Modernize: switch to ruff, remove Python 2 compat

.github/workflows/tests.yml

@@ -27,15 +27,9 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install flake8 pytest pytest-cov coveralls pylint
+          python -m pip install ruff pytest pytest-cov coveralls
           pip install -r requirements.txt
           pip install .
-      - name: Lint with flake8
-        run: |
-          # stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
       - name: Run default linting script
         run: |
           ./lint.sh

gtfparse/__init__.py

@@ -14,20 +14,19 @@
 from .create_missing_features import create_missing_features
 from .parsing_error import ParsingError
 from .read_gtf import (
-    read_gtf, 
+    read_gtf,
     parse_gtf,
-    parse_gtf_pandas, 
-    parse_gtf_and_expand_attributes, 
+    parse_gtf_pandas,
+    parse_gtf_and_expand_attributes,
     REQUIRED_COLUMNS,
 )
 
-__version__ = "2.6.0"
+__version__ = "2.6.2"
 
 __all__ = [
     "__version__",
     "expand_attribute_strings",
     "create_missing_features",
-
     "parse_gtf_and_expand_attributes",
     "REQUIRED_COLUMNS",
     "ParsingError",

lint.sh

@@ -1,8 +1,6 @@
 #!/bin/bash
 set -o errexit
 
-find . -name '*.py' \
-  | xargs pylint \
-  --errors-only 
+ruff check gtfparse/ tests/
 
-echo 'Passes pylint check'
+echo 'Passes ruff check'

pyproject.toml

@@ -25,3 +25,11 @@ packages = ["gtfparse"]
 [project.urls]
 "Homepage" = "https://github.com/openvax/gtfparse"
 "Bug Tracker" = "https://github.com/openvax/gtfparse"
+
+[tool.ruff.lint]
+select = ["E", "F"]
+ignore = ["F821", "E501", "F841", "E731", "E741", "E722", "E721"]
+
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["F401"]
+"test*/*" = ["F401"]