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scoring-matrices - npm Package Compare versions

Comparing version
0.3.1
 to
0.3.2
+8
-1
CHANGELOG.md

@@ -9,5 +9,12 @@ # Changelog

## [Unreleased]
[Unreleased]: https://github.com/althonos/scoring-matrices/compare/v0.3.1...HEAD
[Unreleased]: https://github.com/althonos/scoring-matrices/compare/v0.3.2...HEAD
## [v0.3.2] - 2025-06-16
[v0.3.2]: https://github.com/althonos/scoring-matrices/compare/v0.3.1...v0.3.2
### Fixed
- Exclude `docs` folder from source distribution, causing issues with Windows builds.
## [v0.3.1] - 2025-06-12

@@ -14,0 +21,0 @@ [v0.3.1]: https://github.com/althonos/scoring-matrices/compare/v0.3.0...v0.3.1

+1
-1
PKG-INFO
Metadata-Version: 2.2
Name: scoring-matrices
Version: 0.3.1
Version: 0.3.2
Summary: Dependency free, Cython-compatible scoring matrices to use with biological sequences.

@@ -5,0 +5,0 @@ Keywords: bioinformatics,sequence,substitution,matrix,score

+5
-1
pyproject.toml

@@ -7,3 +7,3 @@ [build-system]

name = "scoring-matrices"
version = "0.3.1"
version = "0.3.2"
description = "Dependency free, Cython-compatible scoring matrices to use with biological sequences."

@@ -54,2 +54,6 @@ readme = "README.md"

editable.verbose = false
sdist.exclude = [
"docs",
"wheelhouse",
]

@@ -56,0 +60,0 @@ [[tool.scikit-build.overrides]]

+7
-7
src/scoring_matrices/lib.pyx

@@ -58,9 +58,9 @@ # distutils: language = c

>>> import argparse
>>> parser = argparse.ArgumentParser()
>>> _ = parser.add_argument(
... "--matrix",
... choices=ScoringMatrix.BUILTIN_MATRICES,
... default="BLOSUM62"
... )
>>> import argparse
>>> parser = argparse.ArgumentParser()
>>> arg = parser.add_argument(
... "--matrix",
... choices=ScoringMatrix.BUILTIN_MATRICES,
... default="BLOSUM62"
... )

@@ -67,0 +67,0 @@ """

-44
docs/_static/js/custom-icon.js
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* Set a custom icon for pypi as it's not available in the fa built-in brands
*/
FontAwesome.library.add(
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prefix: "fa-custom",
iconName: "pypi",
icon: [
17.313, // viewBox width
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"e001", // unicode codepoint - private use area
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],
}),
);
FontAwesome.library.add(
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prefix: "fa-custom",
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icon: [
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256, // viewBox height
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],
}),
);
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)
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-17
docs/_static/json/switcher.json
[
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"name": "v0.3 (latest)",
"version": "0.3.1",
"url": "https://pytantan.readthedocs.io/en/v0.3.1/"
},
{
"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/"
}
]
-1
docs/.gitignore
related.rst
-22
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
-37
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__
-220
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
import urllib.request
# -- 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)
# 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 -----------------------------------------------------
# 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": "Scoring Matrices",
# "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"),
}
-6
docs/guide/copyright.rst
Copyright Notice
================
This library is provided under the MIT license:
.. literalinclude:: ../../COPYING 
-19
docs/guide/index.rst
User Guide
==========
This section contains guides and documents about ``scoring-matrices`` usage.
.. toctree::
:maxdepth: 1
:caption: Getting Started
Installation <install>
Matrices <matrices>
.. toctree::
:maxdepth: 1
:caption: Resources
Contribution Guide <contributing>
Changelog <changes>
Copyright Notice <copyright>
-85
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.
-40
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.
-146
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
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.. 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.
.. include:: related.rst
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>`_.
-35
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 
-20
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)
-15
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