Merge pull request #6 from not-a-feature/dev

Black code formatting

.github/workflows/black.yml

@@ -0,0 +1,12 @@
+name: Black Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: psf/black@stable
+        with:
+            options: "-l 100"

DEPENDENCIES.md

@@ -7,21 +7,6 @@ Any information relevant to third-party vendors listed below are collected using
 
 ## Dependencies
 
-### [flake8 (4.0.1)](https://gitlab.com/pycqa/flake8)
-
-#### Declared Licenses
-MIT
-
-### Package Info
-
-**Package Homepage**: https://gitlab.com/pycqa/flake8
-
-**Package Download URL**: https://files.pythonhosted.org/packages/34/39/cde2c8a227abb4f9ce62fe55586b920f438f1d2903a1a22514d0b982c333/flake8-4.0.1-py2.py3-none-any.whl
-
-**Dependency Paths**:  flake8 
-
----
-
 ### [mypy (0.930)](http://www.mypy-lang.org/)
 
 #### Declared Licenses
@@ -30,11 +15,6 @@ MIT *OR* Python-2.0
 ### Package Info
 
 **Package Homepage**: http://www.mypy-lang.org/
-
-**Package Download URL**: https://files.pythonhosted.org/packages/c0/5c/12591c72af2774dfe08a58cad3b814eb79809297dfc92aae8588a7b22fd7/mypy-0.930-cp310-cp310-macosx_10_9_x86_64.whl
-
-**Dependency Paths**:  mypy 
-
 ---
 
 ### [pytest (7.0.0rc1)](http://pytest.org)
@@ -45,10 +25,6 @@ MIT *OR* Python-2.0
 
 **Package Homepage**: http://pytest.org
 
-**Package Download URL**: https://files.pythonhosted.org/packages/5b/19/90bb3215fd679ead2a93f606e46044d5999eed7271434305c1da60653e1f/pytest-7.0.0rc1-py3-none-any.whl
-
-**Dependency Paths**:  pytest 
-
 ---
 
 ### [pytest-cov (3.0.0)](https://github.com/pytest-dev/pytest-cov)
@@ -60,10 +36,6 @@ MIT
 
 **Package Homepage**: https://github.com/pytest-dev/pytest-cov
 
-**Package Download URL**: https://files.pythonhosted.org/packages/20/49/b3e0edec68d81846f519c602ac38af9db86e1e71275528b3e814ae236063/pytest_cov-3.0.0-py3-none-any.whl
-
-**Dependency Paths**:  pytest-cov 
-
 ---
 
 ### [tox (4.0.0a9)](https://tox.readthedocs.org/)
@@ -74,7 +46,3 @@ MIT
 ### Package Info
 
 **Package Homepage**: https://tox.readthedocs.org/
-
-**Package Download URL**: https://files.pythonhosted.org/packages/9e/1d/62707decc7690dafc1e1ffff6a02ab41ee3806a21ac2e1ca28082c5aed22/tox-4.0.0a9-py3-none-any.whl
-
-**Dependency Paths**:  tox 

README.md

@@ -5,6 +5,7 @@ A small module for easy access to BLOSUM matrices without dependencies.
 ![Test Badge](https://github.com/not-a-feature/blosum/actions/workflows/tests.yml/badge.svg)
 ![Python Version Badge](https://img.shields.io/pypi/pyversions/blosum)
 ![Download Badge](https://img.shields.io/pypi/dm/blosum.svg)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
 The BLOcks SUbstitution Matrices (BLOSUM) are used to score alignments between protein sequences and are therefore mainly used in bioinformatics.
 
@@ -79,7 +80,7 @@ matrix = bl.BLOSUM(62, default=0)
 
 ## License
 ```
-Copyright (C) 2021 by Jules Kreuer - @not_a_feature
+Copyright (C) 2022 by Jules Kreuer - @not_a_feature
 This piece of software is published unter the GNU General Public License v3.0
 TLDR:
 

requirements_dev.txt

@@ -1,4 +1,3 @@
-flake8>=3.9
 pytest>=6.2
 pytest-cov>=2.12
 mypy>=0.910

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = blosum
-version = 1.1.2
+version = 1.1.3
 description = A simple BLOSUM toolbox without dependencies.
 long_description = file: README.md
 long_description_content_type=text/markdown
@@ -28,14 +28,10 @@ zip_safe = no
 testing =
     pytest>=6.0
     pytest-cov>=2.0
-    flake8>=3.9
     tox>=3.20
 
 [options.package_data]
 frameshift_aware_alignment = py.typed
 
-[flake8]
-max-line-length = 120
-
 [pytest]
 xfail_strict=true

src/blosum/__init__.py

@@ -1,4 +1,5 @@
 from ._blosum import BLOSUM
+
 __all__ = [
     "BLOSUM",
 ]

src/blosum/_blosum.py

@@ -11,7 +11,7 @@
 from ._data import default_blosum
 
 
-class BLOSUM():
+class BLOSUM:
     def __init__(self, n, default: float = float("-inf")):
         """
         Object to easily access a blosum matrix.
@@ -40,7 +40,7 @@ def __init__(self, n, default: float = float("-inf")):
             # load custom matrix
             self.__loadMatrix(n)
         else:
-            raise(BaseException("Can't initate empty BLOSUM Object"))
+            raise (BaseException("Can't initate empty BLOSUM Object"))
 
     def __loadMatrix(self, path: str) -> None:
         """
@@ -89,7 +89,7 @@ def __loadMatrix(self, path: str) -> None:
                 blosumDict[f"{linelist[0]}{lab}"] = float(linelist[index])
 
         # Check quadratic
-        if not len(blosumDict) == len(labelslist)**2:
+        if not len(blosumDict) == len(labelslist) ** 2:
             raise EOFError("Blosum file is not quadratic.")
         self.matrix = blosumDict
 
@@ -120,7 +120,7 @@ def __str__(self) -> str:
         """
         Magic method to allow BLOSUM object printing.
         """
-        return f'BLOSUM {self.n}\n{self.matrix}'
+        return f"BLOSUM {self.n}\n{self.matrix}"
 
     def __repr__(self) -> str:
         """
@@ -132,4 +132,4 @@ def __repr__(self) -> str:
             n = self.n
         else:
             n = f'"{self.n}"'
-        return f'BLOSUM({n}, default={d})'
+        return f"BLOSUM({n}, default={d})"