Merge pull request #175 from sanogenetics/feature/lint-and-format-wit…

…h-ruff

Lint and format with Ruff

.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:
@@ -117,7 +120,7 @@ jobs:
       uses: codecov/codecov-action@v3
 
   test-extras:
-    needs: [lint, build-docs]
+    needs: [lint-format, build-docs]
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:

CONTRIBUTING.rst

@@ -65,9 +65,10 @@ To set up ``snps`` 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

@@ -9,7 +9,7 @@ pytest-cov = "*"
 pytest-watch = "*"
 sphinx = "*"
 sphinx-rtd-theme = "*"
-black = "*"
+ruff = "*"
 matplotlib = "*"
 
 [packages]

README.rst

@@ -1,6 +1,6 @@
 .. image:: https://raw.githubusercontent.com/apriha/snps/master/docs/images/snps_banner.png
 
-|ci| |codecov| |docs| |pypi| |python| |downloads| |black|
+|ci| |codecov| |docs| |pypi| |python| |downloads| |ruff|
 
 snps
 ====
@@ -269,6 +269,10 @@ Thanks to Mike Agostino, Padma Reddy, Kevin Arvai, `openSNP <https://opensnp.org
 ``snps`` incorporates code and concepts generated with the assistance of
 `OpenAI's <https://openai.com>`_ `ChatGPT <https://chat.openai.com>`_ (GPT-3.5). ✨
 
+License
+-------
+``snps`` is licensed under the `BSD 3-Clause License <https://github.com/apriha/snps/blob/master/LICENSE.txt>`_.
+
 .. https://github.com/rtfd/readthedocs.org/blob/master/docs/badges.rst
 .. |ci| image:: https://github.com/apriha/snps/actions/workflows/ci.yml/badge.svg?branch=master
    :target: https://github.com/apriha/snps/actions/workflows/ci.yml
@@ -282,5 +286,6 @@ Thanks to Mike Agostino, Padma Reddy, Kevin Arvai, `openSNP <https://opensnp.org
    :target: https://www.python.org
 .. |downloads| image:: https://pepy.tech/badge/snps
    :target: https://pepy.tech/project/snps
-.. |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

analysis/parse-opensnp-files/get_file.py

@@ -1,9 +1,8 @@
-""" Get a file from the openSNP datadump for debugging. """
+"""Get a file from the openSNP datadump for debugging."""
 
 import os
 
 from atomicwrites import atomic_write
-
 from snps.resources import Resources
 from snps.utils import create_dir
 

analysis/parse-opensnp-files/parse_opensnp_files.py

@@ -1,21 +1,21 @@
-""" Parse openSNP datadump files.
+"""Parse openSNP datadump files.
 
 Attempt to parse each file in the openSNP datadump. For files where SNPs were loaded,
 save summary statistics to a dataframe and output as a CSV. For files where no SNPs were
 loaded, save a message for each file indicating the issue and optionally extract these
 files from the datadump for debugging.
+
 """
 
 import logging
 import os
 import random
 
-from atomicwrites import atomic_write
 import pandas as pd
-
+from atomicwrites import atomic_write
 from snps import SNPs
 from snps.resources import Resources
-from snps.utils import Parallelizer, save_df_as_csv, create_dir, clean_str
+from snps.utils import Parallelizer, clean_str, create_dir, save_df_as_csv
 
 OUTPUT_DIR = "output"
 EXTRACT_FILES = True

analysis/xy-chrom-snp-ratios/xy-chrom-snp-ratios.py

@@ -2,15 +2,14 @@
 import os
 import random
 
-from atomicwrites import atomic_write
-import numpy as np
-from matplotlib import patches
 import matplotlib.pyplot as plt
+import numpy as np
 import pandas as pd
-
+from atomicwrites import atomic_write
+from matplotlib import patches
 from snps import SNPs
 from snps.resources import Resources
-from snps.utils import Parallelizer, save_df_as_csv, create_dir
+from snps.utils import Parallelizer, create_dir, save_df_as_csv
 
 OUTPUT_DIR = "output"
 

docs/conf.py

@@ -20,6 +20,8 @@
 import os
 import sys
 
+import snps
+
 # http://docs.readthedocs.io/en/latest/faq.html#i-get-import-errors-on-libraries-that-depend-on-c-modules
 autodoc_mock_imports = [
     "numpy",
@@ -31,8 +33,6 @@
 
 sys.path.insert(0, os.path.abspath("../"))
 
-import snps
-
 # https://samnicholls.net/2016/06/15/how-to-sphinx-readthedocs/
 
 # -- General configuration ------------------------------------------------

pyproject.toml

@@ -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"]

setup.py

@@ -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:
@@ -6,73 +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.
-
-"""
-
-"""
-BSD 3-Clause License
-
-Copyright (c) 2019, Andrew Riha
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
-   list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright notice,
-   this list of conditions and the following disclaimer in the documentation
-   and/or other materials provided with the distribution.
-
-3. Neither the name of the copyright holder nor the names of its
-   contributors may be used to endorse or promote products derived from
-   this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-"""
-
 # 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
 

src/snps/__init__.py

@@ -1,43 +1,10 @@
-""" `snps`
+"""`snps`
 
 tools for reading, writing, merging, and remapping SNPs
 
 """
 
-"""
-BSD 3-Clause License
-
-Copyright (c) 2019, Andrew Riha
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
-   list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright notice,
-   this list of conditions and the following disclaimer in the documentation
-   and/or other materials provided with the distribution.
-
-3. Neither the name of the copyright holder nor the names of its
-   contributors may be used to endorse or promote products derived from
-   this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-"""
-
-from snps.snps import SNPs
+from snps.snps import SNPs as SNPs
 
 # set version string with Versioneer
 from . import _version

src/snps/_version.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]: