From b7f8669e8522a17d341cd87217e9abd1038a7f5f Mon Sep 17 00:00:00 2001
From: James Stevenson <james.stevenson@nationwidechildrens.org>
Date: Wed, 5 Jun 2024 09:38:36 -0400
Subject: [PATCH] style: format with Ruff

---
 .github/workflows/python-package.yml |  4 ++--
 Makefile                             | 12 ++++++------
 pyproject.toml                       |  8 +++++---
 setup.cfg                            |  4 ++--
 src/bioutils/accessions.py           |  1 +
 src/bioutils/normalize.py            |  4 +---
 src/bioutils/seqfetcher.py           |  3 +--
 src/bioutils/sequences.py            |  3 +--
 8 files changed, 19 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 1816684..197b6f1 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -34,9 +34,9 @@ jobs:
       run: |
         isort --check src
 
-    - name: Format check with black
+    - name: Format check with Ruff
       run: |
-        black --check src
+        ruff format --check src
 
     # Disable bandit until issues are resolved
     # - name: Security check with bandit
diff --git a/Makefile b/Makefile
index 86ea9df..e95df5f 100644
--- a/Makefile
+++ b/Makefile
@@ -69,7 +69,7 @@ build: %:
 cqa:
 	flake8 src --count --select=E9,F63,F7,F82 --show-source --statistics
 	isort --profile black --check src
-	black --check src
+	ruff format --check src
 	bandit -ll -r src
 
 #=> test: execute tests
@@ -95,9 +95,9 @@ tox:
 .PHONY: reformat
 reformat:
 	@if ! git diff --cached --exit-code >/dev/null; then echo "Repository not clean" 1>&2; exit 1; fi
-	black src tests
+	ruff format src tests
 	isort src tests
-	git commit -a -m "reformatted with black and isort"
+	git commit -a -m "reformatted with ruff and isort"
 
 #=> rename: rename files and substitute content for new repo name
 .PHONY: rename
@@ -141,13 +141,13 @@ distclean: cleanest
 
 ## <LICENSE>
 ## Copyright 2023 Source Code Committers
-## 
+##
 ## Licensed under the Apache License, Version 2.0 (the "License");
 ## you may not use this file except in compliance with the License.
 ## You may obtain a copy of the License at
-## 
+##
 ##     http://www.apache.org/licenses/LICENSE-2.0
-## 
+##
 ## Unless required by applicable law or agreed to in writing, software
 ## distributed under the License is distributed on an "AS IS" BASIS,
 ## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
diff --git a/pyproject.toml b/pyproject.toml
index 4de0b0a..17c2bbf 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -90,9 +90,6 @@ exclude_lines = [
     "if __name__ == .__main__.:",
 ]
 
-[tool.black]
-line-length = 120
-
 [tool.isort]
 profile = "black"
 
@@ -107,3 +104,8 @@ disable = "R0913"
 
 [tool.pylint.format]
 max-line-length = "120"
+
+
+[tool.ruff]
+src = ["src", "test"]
+line-length = 120
diff --git a/setup.cfg b/setup.cfg
index b6ecf23..40cc960 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -15,20 +15,20 @@ zip_safe = True
 [options.extras_require]
 dev =
     bandit~=1.7
-    black~=22.3
     build~=0.8
     flake8~=4.0
     ipython~=8.4
     isort~=5.10
     mypy
     pylint~=2.14
+    ruff == 0.4.4
 test =
     pytest~=7.1
     pytest-cov~=4.0
     pytest-optional-tests
     tox~=3.25
     vcrpy
-docs = 
+docs =
     mkdocs
 
 [options.packages.find]
diff --git a/src/bioutils/accessions.py b/src/bioutils/accessions.py
index 52c0ab1..7a36e1b 100644
--- a/src/bioutils/accessions.py
+++ b/src/bioutils/accessions.py
@@ -25,6 +25,7 @@
 The string form may be used as a CURIE, in which case the document in
 which the CURIE is used must contain a map of ``{namespace : uri}``.
 """
+
 import re
 
 from .exceptions import BioutilsError
diff --git a/src/bioutils/normalize.py b/src/bioutils/normalize.py
index 7e33c20..2e9cff6 100644
--- a/src/bioutils/normalize.py
+++ b/src/bioutils/normalize.py
@@ -1,7 +1,5 @@
 # -*- coding: utf-8 -*-
-"""Provides functionality for normalizing alleles, ensuring comparable representations.
-
-"""
+"""Provides functionality for normalizing alleles, ensuring comparable representations."""
 
 import copy
 import enum
diff --git a/src/bioutils/seqfetcher.py b/src/bioutils/seqfetcher.py
index a94e294..d0455e2 100644
--- a/src/bioutils/seqfetcher.py
+++ b/src/bioutils/seqfetcher.py
@@ -1,7 +1,6 @@
 # -*- coding: utf-8 -*-
-"""Provides sequence fetching from NCBI and Ensembl.
+"""Provides sequence fetching from NCBI and Ensembl."""
 
-"""
 import logging
 import os
 import random
diff --git a/src/bioutils/sequences.py b/src/bioutils/sequences.py
index e994cea..da948a4 100644
--- a/src/bioutils/sequences.py
+++ b/src/bioutils/sequences.py
@@ -1,6 +1,5 @@
 # -*- coding: utf-8 -*-
-"""Simple functions and lookup tables for nucleic acid and amino acid sequences.
-"""
+"""Simple functions and lookup tables for nucleic acid and amino acid sequences."""
 
 import logging
 import re