Reformat files with Ruff

petasus/masses.py

@@ -3,6 +3,7 @@
 Note that this module is particularly tailored to work with Sage's peptide
 strings. Your mileage with other search engines may vary!
 """
+
 import re
 
 import numba as nb

petasus/petasus.py

@@ -1,4 +1,5 @@
 """The main CLI entry point."""
+
 import sys
 
 import click

petasus/scripts/localize_mods.py

@@ -3,6 +3,7 @@
 This script sanitizes the Sage modification masses and attempts to
 localize them on the peptide using a crude, highest-scoring method.
 """
+
 import json
 import logging
 import time

petasus/scripts/sage2lib.py

@@ -1,4 +1,5 @@
 """Converts a search results to a dlib file"""
+
 from pathlib import Path
 
 import click

petasus/scripts/scan2rt.py

@@ -1,4 +1,5 @@
 """Get the retention times, given scan numbers."""
+
 import gzip
 import logging
 import re

tests/conftest.py

@@ -1,4 +1,5 @@
 """Test fixtures"""
+
 from pathlib import Path
 
 import pytest

tests/system_tests/test_localize_mods.py

@@ -1,4 +1,5 @@
 """Test that localize_mods.py works."""
+
 from pathlib import Path
 
 from click.testing import CliRunner

tests/unit_tests/test_localize_mods_fns.py

@@ -1,4 +1,5 @@
 """Test the localize mods functionality"""
+
 import math
 
 import numpy as np

tests/unit_tests/test_masses.py

@@ -1,4 +1,5 @@
 """Test that mass calculations work correctly."""
+
 import numpy as np
 from petasus import masses