CODECOV_TOKEN }}
+    #     codecov_curl_args: "--globoff"
+    #     verbose: true
+

pyinfernal-0.1.0/.gitignore

@@ -0,0 +1,180 @@
+# Created by https://www.gitignore.io/api/python,c
+# Edit at https://www.gitignore.io/?templates=python,c
+
+.vscode
+*.BAK
+
+### 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.*
+
+# Mprof files
+mprofile_*
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+pyhmmer/*.c
+pyhmmer/*.html
+
+# Cython
+cython_debug/
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+wheelhouse/
+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/
+
+# Jupyter notebooks
+.ipynb_checkpoints/
+
+# End of https://www.gitignore.io/api/python,c

pyinfernal-0.1.0/.gitmodules

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

pyinfernal-0.1.0/.readthedocs.yaml

@@ -0,0 +1,28 @@
+# 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: "3.11"
+
+# 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: .

pyinfernal-0.1.0/CHANGELOG.md

@@ -0,0 +1,14 @@
+# 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/pyinfernal/compare/v0.1.0...HEAD
+
+## [v0.1.0] - 2026-01-24	
+[Unreleased]: https://github.com/althonos/pyinfernal/compare/2cce19c...v0.1.0
+
+Initial release.

pyinfernal-0.1.0/CMakeLists.txt

@@ -0,0 +1,29 @@
+cmake_minimum_required(VERSION 3.20)
+project(${SKBUILD_PROJECT_NAME} VERSION ${SKBUILD_PROJECT_VERSION} LANGUAGES C)
+
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/src/scripts/cmake")
+
+# --- Find PyHMMER -------------------------------------------------------------
+
+find_package(PyHMMER CONFIG REQUIRED)
+set(HMMER_IMPL "${PyHMMER_HMMER_IMPL}")
+set(INFERNAL_IMPL "${PyHMMER_HMMER_IMPL}")
+
+# --- Setup Python folders -----------------------------------------------------
+
+cmake_path(APPEND CMAKE_CURRENT_LIST_DIR "src" OUTPUT_VARIABLE SRC_DIR)
+set_property(GLOBAL PROPERTY PYTHON_EXTENSIONS_SOURCE_DIR "${SRC_DIR}")
+cmake_path(APPEND CMAKE_CURRENT_LIST_DIR "include" OUTPUT_VARIABLE CYTHON_HEADERS_DIR)
+
+# Install shared library objects to `pyinfernal.libs` (like auditwheel repair)
+if(PYINFERNAL_INSTALL_LIBS)
+    set(PYINFERNAL_INSTALL_LIBS_DIR "${CMAKE_PROJECT_NAME}.libs")
+    message(STATUS "Installing shared libraries to ${PYINFERNAL_INSTALL_LIBS_DIR}")
+    install(DIRECTORY ${CYTHON_HEADERS_DIR} DESTINATION ${PYINFERNAL_INSTALL_LIBS_DIR})
+endif()
+
+# --- Compile source code ------------------------------------------------------
+
+add_subdirectory(src)

pyinfernal-0.1.0/CONTRIBUTING.md

@@ -0,0 +1,40 @@
+# Contributing to PyInfernal
+
+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
+
+Make sure you clone the repository in recursive mode, so you also get the
+wrapped code of Infernal, which are exposed as `git` submodules:
+
+```console
+$ git clone --recursive https://github.com/althonos/pyinfernal
+```
+
+## 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 -e . -v --no-build-isolation
+$ python -m unittest pyinfernal.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) or in variable assignments (supported from Python 3.6
+onward). 
+
+### Interfacing with C
+
+When interfacing with C, and in particular with pointers, use assertions
+everywhere you assume the pointer to be non-NULL.