scoring-matrices - npm Package Compare versions

Comparing version 0.3.0 to 0.3.1

docs/.gitignore

+related.rst

docs/guide/matrices.rst

+Matrices
+========
+
+.. currentmodule:: scoring_matrices
+
+The following matrices are distributed with the ``scoring-matrices`` package
+and can be loaded with `ScoringMatrix.from_name`:
+
+
+3DI
+    3di structural alphabet scoring matrix used in Foldseek.
+
+    .. versionadded:: 0.3.1
+
+BENNER6, BENNER22, BENNER74
+    Matrices proposed in Benner, Cohen and Gonnet (1994). 
+
+BLOSUM30, BLOSUM35, BLOSUM40, BLOSUM45, BLOSUM50, BLOSUM55, BLOSUM60, BLOSUM62, BLOSUM65, BLOSUM70, BLOSUM75, BLOSUM80, BLOSUM85, BLOSUM90, BLOSUM100, BLOSUMN
+    BLOcks SUbstitution Matrix series, computed by Henikoff (1992) from databases
+    of local alignments. BLOSUM62 is the default matrix used in the 
+    BLAST algorithm.
+
+DAYHOFF
+    An alias for the PAM-250 with additional B, Z, X and \* scores.
+
+GONNET 
+    PAM 250 matrix recommended by Gonnet, Cohen & Benner (1992).
+
+NUC.4.4 
+    The extended DNA scoring matrix (sometimes also EDNAFULL) created by
+    Todd Lowe (1992).
+
+PAM10, PAM20, PAM30, PAM40, PAM50, PAM60, PAM70, PAM80, PAM90, PAM100, PAM110, PAM120, PAM130, PAM140, PAM150, PAM160, PAM170, PAM180, PAM190, PAM200, PAM210, PAM220, PAM230, PAM240, PAM250, PAM260, PAM270, PAM280, PAM290, PAM300, PAM310, PAM320, PAM330, PAM340, PAM350, PAM360, PAM370, PAM380, PAM390, PAM400, PAM410, PAM420, PAM430, PAM440, PAM450, PAM460, PAM470, PAM480, PAM490, PAM500
+    Point-Accepted Mutation matrix series computed by Dayhoff (1966).
+
+VTML10, VTML20, VTML40, VTML80, VTML120, VTML160
+    Matrices computed with the *resolvent method* developed by Müller and Vingron
+    to improve estimation of exchange frequencies. VTML80 is used by MMseqs2
+    for the k-mer generation process.
+

.github/workflows/package.yml

@@ -12,16 +12,3 @@ name: Package
     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
+    runs-on: ubuntu-22.04-arm
     steps:
@@ -31,16 +18,8 @@ - uses: actions/checkout@v4
         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
+      uses: pypa/cibuildwheel@v3.0.0
       env:
         CIBW_ARCHS: aarch64
-        CIBW_BUILD: ${{ matrix.python-tag }}
+        CIBW_BUILD: '*-manylinux_aarch64'
         CIBW_BUILD_VERBOSITY: 2
-        CIBW_BEFORE_BUILD: pip install cython
-        CIBW_TEST_COMMAND: python -m unittest scoring_matrices.tests -vv
-        CIBW_TEST_REQUIRES: importlib-resources
       with:
@@ -50,3 +29,3 @@ output-dir: dist
       with:
-        name: wheels-${{ matrix.python-tag }}
+        name: wheels-linux-aarch64
         path: dist/*
@@ -56,16 +35,3 @@
     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
+    runs-on: ubuntu-22.04
     steps:
@@ -80,10 +46,7 @@ - uses: actions/checkout@v4
     - name: Build manylinux wheels
-      uses: pypa/cibuildwheel@v2.16.5
+      uses: pypa/cibuildwheel@v3.0.0
       env:
         CIBW_ARCHS: x86_64
-        CIBW_BUILD: ${{ matrix.python-tag }}
-        CIBW_BEFORE_BUILD: pip install cython
+        CIBW_BUILD: '*-manylinux_x86_64'
         CIBW_BUILD_VERBOSITY: 2
-        CIBW_TEST_COMMAND: python -m unittest scoring_matrices.tests -vv
-        CIBW_TEST_REQUIRES: importlib-resources
       with:
@@ -93,3 +56,3 @@ output-dir: dist
       with:
-        name: wheels-${{ matrix.python-tag }}
+        name: wheels-linux-x86_64
         path: dist/*
@@ -99,16 +62,3 @@
     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
+    runs-on: macOS-latest
     steps:
@@ -123,11 +73,7 @@ - uses: actions/checkout@v4
     - name: Build manylinux wheels
-      uses: pypa/cibuildwheel@v2.16.5
+      uses: pypa/cibuildwheel@v3.0.0
       env:
         CIBW_ARCHS: x86_64
-        CIBW_BUILD: ${{ matrix.python-tag }}
-        CIBW_BEFORE_BUILD: pip install cython
+        CIBW_BUILD: '*-macosx_x86_64'
         CIBW_BUILD_VERBOSITY: 2
-        CIBW_TEST_COMMAND: python -m unittest scoring_matrices.tests -vv
-        CIBW_TEST_REQUIRES: importlib-resources
-        CIBW_ENVIRONMENT_MACOS: MACOSX_DEPLOYMENT_TARGET=10.12
       with:
@@ -137,3 +83,3 @@ output-dir: dist
       with:
-        name: wheels-${{ matrix.python-tag }}
+        name: wheels-macos-x86_64
         path: dist/*
@@ -143,11 +89,3 @@
     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
+    runs-on: macOS-latest
     steps:
@@ -163,10 +101,7 @@ - uses: actions/checkout@v4
     - name: Build manylinux wheels
-      uses: pypa/cibuildwheel@v2.16.5
+      uses: pypa/cibuildwheel@v3.0.0
       env:
         CIBW_ARCHS: arm64
-        CIBW_BUILD: ${{ matrix.python-tag }}
-        CIBW_BEFORE_BUILD: pip install cython
+        CIBW_BUILD: '*-macosx_arm64'
         CIBW_BUILD_VERBOSITY: 2
-        CIBW_TEST_COMMAND: python -m unittest scoring_matrices.tests -vv
-        CIBW_TEST_REQUIRES: importlib-resources
       with:
@@ -176,3 +111,3 @@ output-dir: dist
       with:
-        name: wheels-${{ matrix.python-tag }}
+        name: wheels-wheels-macos-aarch64
         path: dist/*
@@ -182,16 +117,3 @@
     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
+    runs-on: windows-latest
     steps:
@@ -206,10 +128,7 @@ - uses: actions/checkout@v4
     - name: Build manylinux wheels
-      uses: pypa/cibuildwheel@v2.16.5
+      uses: pypa/cibuildwheel@v3.0.0
       env:
         CIBW_ARCHS: AMD64
-        CIBW_BUILD: ${{ matrix.python-tag }}
-        CIBW_BEFORE_BUILD: pip install cython
+        CIBW_BUILD: '*-win_amd64'
         CIBW_BUILD_VERBOSITY: 2
-        CIBW_TEST_COMMAND: python -m unittest scoring_matrices.tests -vv
-        CIBW_TEST_REQUIRES: importlib-resources
       with:
@@ -219,3 +138,3 @@ output-dir: dist
       with:
-        name: wheels-${{ matrix.python-tag }}
+        name: wheels-win32-x86_64
         path: dist/*
@@ -230,6 +149,6 @@
         submodules: true
-    - name: Set up Python 3.11
+    - name: Set up Python 3.13
       uses: actions/setup-python@v2
       with:
-        python-version: 3.11
+        python-version: 3.13
     - name: Install build requirements
@@ -251,6 +170,6 @@ run: python -m pip install -r .github/workflows/requirements.txt
     steps:
-    - name: Setup Python 3.11
+    - name: Setup Python 3.13
       uses: actions/setup-python@v2
       with:
-        python-version: '3.11'
+        python-version: '3.13'
     - name: Download source distribution
@@ -325,15 +244,16 @@ uses: actions/download-artifact@v4
         submodules: true
-    - name: Set up Python 3.11
+    - name: Set up Python 3.13
       uses: actions/setup-python@v2
       with:
-        python-version: '3.11'
-    - name: Download built wheels
-      uses: actions/download-artifact@v2
+        python-version: '3.13'
+    - name: Download source distribution
+      uses: actions/download-artifact@v4
       with:
-          name: sdist
-          path: dist
+        name: sdist
+        path: dist/
+        merge-multiple: true
     - name: Extract package version
-      run: echo PKGVER=${{ github.ref }} >> $GITHUB_ENV
+      run: echo PKGVER=$(echo '${{ github.ref }}' | cut -d'v' -f2) >> $GITHUB_ENV
     - name: Compute SHA256 of source distribution
-      run: echo SHA256=$(sha256sum dist/scoring-matrices-${{ env.PKGVER }}.tar.gz | cut -f1 -d' ') >> $GITHUB_ENV
+      run: echo SHA256=$(sha256sum dist/scoring_matrices-${{ env.PKGVER }}.tar.gz | cut -f1 -d' ') >> $GITHUB_ENV
     - name: Generate PKGBUILD
@@ -340,0 +260,0 @@ run: sed -e "s/%pkgver/${{ env.PKGVER }}/g" -e "s/%sha256sum/${{ env.SHA256 }}/g" pkg/aur/PKGBUILD.in > pkg/aur/PKGBUILD

.github/workflows/test.yml

@@ -18,5 +18,2 @@ name: Test
         include:
-        - python-version: 3.7
-          python-release: v3.7
-          python-impl: CPython
         - python-version: 3.8
@@ -37,8 +34,5 @@ python-release: v3.8
           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: 3.13
+          python-release: v3.13
+          python-impl: CPython
         - python-version: pypy-3.9
@@ -78,3 +72,3 @@ python-release: v3.9
     name: Test (OSX)
-    runs-on: macOS-12
+    runs-on: macOS-latest
     env:
@@ -86,5 +80,2 @@ OS: OSX
         include:
-        - python-version: 3.7
-          python-release: v3.7
-          python-impl: CPython
         - python-version: 3.8
@@ -105,8 +96,5 @@ python-release: v3.8
           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: '3.13'
+          python-release: v3.13
+          python-impl: CPython
         - python-version: pypy-3.9
@@ -153,5 +141,2 @@ python-release: v3.9
         include:
-        - python-version: 3.7
-          python-release: v3.7
-          python-impl: CPython
         - python-version: 3.8
@@ -172,8 +157,5 @@ python-release: v3.8
           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: '3.13'
+          python-release: v3.13
+          python-impl: CPython
         - python-version: pypy-3.9
@@ -180,0 +162,0 @@ python-release: v3.9

CHANGELOG.md

@@ -9,5 +9,12 @@ # Changelog
 ## [Unreleased]
-[Unreleased]: https://github.com/althonos/scoring-matrices/compare/v0.3.0...HEAD
+[Unreleased]: https://github.com/althonos/scoring-matrices/compare/v0.3.1...HEAD
 
 
+## [v0.3.1] - 2025-06-12
+[v0.3.1]: https://github.com/althonos/scoring-matrices/compare/v0.3.0...v0.3.1
+
+### Added
+- 3di scoring matrix from Foldseek ([#5](https://github.com/althonos/scoring-matrices/pull/5), by [@apcamargo](https://github.com/apcamargo)).
+
+
 ## [v0.3.0] - 2024-10-20
@@ -14,0 +21,0 @@ [v0.3.0]: https://github.com/althonos/scoring-matrices/compare/v0.2.2...v0.3.0

CMakeLists.txt

@@ -12,6 +12,2 @@ cmake_minimum_required(VERSION 3.20)
 
-# --- Setup include folders ----------------------------------------------------
-
-# set(CYTHON_HEADERS_DIR ${CMAKE_CURRENT_LIST_DIR}/src/scoring_matrices)
-
 # --- Compile source code ------------------------------------------------------
@@ -18,0 +14,0 @@

data/CMakeLists.txt

@@ -15,2 +15,1 @@ file(GLOB MATRICES CONFIGURE_DEPENDS "*.mat")
 
-# install(FILES ${CMAKE_CURRENT_BINARY_DIR}/matrices.h DESTINATION ${SKBUILD_PLATLIB_DIR}/scoring_matrices)

docs/_static/json/switcher.json

 [
     {
         "name": "v0.3 (latest)",
-        "version": "0.3.0",
-        "url": "https://pytantan.readthedocs.io/en/v0.3.0/"
+        "version": "0.3.1",
+        "url": "https://pytantan.readthedocs.io/en/v0.3.1/"
     },
@@ -7,0 +7,0 @@ {

docs/conf.py

@@ -14,2 +14,3 @@ # Configuration file for the Sphinx documentation builder.
 import sys
+import urllib.request
 
@@ -31,2 +32,8 @@ # -- Path setup --------------------------------------------------------------
 
+# Download the *See Also* cards from a centralized location so it can be kept
+# up-to-date across all projects
+with urllib.request.urlopen("https://gist.githubusercontent.com/althonos/5d6bf5a512d64dc951c42a91d5fc3fb3/raw/related.rst") as src:
+    with open("related.rst", "wb") as dst:
+        shutil.copyfileobj(src, dst)
+
 # -- Project information -----------------------------------------------------
@@ -33,0 +40,0 @@ # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information

docs/guide/index.rst

@@ -11,2 +11,3 @@ User Guide
     Installation <install>
+    Matrices <matrices>
 
@@ -13,0 +14,0 @@ .. toctree::

docs/index.rst

@@ -132,101 +132,5 @@ ``scoring-matrices`` |Stars|
 
-.. grid:: 1 3 5 5
-   :gutter: 1
+.. include:: related.rst
 
-   .. 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
@@ -233,0 +137,0 @@ -------

PKG-INFO

@@ -1,4 +0,4 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: scoring-matrices
-Version: 0.3.0
+Version: 0.3.1
 Summary: Dependency free, Cython-compatible scoring matrices to use with biological sequences.
@@ -8,22 +8,23 @@ Keywords: bioinformatics,sequence,substitution,matrix,score
 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.
+         
+         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
@@ -42,2 +43,3 @@ Classifier: Intended Audience :: Developers
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: Implementation :: CPython
@@ -48,8 +50,10 @@ Classifier: Programming Language :: Python :: Implementation :: PyPy
 Project-URL: Documentation, https://scoring-matrices.readthedocs.io/en/stable/
-Project-URL: Bug tracker, https://github.com/althonos/scoring-matrices/issues
+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
+Project-URL: PyPI, https://pypi.org/project/scoring-matrices
 Requires-Python: >=3.7
+Provides-Extra: test
+Requires-Dist: importlib-resources; python_version < "3.9" and extra == "test"
 Description-Content-Type: text/markdown
@@ -56,0 +60,0 @@

pkg/aur/PKGBUILD.in

@@ -14,3 +14,3 @@ # Maintainer: Martin Larralde <[e-mail]>
 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")
+source=("https://files.pythonhosted.org/packages/source/${_name::1}/$_name/$_module-$pkgver.tar.gz")
 sha256sums=(%sha256sum)
@@ -17,0 +17,0 @@

pyproject.toml

@@ -7,3 +7,3 @@ [build-system]
 name = "scoring-matrices"
-version = "0.3.0"
+version = "0.3.1"
 description = "Dependency free, Cython-compatible scoring matrices to use with biological sequences."
@@ -31,2 +31,3 @@ readme = "README.md"
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Programming Language :: Python :: Implementation :: CPython",
@@ -47,2 +48,5 @@ "Programming Language :: Python :: Implementation :: PyPy",
 
+[project.optional-dependencies]
+test = ["importlib-resources ; python_version < '3.9'"]
+
 [tool.scikit-build]
@@ -53,7 +57,2 @@ build-dir = "build/{build_type}"
 
-[[tool.scikit-build.generate]]
-path = "src/scoring_matrices/_version.py"
-template = '__version__ = "${version}"'
-location = 'source'
-
 [[tool.scikit-build.overrides]]
@@ -75,2 +74,9 @@ if.state = "editable"
 
+[tool.cibuildwheel]
+before-build = "pip install scikit-build-core cython"
+build-frontend = { name = "pip", args = ["--no-build-isolation"] }
+build-verbosity = 1
+test-command = "python -m unittest scoring_matrices.tests -vv"
+test-extras = ["test"]
+
 [tool.coverage.report]
@@ -77,0 +83,0 @@ include = ["src/scoring_matrices/*"]

src/scoring_matrices/__init__.py

@@ -1,9 +0,6 @@
-from ._version import __version__
+from . import lib
+from .lib import ScoringMatrix, __version__
 
 __author__ = "Martin Larralde <[e-mail]>"
 __license__ = "MIT"
-
-from . import lib
-from .lib import ScoringMatrix
-
 __doc__ = lib.__doc__

src/scoring_matrices/lib.pyi

 import typing
 from typing import ClassVar, List, Optional, Sequence, TextIO, Tuple, Type, TypeVar
 
+__version__: str
+
 S = TypeVar("S")
@@ -5,0 +7,0 @@

src/scoring_matrices/lib.pyx

@@ -19,2 +19,3 @@ # distutils: language = c
 
+__version__ = PROJECT_VERSION
 
@@ -39,8 +40,9 @@ cdef dict _INDICES = {
 
+        This library comes with built-in matrices including the PAM, BLOSUM,
+        VTML or BENNER matrix series. See the :doc:`Matrices </guide/matrices>`
+        page of the documentation for a comprehensive list. 
+
         Arguments:
             name (`str`): The name of the scoring matrix.
 
-        Example:
-            >>> blosum62 = ScoringMatrix.from_name("BLOSUM62")
-
         Raises:
@@ -50,2 +52,18 @@ `ValueError`: When no scoring matrix with the given ``name``
 
+        Example:
+            >>> blosum62 = ScoringMatrix.from_name("BLOSUM62")
+
+        Note:
+            The `ScoringMatrix.BUILTIN_MATRICES` frozenset contains the names
+            of every available matrix, which can be useful for checking 
+            allowed matrix names::
+
+            >>> import argparse
+            >>> parser = argparse.ArgumentParser()
+            >>> _ = parser.add_argument(
+            ...     "--matrix", 
+            ...     choices=ScoringMatrix.BUILTIN_MATRICES,
+            ...     default="BLOSUM62" 
+            ... ) 
+
         """
@@ -52,0 +70,0 @@ cdef size_t i

src/scoring_matrices/_version.py

-__version__ = "0.3.0"

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Improved metrics

Number of package files

122

1.67%

Lines of code

570

1.06%

Worsened metrics

Total package byte prevSize

279985

-0.13%