Merge pull request #117 from apriha/feature/lint-and-format-with-ruff

Lint and format with Ruff

Author: apriha

.github/workflows/ci.yml

@@ -25,20 +25,23 @@ jobs:
       - name: Enable workflow based on preconditions
         run: echo "Workflow enabled."
 
-  lint:
+  lint-format:
     needs: [enable-workflow]
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
       with:
         python-version: '3.12'
-    - name: Install Black
+    - name: Install Ruff
       run: |
-        pip install black
-    - name: Lint with Black
+        pip install ruff
+    - name: Lint with Ruff
       run: |
-        black --check --diff .
+        ruff check
+    - name: Format with Ruff
+      run: |
+        ruff format --check
 
   build-docs:
     needs: [enable-workflow]
@@ -57,7 +60,7 @@ jobs:
         sphinx-build -W --keep-going -T -E -D language=en docs docs/_build
 
   test:
-    needs: [lint, build-docs]
+    needs: [lint-format, build-docs]
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:

CONTRIBUTING.rst

@@ -65,9 +65,10 @@ To set up ``lineage`` for local development:
    .. note:: After running the tests, a coverage report can be viewed by opening
              ``htmlcov/index.html`` in a browser.
 
-6. Check code formatting::
+6. Perform code linting and formatting::
 
-    $ pipenv run black --check --diff .
+    $ pipenv run ruff check --fix
+    $ pipenv run ruff format
 
 7. Commit your changes and push your branch to GitHub::
 

Pipfile

@@ -8,7 +8,7 @@ pytest = "*"
 pytest-cov = "*"
 sphinx = "*"
 sphinx-rtd-theme = "*"
-black = "*"
+ruff = "*"
 
 [packages]
 lineage = {editable = true,path = "."}

Pipfile.lock

@@ -1,6 +1,6 @@
 .. image:: https://raw.githubusercontent.com/apriha/lineage/master/docs/images/lineage_banner.png
 
-|ci| |codecov| |docs| |pypi| |python| |downloads| |license| |black|
+|ci| |codecov| |docs| |pypi| |python| |downloads| |license| |ruff|
 
 lineage
 =======
@@ -249,6 +249,10 @@ Thanks to Whit Athey, Ryan Dale, Binh Bui, Jeff Gill, Gopal Vashishtha,
 ``lineage`` incorporates code and concepts generated with the assistance of
 `OpenAI's <https://openai.com>`_ `ChatGPT <https://chatgpt.com>`_ . ✨
 
+License
+-------
+``lineage`` is licensed under the `MIT License <https://github.com/apriha/lineage/blob/master/LICENSE.txt>`_.
+
 .. https://github.com/rtfd/readthedocs.org/blob/master/docs/badges.rst
 .. |ci| image:: https://github.com/apriha/lineage/actions/workflows/ci.yml/badge.svg?branch=master
    :target: https://github.com/apriha/lineage/actions/workflows/ci.yml
@@ -264,5 +268,6 @@ Thanks to Whit Athey, Ryan Dale, Binh Bui, Jeff Gill, Gopal Vashishtha,
    :target: https://pepy.tech/project/lineage
 .. |license| image:: https://img.shields.io/pypi/l/lineage.svg
    :target: https://github.com/apriha/lineage/blob/master/LICENSE.txt
-.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
-   :target: https://github.com/psf/black
+.. |ruff| image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json
+   :target: https://github.com/astral-sh/ruff
+   :alt: Ruff

README.rst

@@ -21,6 +21,8 @@
 import sys
 from unittest.mock import MagicMock
 
+import lineage
+
 # http://docs.readthedocs.io/en/latest/faq.html#i-get-import-errors-on-libraries-that-depend-on-c-modules
 autodoc_mock_imports = [
     "numpy",
@@ -43,8 +45,6 @@ def __getattr__(cls, name):
 for mod_name in autodoc_mock_imports:
     sys.modules[mod_name] = Mock()
 
-import lineage
-
 # https://samnicholls.net/2016/06/15/how-to-sphinx-readthedocs/
 
 # -- General configuration ------------------------------------------------

docs/conf.py

@@ -1,3 +1,7 @@
 [build-system]
 requires = ["setuptools", "wheel"]
-build-backend = "setuptools.build_meta:__legacy__"
+build-backend = "setuptools.build_meta:__legacy__"
+
+# https://github.com/astral-sh/ruff/issues/465#issuecomment-1783684428
+[tool.ruff.lint]
+extend-select = ["I"]

pyproject.toml

@@ -1,3 +1,23 @@
+# Copyright (c) 2016 The Python Packaging Authority (PyPA)
+#
+# 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.
+
 """A setuptools based setup module.
 
 See:
@@ -6,65 +26,12 @@
 
 """
 
-"""
-Copyright (c) 2016 The Python Packaging Authority (PyPA)
-
-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.
-
-"""
-
-"""
-MIT License
-
-Copyright (c) 2016 Andrew Riha
-
-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.
-
-"""
-
 # To use a consistent encoding
 from codecs import open
 from glob import glob
-from os.path import abspath
-from os.path import basename
-from os.path import dirname
-from os.path import join
-from os.path import splitext
+from os.path import abspath, basename, dirname, join, splitext
 
-from setuptools import find_packages
-from setuptools import setup
+from setuptools import find_packages, setup
 
 import versioneer
 

setup.py

@@ -1,38 +1,13 @@
-""" lineage
+"""lineage
 
 tools for genetic genealogy and the analysis of consumer DNA test results
 
 """
 
-"""
-MIT License
-
-Copyright (c) 2016 Andrew Riha
-
-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.
-
-"""
-
 import datetime
-from itertools import chain, combinations
 import logging
 import os
+from itertools import chain, combinations
 
 import numpy as np
 import pandas as pd

src/lineage/__init__.py

@@ -11,12 +11,12 @@
 """Git implementation of _version.py."""
 
 import errno
+import functools
 import os
 import re
 import subprocess
 import sys
 from typing import Any, Callable, Dict, List, Optional, Tuple
-import functools
 
 
 def get_keywords() -> Dict[str, str]:

src/lineage/_version.py

@@ -1,29 +1,5 @@
-""" Class for representing individuals within the `lineage` framework. """
+"""Class for representing individuals within the `lineage` framework."""
 
-"""
-MIT License
-
-Copyright (c) 2016 Andrew Riha
-
-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.
-
-"""
 import inspect
 
 from snps import SNPs

src/lineage/individual.py

@@ -1,4 +1,4 @@
-""" Class for downloading and loading required external resources.
+"""Class for downloading and loading required external resources.
 
 `lineage` uses tables and data from UCSC's Genome Browser:
 
@@ -29,31 +29,6 @@
 
 """
 
-"""
-MIT License
-
-Copyright (c) 2017 Andrew Riha
-
-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.
-
-"""
-
 import logging
 import tarfile