Update to black 2024 stable style

lib/bx/align/core.py

@@ -1,6 +1,7 @@
 """
 Classes that represent alignments between multiple sequences.
 """
+
 import random
 import weakref
 

lib/bx/align/epo.py

@@ -1,6 +1,5 @@
 """Classes and utilities for mutliple alignments from the EPO pipeline"""
 
-
 import logging
 import os
 import pickle as cPickle

lib/bx/align/maf.py

@@ -4,6 +4,7 @@
 .. _MAF: http://genome.ucsc.edu/FAQ/FAQformat.html#format5
 .. _multiz: http://www.bx.psu.edu/miller_lab/
 """
+
 from io import (
     StringIO,
     TextIOWrapper,

lib/bx/align/score_tests.py

@@ -1,6 +1,7 @@
 """
 Tests for `bx.align.score`.
 """
+
 import unittest
 from io import StringIO
 

lib/bx/align/sitemask/sitemask_tests.py

@@ -1,6 +1,7 @@
 """
 Tests for `bx.align.maf.sitemask`.
 """
+
 import tempfile
 from io import StringIO
 

lib/bx/interval_index_file.py

@@ -80,6 +80,7 @@
 ...          ...           ...
 ============ ===========   =================================================
 """
+
 import os.path
 import sys
 from bisect import (

lib/bx/intervals/operations/merge.py

@@ -2,7 +2,6 @@
 Merge overlapping regions in two sets of genomic intervals.
 """
 
-
 from bx.intervals.io import BitsetSafeReaderWrapper
 from bx.intervals.operations import (
     bits_set_in_range,

lib/bx/misc/binary_file.py

@@ -1,6 +1,7 @@
 """
 Wrappers for doing binary IO on file-like objects
 """
+
 import struct
 import sys
 

lib/bx/misc/seekbzip2.py

@@ -1,6 +1,7 @@
 """
 Semi-random access to bz2 compressed data.
 """
+
 import bisect
 
 from ._seekbzip2 import SeekBzip2

lib/bx/misc/seekbzip2_tests.py

@@ -1,6 +1,7 @@
 """
 Tests for `bx.misc.seekbzip2`.
 """
+
 import bz2
 import os
 import random

lib/bx/motif/pwm.py

@@ -1,6 +1,7 @@
 """
 Classes for working with position specific matrices.
 """
+
 from copy import copy
 
 import numpy

lib/bx/seq/qdna.py

@@ -39,6 +39,7 @@
 Recognized properties (at present only one):
   - codebook: A string in qdna code file format (see QdnaCodebook class for details).
 """
+
 import struct
 from io import StringIO
 

lib/bx/seq/twobit.py

@@ -1,6 +1,7 @@
 """
 Access to files containing sequence data in 'twobit' format.
 """
+
 from collections.abc import Mapping
 from struct import (
     calcsize,

lib/bx/seqmapping_tests.py

@@ -1,6 +1,7 @@
 """
 Tests for `bx.seqmapping`.
 """
+
 import unittest
 from io import StringIO
 

lib/bx/tabular/io.py

@@ -1,6 +1,7 @@
 """
 Reading and writing delimited data files (with headers and comments).
 """
+
 from itertools import count
 
 FIRST_LINE_IS_HEADER = object()

lib/bx/wiggle_tests.py

@@ -1,6 +1,7 @@
 """
 Tests for `bx.wiggle`.
 """
+
 import unittest
 from io import StringIO
 

setup.cfg

@@ -48,7 +48,7 @@ snapshot = egg_info -rb_DEV bdist_egg rotate -m.egg -k1
 build_docs = build_sphinx build_apidocs
 
 [flake8]
-ignore = E203,E501,E741,W503
+ignore = E203,E501,E701,E704,E741,W503
 exclude = .git,.tox,.venv,build,doc/source/conf.py
 import-order-style = smarkets
 application-import-names = bx,bx_extras