blosum - npm Package Compare versions

Comparing version 2.0.3 to 2.2.0

PKG-INFO

@@ -1,8 +0,10 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: blosum
-Version: 2.0.3
+Version: 2.2.0
 Summary: A simple BLOSUM toolbox without dependencies.
 Home-page: https://github.com/not-a-feature/blosum
 Author: Jules Kreuer / not_a_feature
-License: gpl-3.0
+License: GPL-3.0
+Project-URL: Homepage, https://github.com/not-a-feature/blosum
+Project-URL: Repository, https://github.com/not-a-feature/blosum
 Keywords: BLOSUM,reader,bio,bioinformatics,blosum62,blosum45,blosum50,blosum90
@@ -15,14 +17,22 @@ Platform: unix
 Classifier: Programming Language :: Python :: 3
+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 :: 3.13
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Operating System :: OS Independent
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Provides-Extra: testing
-Requires-Dist: pytest>=6.0; extra == "testing"
-Requires-Dist: pytest-cov>=2.0; extra == "testing"
-Requires-Dist: tox>=3.20; extra == "testing"
+Provides-Extra: dev
+Requires-Dist: pytest>=6.2; extra == "dev"
+Requires-Dist: pytest-cov>=2.12; extra == "dev"
+Requires-Dist: mypy>=0.910; extra == "dev"
+Requires-Dist: tox>=3.24; extra == "dev"
+Dynamic: license-file
 
-![blosum](https://github.com/not-a-feature/blosum/raw/main/blosum.png)
+<img src="https://github.com/not-a-feature/blosum/raw/main/blosum.png" width=300px alt="blosum logo"></img>
 
-A small module for easy access to BLOSUM matrices without dependencies.
-
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7084916.svg)](https://doi.org/10.5281/zenodo.7084916)
@@ -29,0 +39,0 @@ [![Citation Badge](https://api.juleskreuer.eu/citation-badge.php?doi=10.5281/zenodo.7748749)](https://juleskreuer.eu/projekte/citation-badge/)

pyproject.toml

 [build-system]
-requires = ["setuptools>=42.0", "wheel"]
+requires = ["setuptools>=61.0", "wheel"]
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "blosum"
+version = "2.2.0"
+description = "A simple BLOSUM toolbox without dependencies."
+readme = "README.md"
+requires-python = ">=3.8"
+license = {text = "GPL-3.0"}
+keywords = ["BLOSUM", "reader", "bio", "bioinformatics", "blosum62", "blosum45", "blosum50", "blosum90"]
+authors = [
+    {name = "Jules Kreuer / not_a_feature"}
+]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "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 :: 3.13",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Operating System :: OS Independent",
+]
+
+[project.urls]
+Homepage = "https://github.com/not-a-feature/blosum"
+Repository = "https://github.com/not-a-feature/blosum"
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=6.2",
+    "pytest-cov>=2.12",
+    "mypy>=0.910",
+    "tox>=3.24",
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+blosum = ["py.typed"]
+
 [tool.pytest.ini_options]
@@ -10,2 +51,3 @@ addopts = "--cov=blosum"
 ]
+xfail_strict = true
 
@@ -12,0 +54,0 @@ [tool.mypy]

README.md

@@ -1,5 +0,3 @@
-![blosum](https://github.com/not-a-feature/blosum/raw/main/blosum.png)
+<img src="https://github.com/not-a-feature/blosum/raw/main/blosum.png" width=300px alt="blosum logo"></img>
 
-A small module for easy access to BLOSUM matrices without dependencies.
-
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7084916.svg)](https://doi.org/10.5281/zenodo.7084916)
@@ -6,0 +4,0 @@ [![Citation Badge](https://api.juleskreuer.eu/citation-badge.php?doi=10.5281/zenodo.7748749)](https://juleskreuer.eu/projekte/citation-badge/)

setup.cfg

 [metadata]
 name = blosum
-version = 2.0.3
+version = 2.2.0
 description = A simple BLOSUM toolbox without dependencies.
@@ -30,8 +30,2 @@ long_description = file: README.md
 
-[options.package_data]
-frameshift_aware_alignment = py.typed
-
-[pytest]
-xfail_strict = true
-
 [egg_info]
@@ -38,0 +32,0 @@ tag_build =

src/blosum.egg-info/PKG-INFO

@@ -1,8 +0,10 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: blosum
-Version: 2.0.3
+Version: 2.2.0
 Summary: A simple BLOSUM toolbox without dependencies.
 Home-page: https://github.com/not-a-feature/blosum
 Author: Jules Kreuer / not_a_feature
-License: gpl-3.0
+License: GPL-3.0
+Project-URL: Homepage, https://github.com/not-a-feature/blosum
+Project-URL: Repository, https://github.com/not-a-feature/blosum
 Keywords: BLOSUM,reader,bio,bioinformatics,blosum62,blosum45,blosum50,blosum90
@@ -15,14 +17,22 @@ Platform: unix
 Classifier: Programming Language :: Python :: 3
+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 :: 3.13
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Operating System :: OS Independent
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Provides-Extra: testing
-Requires-Dist: pytest>=6.0; extra == "testing"
-Requires-Dist: pytest-cov>=2.0; extra == "testing"
-Requires-Dist: tox>=3.20; extra == "testing"
+Provides-Extra: dev
+Requires-Dist: pytest>=6.2; extra == "dev"
+Requires-Dist: pytest-cov>=2.12; extra == "dev"
+Requires-Dist: mypy>=0.910; extra == "dev"
+Requires-Dist: tox>=3.24; extra == "dev"
+Dynamic: license-file
 
-![blosum](https://github.com/not-a-feature/blosum/raw/main/blosum.png)
+<img src="https://github.com/not-a-feature/blosum/raw/main/blosum.png" width=300px alt="blosum logo"></img>
 
-A small module for easy access to BLOSUM matrices without dependencies.
-
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7084916.svg)](https://doi.org/10.5281/zenodo.7084916)
@@ -29,0 +39,0 @@ [![Citation Badge](https://api.juleskreuer.eu/citation-badge.php?doi=10.5281/zenodo.7748749)](https://juleskreuer.eu/projekte/citation-badge/)

src/blosum.egg-info/requires.txt

 
-[testing]
-pytest>=6.0
-pytest-cov>=2.0
-tox>=3.20
+[dev]
+pytest>=6.2
+pytest-cov>=2.12
+mypy>=0.910
+tox>=3.24

src/blosum/_blosum.py

@@ -22,15 +22,23 @@ """
 
-        Input
-        -----
-            Either n ϵ {45,50,62,80,90} or path
+        Parameters
+        ----------
+            n: int or str
+                * If an integer (45, 50, 62, 80, or 90), selects the corresponding
+                standard BLOSUM matrix.
+                * If a string, provides a filepath to a custom BLOSUM matrix file.
+            default: float
+                The default value for missing entries in the matrix.
+                Defaults to -inf.
 
-            n: int, which BLOSUM Matrix to use.
-                Choice between: 45,50,62,80 and 90
-                Data gathered from https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/
+        Attributes
+        ----------
+            n: int or str
+                The BLOSUM matrix identifier (version number or filepath).
+            default: float
+                The default value for missing entries.
 
-            path: string, path to a Blosum matrix.
-                File in a format like:
-                https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/BLOSUM62
-
-            default: float, default -inf
+        Examples
+        --------
+            >>> blosum62 = BLOSUM(62)
+            >>> score = blosum62['W']['Y']  # Get the score for substituting W with Y
         """
@@ -89,13 +97,15 @@
     Reads a Blosum matrix from file.
-    File in a format like:
-        https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/BLOSUM62
+    File in a format like: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/BLOSUM62
 
-    Input
-    -----
-        path: str, path to a file.
-        default: float, default value "-inf"
+    Parameters
+    ----------
+        path: str
+             Path to the file.
+        default: float
+            Default value "-inf".
 
     Returns
     -------
-        blosumDict: Dictionary, The blosum dict
+        blosumDict: dict
+            The blosum dict.
     """
@@ -102,0 +112,0 @@

Alert delta unavailable

Currently unable to show alert delta for PyPI packages.

Improved metrics

Total package byte prevSize

132242

1.93%

Lines of code

3587

0.31%