Modify and Test tests.yml

.flake8

@@ -0,0 +1,8 @@
+[flake8]
+# Black by its default setting the maximum length to 88
+max-line-length = 88
+extend-ignore = 
+    # also the Black's default, whitespace before ':'
+    E203,
+    # this is for the line length, all the lines too long are comments now
+    E501

.github/workflows/tests.yml

@@ -35,8 +35,8 @@ jobs:
             - name: Build SDist and wheel
               run: python3 -m build
 
-            - name: Install AlphaPeel
-              run: pip install dist/AlphaPeel-1.1.3-py3-none-any.whl
+            - name: Install AlphaImpute2
+              run: pip install dist/AlphaImpute2-0.0.3-py3-none-any.whl
 
             - name: Install pytest
               run: |

.pre-commit-config.yaml

@@ -0,0 +1,9 @@
+repos:
+-   repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+    -   id: black
+-   repo: https://github.com/PyCQA/flake8
+    rev: 6.0.0
+    hooks:
+    -   id: flake8

docs/source/conf.py

@@ -17,21 +17,20 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'AlphaImpute2'
-copyright = '2020, Andrew Whalen'
-author = 'Andrew Whalen'
+project = "AlphaImpute2"
+copyright = "2020, Andrew Whalen"
+author = "Andrew Whalen"
 
 
 # -- 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 = [
-]
+extensions = []
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -44,29 +43,25 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = "alabaster"
 
 # 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']
+html_static_path = ["_static"]
 
 latex_elements = {
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
-    'extraclassoptions': 'openany,oneside'
-
+    "extraclassoptions": "openany,oneside"
 }

setup.py

@@ -2,13 +2,7 @@
 
 from setuptools import setup
 
-from setuptools import Extension, find_packages
-# import numpy
-import os
-import glob
-from sys import platform
-import sys
-import sysconfig
+
 # py_modules = ['alphaimpute2']
 
 # py_modules += [os.path.join('src','General', 'InputOutput')]
@@ -30,20 +24,13 @@
     long_description_content_type="text/markdown",
     url="",
     license="MIT license",
-
-    packages=['alphaimpute2', 'alphaimpute2.tinyhouse','alphaimpute2.Imputation'],
-    package_dir={'': 'src'},
-
+    packages=["alphaimpute2", "alphaimpute2.tinyhouse", "alphaimpute2.Imputation"],
+    package_dir={"": "src"},
     classifiers=[
         "Programming Language :: Python :: 3",
     ],
-    entry_points = {
-    'console_scripts': [
-        'AlphaImpute2=alphaimpute2.alphaimpute2:main'
-        ],
+    entry_points={
+        "console_scripts": ["AlphaImpute2=alphaimpute2.alphaimpute2:main"],
     },
-    install_requires=[
-        'numpy>=1.19',
-        'numba>=0.49.0'
-    ]
+    install_requires=["numpy>=1.19", "numba>=0.49.0"],
 )

src/alphaimpute2-script.py

@@ -1,6 +1,9 @@
 from alphaimpute2 import alphaimpute2
+
+
 def main():
     alphaimpute2.main()
 
+
 if __name__ == "__main__":
-    main()
+    main()