Apply isort (forcing single lines, not sorting by type) via ruff

$ ruff check --fix --select=I \
  --config=lint.isort.force-single-line=true \
  --config=lint.isort.order-by-type=false \
  BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py

Using ruff version 0.4.10

Bio/Align/Applications/_ClustalOmega.py

@@ -7,7 +7,9 @@
 # package.
 """Command line wrapper for the multiple alignment program Clustal Omega."""
 
-from Bio.Application import _Option, _Switch, AbstractCommandline
+from Bio.Application import _Option
+from Bio.Application import _Switch
+from Bio.Application import AbstractCommandline
 
 
 class ClustalOmegaCommandline(AbstractCommandline):

Bio/Align/Applications/_Clustalw.py

@@ -7,7 +7,10 @@
 """Command line wrapper for the multiple alignment program Clustal W."""
 
 import os
-from Bio.Application import _Option, _Switch, AbstractCommandline
+
+from Bio.Application import _Option
+from Bio.Application import _Switch
+from Bio.Application import AbstractCommandline
 
 
 class ClustalwCommandline(AbstractCommandline):

Bio/Align/Applications/_Dialign.py

@@ -6,7 +6,10 @@
 # package.
 """Command line wrapper for the multiple alignment program DIALIGN2-2."""
 
-from Bio.Application import _Option, _Argument, _Switch, AbstractCommandline
+from Bio.Application import _Argument
+from Bio.Application import _Option
+from Bio.Application import _Switch
+from Bio.Application import AbstractCommandline
 
 
 class DialignCommandline(AbstractCommandline):

Bio/Align/Applications/_MSAProbs.py

@@ -6,7 +6,10 @@
 # package.
 """Command line wrapper for the multiple sequence alignment program MSAProbs."""
 
-from Bio.Application import _Argument, _Option, _Switch, AbstractCommandline
+from Bio.Application import _Argument
+from Bio.Application import _Option
+from Bio.Application import _Switch
+from Bio.Application import AbstractCommandline
 
 
 class MSAProbsCommandline(AbstractCommandline):

Bio/Align/Applications/_Mafft.py

@@ -6,7 +6,10 @@
 # package.
 """Command line wrapper for the multiple alignment programme MAFFT."""
 
-from Bio.Application import _Option, _Switch, _Argument, AbstractCommandline
+from Bio.Application import _Argument
+from Bio.Application import _Option
+from Bio.Application import _Switch
+from Bio.Application import AbstractCommandline
 
 
 class MafftCommandline(AbstractCommandline):

Bio/Align/Applications/_Muscle.py

@@ -6,7 +6,9 @@
 # package.
 """Command line wrapper for the multiple alignment program MUSCLE."""
 
-from Bio.Application import _Option, _Switch, AbstractCommandline
+from Bio.Application import _Option
+from Bio.Application import _Switch
+from Bio.Application import AbstractCommandline
 
 
 class MuscleCommandline(AbstractCommandline):

Bio/Align/Applications/_Prank.py

@@ -6,7 +6,9 @@
 # package.
 """Command line wrapper for the multiple alignment program PRANK."""
 
-from Bio.Application import _Option, _Switch, AbstractCommandline
+from Bio.Application import _Option
+from Bio.Application import _Switch
+from Bio.Application import AbstractCommandline
 
 
 class PrankCommandline(AbstractCommandline):

Bio/Align/Applications/_Probcons.py

@@ -6,7 +6,10 @@
 # package.
 """Command line wrapper for the multiple alignment program PROBCONS."""
 
-from Bio.Application import _Option, _Switch, _Argument, AbstractCommandline
+from Bio.Application import _Argument
+from Bio.Application import _Option
+from Bio.Application import _Switch
+from Bio.Application import AbstractCommandline
 
 
 class ProbconsCommandline(AbstractCommandline):

Bio/Align/Applications/_TCoffee.py

@@ -6,7 +6,9 @@
 # package.
 """Command line wrapper for the multiple alignment program TCOFFEE."""
 
-from Bio.Application import _Option, _Switch, AbstractCommandline
+from Bio.Application import _Option
+from Bio.Application import _Switch
+from Bio.Application import AbstractCommandline
 
 
 class TCoffeeCommandline(AbstractCommandline):

Bio/Align/Applications/__init__.py

@@ -10,15 +10,15 @@ We have decided to remove this module in future, and instead recommend
 building your command and invoking it via the subprocess module directly.
 """
 
-from ._Muscle import MuscleCommandline
-from ._Clustalw import ClustalwCommandline
 from ._ClustalOmega import ClustalOmegaCommandline
-from ._Prank import PrankCommandline
-from ._Mafft import MafftCommandline
+from ._Clustalw import ClustalwCommandline
 from ._Dialign import DialignCommandline
+from ._Mafft import MafftCommandline
+from ._MSAProbs import MSAProbsCommandline
+from ._Muscle import MuscleCommandline
+from ._Prank import PrankCommandline
 from ._Probcons import ProbconsCommandline
 from ._TCoffee import TCoffeeCommandline
-from ._MSAProbs import MSAProbsCommandline
 
 # Make this explicit, then they show up in the API docs
 __all__ = (

Bio/Align/__init__.py

@@ -13,18 +13,18 @@ class, used in the Bio.AlignIO module.
 
 """
 
-import sys
 import collections
 import copy
 import importlib
+import numbers
+import sys
 import types
 import warnings
-import numbers
+from abc import ABC
+from abc import abstractmethod
 from itertools import zip_longest
-from abc import ABC, abstractmethod
 from typing import Dict
 
-
 try:
     import numpy as np
 except ImportError:
@@ -37,13 +37,17 @@ except ImportError:
 
 from Bio import BiopythonDeprecationWarning
 from Bio.Align import _aligncore  # type: ignore
-from Bio.Align import _pairwisealigner  # type: ignore
 from Bio.Align import _codonaligner  # type: ignore
+from Bio.Align import _pairwisealigner  # type: ignore
 from Bio.Align import substitution_matrices
 from Bio.Data import CodonTable
-from Bio.Seq import Seq, MutableSeq, reverse_complement, UndefinedSequenceError
+from Bio.Seq import MutableSeq
+from Bio.Seq import reverse_complement
+from Bio.Seq import Seq
 from Bio.Seq import translate
-from Bio.SeqRecord import SeqRecord, _RestrictedDict
+from Bio.Seq import UndefinedSequenceError
+from Bio.SeqRecord import _RestrictedDict
+from Bio.SeqRecord import SeqRecord
 
 # Import errors may occur here if a compiled _pairwisealigner.c file or
 # compiled _codonaligner.c file (_pairwisealigner.pyd or _pairwisealigner.so,
@@ -357,6 +361,7 @@ class MultipleSeqAlignment:
         """
         if format_spec:
             from io import StringIO
+
             from Bio import AlignIO
 
             handle = StringIO()

Bio/Align/analysis.py

@@ -7,10 +7,16 @@
 """Code for performing calculations on codon alignments."""
 
 import sys
-from math import sqrt, erfc, log, floor
-from heapq import heapify, heappop, heappush
+from collections import Counter
+from collections import defaultdict
+from heapq import heapify
+from heapq import heappop
+from heapq import heappush
 from itertools import permutations
-from collections import defaultdict, Counter
+from math import erfc
+from math import floor
+from math import log
+from math import sqrt
 
 import numpy as np
 

Bio/Align/bed.py

@@ -27,8 +27,8 @@ zero-based end position. We can therefore manipulate ``start`` and
 """
 
 import sys
-import numpy as np
 
+import numpy as np
 
 from Bio.Align import Alignment
 from Bio.Align import interfaces

Bio/Align/bigbed.py

@@ -50,24 +50,23 @@ You are expected to use this module via the Bio.Align functions.
 # CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 # ------------------------------------------------------------------------------
 
-import sys
-import io
-import copy
 import array
+import copy
+import io
 import itertools
 import struct
+import sys
 import zlib
 from collections import namedtuple
 from io import BytesIO
-import numpy as np
 
+import numpy as np
 
 from Bio.Align import Alignment
 from Bio.Align import interfaces
 from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
 
-
 Field = namedtuple("Field", ("as_type", "name", "comment"))
 
 

Bio/Align/bigmaf.py

@@ -17,17 +17,17 @@ import re
 import struct
 import zlib
 
-
-from Bio.Align import Alignment, Alignments
-from Bio.Align import bigbed, maf
-from Bio.Align import _aligncore  # type: ignore
-from Bio.Align.bigbed import AutoSQLTable, Field
-from Bio.Seq import Seq
-from Bio.SeqRecord import SeqRecord
-
-
 import numpy as np
 
+from Bio.Align import _aligncore  # type: ignore
+from Bio.Align import Alignment
+from Bio.Align import Alignments
+from Bio.Align import bigbed
+from Bio.Align import maf
+from Bio.Align.bigbed import AutoSQLTable
+from Bio.Align.bigbed import Field
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
 
 declaration = AutoSQLTable(
     "bedMaf",

Bio/Align/bigpsl.py

@@ -20,15 +20,19 @@ You are expected to use this module via the Bio.Align functions.
 
 import numpy as np
 
-
-from Bio.Align import Alignment, Alignments
-from Bio.Align import bigbed, psl
-from Bio.Align.bigbed import AutoSQLTable, Field
-from Bio.Seq import Seq, reverse_complement, UndefinedSequenceError
-from Bio.SeqRecord import SeqRecord
-from Bio.SeqFeature import SeqFeature, Location
+from Bio.Align import Alignment
+from Bio.Align import Alignments
+from Bio.Align import bigbed
+from Bio.Align import psl
+from Bio.Align.bigbed import AutoSQLTable
+from Bio.Align.bigbed import Field
+from Bio.Seq import reverse_complement
+from Bio.Seq import Seq
+from Bio.Seq import UndefinedSequenceError
+from Bio.SeqFeature import Location
+from Bio.SeqFeature import SeqFeature
 from Bio.SeqIO.InsdcIO import _insdc_location_string
-
+from Bio.SeqRecord import SeqRecord
 
 declaration = AutoSQLTable(
     "bigPsl",

Bio/Align/chain.py

@@ -21,7 +21,6 @@ positions (like Python) and aligning region sizes.
 
 import numpy as np
 
-
 from Bio.Align import Alignment
 from Bio.Align import interfaces
 from Bio.Seq import Seq

Bio/Align/exonerate.py

@@ -29,7 +29,6 @@ You are expected to use this module via the Bio.Align functions.
 
 import numpy as np
 
-
 from Bio.Align import Alignment
 from Bio.Align import interfaces
 from Bio.Seq import Seq

Bio/Align/interfaces.py

@@ -17,7 +17,8 @@ from abc import abstractmethod
 from typing import Optional
 
 from Bio import StreamModeError
-from Bio.Align import Alignments, AlignmentsAbstractBaseClass
+from Bio.Align import Alignments
+from Bio.Align import AlignmentsAbstractBaseClass
 
 
 class AlignmentIterator(AlignmentsAbstractBaseClass):

Bio/Align/maf.py

@@ -29,13 +29,13 @@ zero-based end position. We can therefore manipulate ``start`` and
 ``start + size`` as python list slice boundaries.
 """
 
-import shlex
 import itertools
-
+import shlex
 
 from Bio.Align import Alignment
 from Bio.Align import interfaces
-from Bio.Seq import Seq, reverse_complement
+from Bio.Seq import reverse_complement
+from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
 
 

Bio/Align/mauve.py

@@ -11,7 +11,8 @@ You are expected to use this module via the Bio.Align functions.
 
 from Bio.Align import Alignment
 from Bio.Align import interfaces
-from Bio.Seq import Seq, reverse_complement
+from Bio.Seq import reverse_complement
+from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
 
 

Bio/Align/msf.py

@@ -15,13 +15,12 @@ You are expected to use this module via the Bio.Align functions.
 
 import warnings
 
+from Bio import BiopythonParserWarning
 from Bio.Align import Alignment
 from Bio.Align import interfaces
 from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
 
-from Bio import BiopythonParserWarning
-
 
 class AlignmentIterator(interfaces.AlignmentIterator):
     """GCG MSF alignment iterator."""

Bio/Align/nexus.py

@@ -20,9 +20,9 @@ import numpy as np
 
 from Bio.Align import Alignment
 from Bio.Align import interfaces
+from Bio.Nexus import Nexus
 from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
-from Bio.Nexus import Nexus
 
 
 class AlignmentWriter(interfaces.AlignmentWriter):

Bio/Align/phylip.py

@@ -14,7 +14,6 @@ from Bio.Align import interfaces
 from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
 
-
 _PHYLIP_ID_WIDTH = 10
 
 

Bio/Align/psl.py

@@ -27,14 +27,19 @@ zero-based end position. We can therefore manipulate ``start`` and
 """
 
 from itertools import chain
-import numpy as np
 
+import numpy as np
 
 from Bio.Align import Alignment
 from Bio.Align import interfaces
-from Bio.Seq import Seq, reverse_complement, UndefinedSequenceError
+from Bio.Seq import reverse_complement
+from Bio.Seq import Seq
+from Bio.Seq import UndefinedSequenceError
+from Bio.SeqFeature import CompoundLocation
+from Bio.SeqFeature import ExactPosition
+from Bio.SeqFeature import SeqFeature
+from Bio.SeqFeature import SimpleLocation
 from Bio.SeqRecord import SeqRecord
-from Bio.SeqFeature import SeqFeature, ExactPosition, SimpleLocation, CompoundLocation
 
 
 class AlignmentWriter(interfaces.AlignmentWriter):

Bio/Align/sam.py

@@ -22,14 +22,16 @@ positions; the parser converts these to zero-based coordinates to be consistent
 with Python and other alignment formats.
 """
 
-from itertools import chain
 import copy
+from itertools import chain
 
 import numpy as np
 
 from Bio.Align import Alignment
 from Bio.Align import interfaces
-from Bio.Seq import Seq, reverse_complement, UndefinedSequenceError
+from Bio.Seq import reverse_complement
+from Bio.Seq import Seq
+from Bio.Seq import UndefinedSequenceError
 from Bio.SeqRecord import SeqRecord
 
 

Bio/Align/substitution_matrices/__init__.py

@@ -9,6 +9,7 @@
 
 import os
 import string
+
 import numpy as np
 
 from Bio.File import as_handle

Bio/Align/tabular.py

@@ -11,9 +11,11 @@ This module contains a parser for tabular output from BLAST run with the
 FASTA alignment tools using the '-m 8CB' or '-m 8CC' arguments.
 """
 
-import re
 import enum
+import re
+
 import numpy as np
+
 from Bio.Align import Alignment
 from Bio.Align import interfaces
 from Bio.Seq import Seq

Bio/AlignIO/FastaIO.py

@@ -305,6 +305,7 @@ handle.name: {handle.name}
                 key, value = (s.strip() for s in line[2:].split(": ", 1))
             else:
                 import warnings
+
                 from Bio import BiopythonParserWarning
 
                 # Seen in lalign36, specifically version 36.3.4 Apr, 2011

Bio/AlignIO/MafIO.py

@@ -34,7 +34,6 @@ A 1-column wide alignment would have ``start == end``.
 """
 
 import os
-
 from itertools import islice
 
 try:

Bio/AlignIO/MauveIO.py

@@ -78,7 +78,6 @@ the annotation attribute of each record::
 """
 
 import re
-
 from typing import List
 
 from Bio.Align import MultipleSeqAlignment
@@ -88,7 +87,6 @@ from Bio.SeqRecord import SeqRecord
 from .Interfaces import AlignmentIterator
 from .Interfaces import SequentialAlignmentWriter
 
-
 XMFA_HEADER_REGEX = re.compile(
     r"> (?P<id>\d+):(?P<start>\d+)-(?P<end>\d+) (?P<strand>[+-]) (?P<name>.*)"
 )

Bio/AlignIO/MsfIO.py

@@ -309,6 +309,7 @@ class MsfIterator(AlignmentIterator):
                 seqs[idx] = s + "-" * (aln_length - len(s))
         if padded:
             import warnings
+
             from Bio import BiopythonParserWarning
 
             warnings.warn(

Bio/AlignIO/NexusIO.py

@@ -14,14 +14,15 @@ as this offers more than just accessing the alignment or its
 sequences as SeqRecord objects.
 """
 
-from typing import IO, Iterator, Optional
+from typing import IO
+from typing import Iterator
+from typing import Optional
 
 from Bio.Align import MultipleSeqAlignment
 from Bio.AlignIO.Interfaces import AlignmentWriter
 from Bio.Nexus import Nexus
 from Bio.SeqRecord import SeqRecord
 
-
 # You can get a couple of example files here:
 # http://www.molecularevolution.org/resources/fileformats/
 

Bio/AlignIO/PhylipIO.py

@@ -44,7 +44,6 @@ from Bio.SeqRecord import SeqRecord
 from .Interfaces import AlignmentIterator
 from .Interfaces import SequentialAlignmentWriter
 
-
 _PHYLIP_ID_WIDTH = 10
 _NO_DOTS = "PHYLIP format no longer allows dots in sequence"
 

Bio/Application/__init__.py

@@ -29,15 +29,13 @@ with the subprocess module.
 
 import os
 import platform
-import sys
-import subprocess
 import re
+import subprocess
+import sys
 import warnings
 
-
 from Bio import BiopythonDeprecationWarning
 
-
 warnings.warn(
     """\
 The Bio.Application modules and modules relying on it have been deprecated.

Bio/Blast/Applications.py

@@ -32,7 +32,9 @@ We have decided to remove this module in future, and instead recommend
 building your command and invoking it via the subprocess module directly.
 """
 
-from Bio.Application import _Option, AbstractCommandline, _Switch
+from Bio.Application import _Option
+from Bio.Application import _Switch
+from Bio.Application import AbstractCommandline
 
 
 class _NcbibaseblastCommandline(AbstractCommandline):

Bio/Blast/NCBIWWW.py

@@ -20,16 +20,16 @@ Variables:
 
 """
 
-import warnings
-
-from io import StringIO
 import time
-
+import warnings
+from io import StringIO
 from urllib.parse import urlencode
-from urllib.request import build_opener, install_opener
-from urllib.request import urlopen
-from urllib.request import HTTPPasswordMgrWithDefaultRealm, HTTPBasicAuthHandler
+from urllib.request import build_opener
+from urllib.request import HTTPBasicAuthHandler
+from urllib.request import HTTPPasswordMgrWithDefaultRealm
+from urllib.request import install_opener
 from urllib.request import Request
+from urllib.request import urlopen
 
 from Bio import BiopythonWarning
 from Bio._utils import function_with_previous

Bio/Blast/NCBIXML.py

@@ -32,9 +32,9 @@ Parameters         Holds information from the parameters.
 import xml.sax
 from xml.sax.handler import ContentHandler
 
+from Bio.Align import MultipleSeqAlignment
 from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
-from Bio.Align import MultipleSeqAlignment
 
 
 def fmt_(value, format_spec="%s", default_str="<unknown>"):

Bio/Blast/__init__.py

@@ -22,29 +22,28 @@ Variables:
 
 """
 
-import warnings
-
 import io
 import textwrap
 import time
+import warnings
+from collections import UserList
+from urllib.parse import urlencode
+from urllib.request import build_opener
+from urllib.request import HTTPBasicAuthHandler
+from urllib.request import HTTPPasswordMgrWithDefaultRealm
+from urllib.request import install_opener
+from urllib.request import Request
+from urllib.request import urlopen
+from xml.parsers import expat
 
 import numpy as np
 
-from collections import UserList
-from urllib.parse import urlencode
-from urllib.request import build_opener, install_opener
-from urllib.request import urlopen
-from urllib.request import HTTPPasswordMgrWithDefaultRealm, HTTPBasicAuthHandler
-from urllib.request import Request
-from xml.parsers import expat
-
-
 from Bio import BiopythonWarning
 from Bio import StreamModeError
-from Bio.Align import Alignment, Alignments
-from Bio.Blast import _writers
 from Bio._utils import function_with_previous
-
+from Bio.Align import Alignment
+from Bio.Align import Alignments
+from Bio.Blast import _writers
 
 email = None
 tool = "biopython"

Bio/Blast/_parser.py

@@ -14,18 +14,23 @@ The BLAST XML DTD file is available on the NCBI site at:
 https://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd
 """
 
-import os.path
 import html
+import os.path
 from collections import deque
+from typing import Callable
+from typing import Dict
 from xml.parsers import expat
-from typing import Dict, Callable
 
-from Bio.Blast import Record, Hit, HSP
-from Bio.Seq import Seq, reverse_complement
-from Bio.SeqRecord import SeqRecord
-from Bio.SeqFeature import SeqFeature, SimpleLocation
-from Bio.Align import Alignment
 from Bio import Entrez
+from Bio.Align import Alignment
+from Bio.Blast import Hit
+from Bio.Blast import HSP
+from Bio.Blast import Record
+from Bio.Seq import reverse_complement
+from Bio.Seq import Seq
+from Bio.SeqFeature import SeqFeature
+from Bio.SeqFeature import SimpleLocation
+from Bio.SeqRecord import SeqRecord
 
 
 class DTDHandler:

Bio/Blast/_writers.py

@@ -1,6 +1,7 @@
-import html
 import codecs
-from abc import ABC, abstractmethod
+import html
+from abc import ABC
+from abc import abstractmethod
 
 from Bio.Seq import UndefinedSequenceError
 

Bio/Data/CodonTable.py

@@ -13,9 +13,11 @@ using Scripts/update_ncbi_codon_table.py
 Last updated at Version 4.4 (May 2019)
 """
 
-from Bio.Data import IUPACData
+from typing import Dict
+from typing import List
+from typing import Optional
 
-from typing import Dict, List, Optional
+from Bio.Data import IUPACData
 
 unambiguous_dna_by_name = {}
 unambiguous_dna_by_id = {}

Bio/Emboss/Applications.py

@@ -16,7 +16,9 @@ We have decided to remove this module in future, and instead recommend
 building your command and invoking it via the subprocess module directly.
 """
 
-from Bio.Application import _Option, _Switch, AbstractCommandline
+from Bio.Application import _Option
+from Bio.Application import _Switch
+from Bio.Application import AbstractCommandline
 
 
 class _EmbossMinimalCommandLine(AbstractCommandline):

Bio/Entrez/Parser.py

@@ -40,18 +40,16 @@ with parsing the DTD, and the other half with the XML itself.
 
 import os
 import warnings
-from collections import Counter
-from xml.parsers import expat
-from io import BytesIO
 import xml.etree.ElementTree as ET
+from collections import Counter
+from io import BytesIO
+from urllib.parse import urlparse
+from urllib.request import urlopen
+from xml.parsers import expat
 from xml.sax.saxutils import escape
 
-from urllib.request import urlopen
-from urllib.parse import urlparse
-
 from Bio import StreamModeError
 
-
 # The following four classes are used to add a member .attributes to integers,
 # strings, lists, and dictionaries, respectively.
 

Bio/Entrez/__init__.py

@@ -127,12 +127,14 @@ Functions:
 
 """
 
+import io
 import time
 import warnings
-import io
-from urllib.error import URLError, HTTPError
+from urllib.error import HTTPError
+from urllib.error import URLError
 from urllib.parse import urlencode
-from urllib.request import urlopen, Request
+from urllib.request import Request
+from urllib.request import urlopen
 
 from Bio import BiopythonDeprecationWarning
 from Bio._utils import function_with_previous

Bio/ExPASy/ScanProsite.py

@@ -6,9 +6,8 @@
 """Code for calling and parsing ScanProsite from ExPASy."""
 
 # Importing these functions with leading underscore as not intended for reuse
-from urllib.request import urlopen
 from urllib.parse import urlencode
-
+from urllib.request import urlopen
 from xml.sax import handler
 from xml.sax.expatreader import ExpatParser
 

Bio/ExPASy/__init__.py

@@ -17,8 +17,8 @@ Functions:
 """
 
 import io
-from urllib.request import urlopen
 from urllib.error import HTTPError
+from urllib.request import urlopen
 
 
 def get_prodoc_entry(

Bio/File.py

@@ -11,12 +11,12 @@ Bio.File defines private classes used in Bio.SeqIO and Bio.SearchIO for
 indexing files. These are not intended for direct use.
 """
 
-import os
+import collections.abc
 import contextlib
 import itertools
-import collections.abc
-
-from abc import ABC, abstractmethod
+import os
+from abc import ABC
+from abc import abstractmethod
 
 try:
     import sqlite3

Bio/GenBank/Scanner.py

@@ -27,17 +27,16 @@ Feature Table Documentation:
 # for more details of this format, and an example.
 # Added by Ying Huang & Iddo Friedberg
 
-import warnings
 import re
 import sys
+import warnings
 from collections import defaultdict
+from typing import List
 
+from Bio import BiopythonParserWarning
 from Bio.File import as_handle
 from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
-from Bio import BiopythonParserWarning
-
-from typing import List
 
 
 class InsdcScanner:

Bio/GenBank/__init__.py

@@ -43,15 +43,15 @@ import warnings
 from Bio import BiopythonParserWarning
 from Bio.Seq import Seq
 from Bio.SeqFeature import Location
+from Bio.SeqFeature import LocationParserError
 from Bio.SeqFeature import Reference
 from Bio.SeqFeature import SeqFeature
 from Bio.SeqFeature import SimpleLocation
-from Bio.SeqFeature import LocationParserError
+
+from .Scanner import GenBankScanner
 
 # other Bio.GenBank stuff
 from .utils import FeatureValueCleaner
-from .Scanner import GenBankScanner
-
 
 # Constants used to parse GenBank header lines
 GENBANK_INDENT = 12

Bio/Graphics/BasicChromosome.py

@@ -34,18 +34,21 @@ reportlab's renderPM module installed you can also use PNG etc.
 """
 
 # reportlab
+from reportlab.graphics.shapes import ArcPath
+from reportlab.graphics.shapes import Drawing
+from reportlab.graphics.shapes import Line
+from reportlab.graphics.shapes import Rect
+from reportlab.graphics.shapes import String
+from reportlab.graphics.shapes import Wedge
+from reportlab.graphics.widgetbase import Widget
+from reportlab.lib import colors
 from reportlab.lib.pagesizes import letter
 from reportlab.lib.units import inch
-from reportlab.lib import colors
 from reportlab.pdfbase.pdfmetrics import stringWidth
 
-from reportlab.graphics.shapes import Drawing, String, Line, Rect, Wedge, ArcPath
-from reportlab.graphics.widgetbase import Widget
-
 from Bio.Graphics import _write
 from Bio.Graphics.GenomeDiagram import _Colors
 
-
 _color_trans = _Colors.ColorTranslator()
 
 
@@ -538,6 +541,7 @@ def _spring_layout(desired, minimum, maximum, gap=0):
 
     if equal_step < gap:
         import warnings
+
         from Bio import BiopythonWarning
 
         warnings.warn("Too many labels to avoid overlap", BiopythonWarning)

Bio/Graphics/ColorSpiral.py

@@ -21,8 +21,11 @@ categories to be coloured).
 
 # standard library
 import colorsys  # colour format conversions
-from math import log, exp, floor, pi
 import random  # for jitter values
+from math import exp
+from math import floor
+from math import log
+from math import pi
 
 
 class ColorSpiral:

Bio/Graphics/Comparative.py

@@ -12,16 +12,19 @@ two variables in a traditional scatter plot.
 """
 
 # reportlab
-from reportlab.lib import colors
 from reportlab.graphics.charts.lineplots import LinePlot
+from reportlab.graphics.charts.markers import makeEmptyCircle
+from reportlab.graphics.charts.markers import makeEmptySquare
+from reportlab.graphics.charts.markers import makeFilledCircle
+from reportlab.graphics.charts.markers import makeFilledDiamond
+from reportlab.graphics.charts.markers import makeFilledSquare
+from reportlab.graphics.charts.markers import makeSmiley
+from reportlab.graphics.shapes import Drawing
+from reportlab.graphics.shapes import String
+from reportlab.lib import colors
 from reportlab.lib.pagesizes import letter
 from reportlab.lib.units import inch
 
-from reportlab.graphics.shapes import Drawing, String
-from reportlab.graphics.charts.markers import makeEmptySquare, makeFilledSquare
-from reportlab.graphics.charts.markers import makeFilledDiamond, makeSmiley
-from reportlab.graphics.charts.markers import makeFilledCircle, makeEmptyCircle
-
 from Bio.Graphics import _write
 
 

Bio/Graphics/DisplayRepresentation.py

@@ -17,7 +17,6 @@ from reportlab.lib import colors
 from Bio.Graphics.BasicChromosome import ChromosomeSegment
 from Bio.Graphics.BasicChromosome import TelomereSegment
 
-
 # --- constants
 # This is a default color scheme based on the light spectrum.
 # Based on my vague recollections from biology, this is our friend ROY G. BIV

Bio/Graphics/Distribution.py

@@ -17,15 +17,16 @@ Reportlab is used for producing the graphical output.
 # standard library
 import math
 
+from reportlab.graphics.charts.barcharts import BarChartProperties
+from reportlab.graphics.charts.barcharts import VerticalBarChart
+from reportlab.graphics.shapes import Drawing
+from reportlab.graphics.shapes import String
+from reportlab.graphics.widgetbase import TypedPropertyCollection
+from reportlab.lib import colors
+
 # reportlab
 from reportlab.lib.pagesizes import letter
 from reportlab.lib.units import inch
-from reportlab.lib import colors
-
-from reportlab.graphics.shapes import Drawing, String
-from reportlab.graphics.charts.barcharts import VerticalBarChart
-from reportlab.graphics.charts.barcharts import BarChartProperties
-from reportlab.graphics.widgetbase import TypedPropertyCollection
 
 from Bio.Graphics import _write
 

Bio/Graphics/GenomeDiagram/_AbstractDrawer.py

@@ -34,12 +34,14 @@ like SeqFeatures.
 
 # ReportLab imports
 
-from reportlab.lib import pagesizes
-from reportlab.lib import colors
-from reportlab.graphics.shapes import Polygon
-
-from math import pi, sin, cos
 from itertools import islice
+from math import cos
+from math import pi
+from math import sin
+
+from reportlab.graphics.shapes import Polygon
+from reportlab.lib import colors
+from reportlab.lib import pagesizes
 
 ################################################################################
 # METHODS

Bio/Graphics/GenomeDiagram/_CircularDrawer.py

@@ -15,18 +15,28 @@
 
 # ReportLab imports
 
-from reportlab.graphics.shapes import Drawing, String, Group, Line, Circle, Polygon
-from reportlab.lib import colors
+from math import cos
+from math import pi
+from math import sin
+
 from reportlab.graphics.shapes import ArcPath
+from reportlab.graphics.shapes import Circle
+from reportlab.graphics.shapes import Drawing
+from reportlab.graphics.shapes import Group
+from reportlab.graphics.shapes import Line
+from reportlab.graphics.shapes import Polygon
+from reportlab.graphics.shapes import String
+from reportlab.lib import colors
+
+from ._AbstractDrawer import _stroke_and_fill_colors
 
 # GenomeDiagram imports
-from ._AbstractDrawer import AbstractDrawer, draw_polygon, intermediate_points
-from ._AbstractDrawer import _stroke_and_fill_colors
+from ._AbstractDrawer import AbstractDrawer
+from ._AbstractDrawer import draw_polygon
+from ._AbstractDrawer import intermediate_points
 from ._FeatureSet import FeatureSet
 from ._GraphSet import GraphSet
 
-from math import pi, cos, sin
-
 
 class CircularDrawer(AbstractDrawer):
     """Object for drawing circular diagrams.

Bio/Graphics/GenomeDiagram/_Diagram.py

@@ -28,12 +28,12 @@ except ImportError:
     # This is an optional part of ReportLab, so may not be installed.
     renderPM = None
 
-from ._LinearDrawer import LinearDrawer
-from ._CircularDrawer import CircularDrawer
-from ._Track import Track
-
 from Bio.Graphics import _write
 
+from ._CircularDrawer import CircularDrawer
+from ._LinearDrawer import LinearDrawer
+from ._Track import Track
+
 
 def _first_defined(*args):
     """Return the first non-null argument (PRIVATE)."""

Bio/Graphics/GenomeDiagram/_FeatureSet.py

@@ -25,11 +25,11 @@ the diagram: http://www.reportlab.com
 """
 
 # GenomeDiagram
-from ._Feature import Feature
-
 # Builtins
 import re
 
+from ._Feature import Feature
+
 
 class FeatureSet:
     """FeatureSet object."""

Bio/Graphics/GenomeDiagram/_Graph.py

@@ -23,10 +23,10 @@ the diagram: http://www.reportlab.com
 
 # ReportLab imports
 
-from reportlab.lib import colors
-
 from math import sqrt
 
+from reportlab.lib import colors
+
 
 class GraphData:
     """Graph Data.

Bio/Graphics/GenomeDiagram/_LinearDrawer.py

@@ -22,18 +22,28 @@ the diagram: http://www.reportlab.com
 
 # ReportLab imports
 
-from reportlab.graphics.shapes import Drawing, Line, String, Group, Polygon
+from math import ceil
+
+from reportlab.graphics.shapes import Drawing
+from reportlab.graphics.shapes import Group
+from reportlab.graphics.shapes import Line
+from reportlab.graphics.shapes import Polygon
+from reportlab.graphics.shapes import String
 from reportlab.lib import colors
 
+from ._AbstractDrawer import _stroke_and_fill_colors
+
 # GenomeDiagram imports
-from ._AbstractDrawer import AbstractDrawer, draw_box, draw_arrow
-from ._AbstractDrawer import draw_cut_corner_box, _stroke_and_fill_colors
-from ._AbstractDrawer import intermediate_points, angle2trig, deduplicate
+from ._AbstractDrawer import AbstractDrawer
+from ._AbstractDrawer import angle2trig
+from ._AbstractDrawer import deduplicate
+from ._AbstractDrawer import draw_arrow
+from ._AbstractDrawer import draw_box
+from ._AbstractDrawer import draw_cut_corner_box
+from ._AbstractDrawer import intermediate_points
 from ._FeatureSet import FeatureSet
 from ._GraphSet import GraphSet
 
-from math import ceil
-
 
 class LinearDrawer(AbstractDrawer):
     """Linear Drawer.

Bio/Graphics/GenomeDiagram/__init__.py

@@ -16,14 +16,14 @@
 # Local imports, to make these classes available directly under the
 # Bio.Graphics.GenomeDiagram namespace:
 
-from ._Diagram import Diagram
-from ._Track import Track
-from ._FeatureSet import FeatureSet
-from ._GraphSet import GraphSet
-from ._CrossLink import CrossLink
 from ._Colors import ColorTranslator
+from ._CrossLink import CrossLink
+from ._Diagram import Diagram
 from ._Feature import Feature
+from ._FeatureSet import FeatureSet
 from ._Graph import GraphData
+from ._GraphSet import GraphSet
+from ._Track import Track
 
 __all__ = (
     "Diagram",

Bio/Graphics/__init__.py

@@ -43,7 +43,9 @@ def _write(drawing, output_file, format, dpi=72):
 
     No return value.
     """
-    from reportlab.graphics import renderPS, renderPDF, renderSVG
+    from reportlab.graphics import renderPDF
+    from reportlab.graphics import renderPS
+    from reportlab.graphics import renderSVG
 
     try:
         from reportlab.graphics import renderPM

Bio/HMM/MarkovModel.py

@@ -11,11 +11,11 @@
 import copy
 import math
 import random
-from collections import defaultdict
 import warnings
+from collections import defaultdict
 
-from Bio.Seq import Seq
 from Bio import BiopythonDeprecationWarning
+from Bio.Seq import Seq
 
 warnings.warn(
     "The 'Bio.HMM.MarkovModule' module is deprecated and will be "

Bio/HMM/Trainer.py

@@ -24,11 +24,11 @@ This aims to estimate two parameters:
 import math
 import warnings
 
+from Bio import BiopythonDeprecationWarning
+
 # local stuff
 from .DynamicProgramming import ScaledDPAlgorithms
 
-from Bio import BiopythonDeprecationWarning
-
 warnings.warn(
     "The 'Bio.HMM.Trainer' module is deprecated and will be removed "
     "in a future release of Biopython. Consider using the hmmlearn "

Bio/HMM/Utilities.py

@@ -15,7 +15,6 @@ import warnings
 
 from Bio import BiopythonDeprecationWarning
 
-
 warnings.warn(
     "The 'Bio.HMM.Utilities' module is deprecated and will be "
     "removed in a future release of Biopython. Consider using the "

Bio/KEGG/Compound/__init__.py

@@ -15,8 +15,10 @@ Classes:
  - Record - A representation of a KEGG Ligand/Compound.
 """
 
-from Bio.KEGG import _default_wrap, _struct_wrap, _wrap_kegg, _write_kegg
-
+from Bio.KEGG import _default_wrap
+from Bio.KEGG import _struct_wrap
+from Bio.KEGG import _wrap_kegg
+from Bio.KEGG import _write_kegg
 
 # Set up line wrapping rules (see Bio.KEGG._wrap_kegg)
 name_wrap = [0, "", (" ", "$", 1, 1), ("-", "$", 1, 1)]

Bio/KEGG/Enzyme/__init__.py

@@ -13,8 +13,10 @@ Classes:
  - Record - Holds the information from a KEGG Enzyme record.
 """
 
-from Bio.KEGG import _default_wrap, _struct_wrap, _wrap_kegg, _write_kegg
-
+from Bio.KEGG import _default_wrap
+from Bio.KEGG import _struct_wrap
+from Bio.KEGG import _wrap_kegg
+from Bio.KEGG import _write_kegg
 
 # Set up line wrapping rules (see Bio.KEGG._wrap_kegg)
 rxn_wrap = [

Bio/KEGG/Gene/__init__.py

@@ -15,8 +15,9 @@ Classes:
 
 """
 
-from Bio.KEGG import _default_wrap, _wrap_kegg, _write_kegg
-
+from Bio.KEGG import _default_wrap
+from Bio.KEGG import _wrap_kegg
+from Bio.KEGG import _write_kegg
 
 # Set up line wrapping rules (see Bio.KEGG._wrap_kegg)
 name_wrap = [0, "", (" ", "$", 1, 1), ("-", "$", 1, 1)]

Bio/KEGG/KGML/KGML_parser.py

@@ -18,12 +18,15 @@ Functions:
 
 """
 
+from io import StringIO
 from xml.etree import ElementTree
 
-from io import StringIO
-
-from Bio.KEGG.KGML.KGML_pathway import Component, Entry, Graphics
-from Bio.KEGG.KGML.KGML_pathway import Pathway, Reaction, Relation
+from Bio.KEGG.KGML.KGML_pathway import Component
+from Bio.KEGG.KGML.KGML_pathway import Entry
+from Bio.KEGG.KGML.KGML_pathway import Graphics
+from Bio.KEGG.KGML.KGML_pathway import Pathway
+from Bio.KEGG.KGML.KGML_pathway import Reaction
+from Bio.KEGG.KGML.KGML_pathway import Relation
 
 
 def read(handle):
@@ -174,6 +177,7 @@ class KGMLParser:
             else:
                 # This should warn us of any unimplemented tags
                 import warnings
+
                 from Bio import BiopythonParserWarning
 
                 warnings.warn(

Bio/KEGG/KGML/KGML_pathway.py

@@ -23,9 +23,9 @@ Classes:
 """
 
 import time
+import xml.etree.ElementTree as ET
 from itertools import chain
 from xml.dom import minidom
-import xml.etree.ElementTree as ET
 
 
 # Pathway

Bio/KEGG/REST.py

@@ -30,8 +30,9 @@ Nucleic Acids Res. 28, 29-34 (2000).
 """
 
 import io
-from urllib.request import urlopen
 import time
+from urllib.request import urlopen
+
 from Bio._utils import function_with_previous
 
 

Bio/LogisticRegression.py

@@ -20,6 +20,7 @@ instead.
 """
 
 import warnings
+
 from Bio import BiopythonDeprecationWarning
 
 warnings.warn(

Bio/MarkovModel.py

@@ -23,6 +23,7 @@ MarkovModel     Holds the description of a markov model
 """
 
 import warnings
+
 from Bio import BiopythonDeprecationWarning
 
 warnings.warn(

Bio/MaxEntropy.py

@@ -10,8 +10,8 @@ Uses Improved Iterative Scaling.
 """
 # TODO Define terminology
 
-from functools import reduce
 import warnings
+from functools import reduce
 
 try:
     import numpy as np

Bio/NaiveBayes.py

@@ -29,6 +29,7 @@ Functions:
 """
 
 import warnings
+
 from Bio import BiopythonDeprecationWarning
 
 warnings.warn(

Bio/Nexus/Nexus.py

@@ -12,22 +12,20 @@ Based upon 'NEXUS: An extensible file format for systematic information'
 Maddison, Swofford, Maddison. 1997. Syst. Biol. 46(4):590-621
 """
 
-from functools import reduce
 import copy
 import math
 import random
 import sys
 import warnings
+from functools import reduce
 
+from Bio import BiopythonDeprecationWarning
+from Bio import BiopythonWarning
 from Bio import File
 from Bio.Data import IUPACData
-from Bio.Seq import Seq
-from Bio import BiopythonDeprecationWarning, BiopythonWarning
-
-
 from Bio.Nexus.StandardData import StandardData
 from Bio.Nexus.Trees import Tree
-
+from Bio.Seq import Seq
 
 INTERLEAVE = 70
 SPECIAL_COMMANDS = [

Bio/Nexus/Nodes.py

@@ -16,7 +16,9 @@ Subclassed by Nexus.Trees to store phylogenetic trees.
 Bug reports to Frank Kauff (fkauff@biologie.uni-kl.de)
 """
 
-from typing import Dict, List, Optional
+from typing import Dict
+from typing import List
+from typing import Optional
 
 
 class ChainException(Exception):

Bio/Nexus/Trees.py

@@ -16,8 +16,8 @@ nodes).
 import random
 import re
 import sys
-from . import Nodes
 
+from . import Nodes
 
 PRECISION_BRANCHLENGTH = 6
 PRECISION_SUPPORT = 6

Bio/PDB/Atom.py

@@ -9,16 +9,18 @@
 
 import copy
 import sys
-from typing import Optional, TYPE_CHECKING, TypeVar
 import warnings
+from typing import Optional
+from typing import TYPE_CHECKING
+from typing import TypeVar
 
 import numpy as np
 
 import Bio.PDB.Atom
+from Bio.Data import IUPACData
 from Bio.PDB.Entity import DisorderedEntityWrapper
 from Bio.PDB.PDBExceptions import PDBConstructionWarning
 from Bio.PDB.vectors import Vector
-from Bio.Data import IUPACData
 
 if TYPE_CHECKING:
     from Bio.PDB.Residue import Residue

Bio/PDB/Chain.py

@@ -7,11 +7,12 @@
 
 """Chain class, used in Structure objects."""
 
+from typing import Optional
+from typing import TYPE_CHECKING
+
 from Bio.PDB.Entity import Entity
 from Bio.PDB.internal_coords import IC_Chain
 
-from typing import Optional, TYPE_CHECKING
-
 if TYPE_CHECKING:
     from Bio.PDB.Model import Model
     from Bio.PDB.Residue import Residue

Bio/PDB/DSSP.py

@@ -90,17 +90,18 @@ The dssp data returned for a single residue is a tuple in the form:
 
 """
 
-import re
 import os
-from io import StringIO
+import re
 import subprocess
 import warnings
+from io import StringIO
 
+from Bio.Data.PDBData import protein_letters_3to1
+from Bio.Data.PDBData import residue_sasa_scales
 from Bio.PDB.AbstractPropertyMap import AbstractResiduePropertyMap
+from Bio.PDB.MMCIF2Dict import MMCIF2Dict
 from Bio.PDB.PDBExceptions import PDBException
 from Bio.PDB.PDBParser import PDBParser
-from Bio.Data.PDBData import protein_letters_3to1, residue_sasa_scales
-from Bio.PDB.MMCIF2Dict import MMCIF2Dict
 
 # Match C in DSSP
 _dssp_cys = re.compile("[a-z]")

Bio/PDB/Dice.py

@@ -13,8 +13,8 @@ This module is used internally by the Bio.PDB.extract() function.
 import re
 import warnings
 
-from Bio.PDB.PDBIO import PDBIO
 from Bio import BiopythonWarning
+from Bio.PDB.PDBIO import PDBIO
 
 _hydrogen = re.compile("[123 ]*H.*")
 

Bio/PDB/Entity.py

@@ -10,10 +10,16 @@ It is a simple container class, with list and dictionary like properties.
 """
 
 import warnings
-
 from collections import deque
 from copy import copy
-from typing import TYPE_CHECKING, Any, Dict, Generic, List, Optional, TypeVar, Union
+from typing import Any
+from typing import Dict
+from typing import Generic
+from typing import List
+from typing import Optional
+from typing import TYPE_CHECKING
+from typing import TypeVar
+from typing import Union
 
 import numpy as np
 

Bio/PDB/FragmentMapper.py

@@ -44,11 +44,9 @@ The library files can be found in directory 'fragment_data'.
 
 import numpy as np
 
-from Bio.SVDSuperimposer import SVDSuperimposer
-
 from Bio.PDB.PDBExceptions import PDBException
 from Bio.PDB.Polypeptide import PPBuilder
-
+from Bio.SVDSuperimposer import SVDSuperimposer
 
 # fragment file (lib_SIZE_z_LENGTH.txt)
 # SIZE=number of fragments

Bio/PDB/HSExposure.py

@@ -11,7 +11,8 @@ import warnings
 from math import pi
 
 from Bio.PDB.AbstractPropertyMap import AbstractPropertyMap
-from Bio.PDB.Polypeptide import CaPPBuilder, is_aa
+from Bio.PDB.Polypeptide import CaPPBuilder
+from Bio.PDB.Polypeptide import is_aa
 from Bio.PDB.vectors import rotaxis
 
 

Bio/PDB/MMCIFParser.py

@@ -5,15 +5,15 @@
 
 """mmCIF parsers."""
 
-import numpy as np
 import warnings
 
-from Bio.File import as_handle
+import numpy as np
 
+from Bio.File import as_handle
 from Bio.PDB.MMCIF2Dict import MMCIF2Dict
-from Bio.PDB.StructureBuilder import StructureBuilder
 from Bio.PDB.PDBExceptions import PDBConstructionException
 from Bio.PDB.PDBExceptions import PDBConstructionWarning
+from Bio.PDB.StructureBuilder import StructureBuilder
 
 
 class MMCIFParser:

Bio/PDB/Model.py

@@ -5,11 +5,11 @@
 
 """Model class, used in Structure objects."""
 
+from typing import TYPE_CHECKING
+
 from Bio.PDB.Entity import Entity
 from Bio.PDB.internal_coords import IC_Chain
 
-from typing import TYPE_CHECKING
-
 if TYPE_CHECKING:
     from Bio.PDB.Chain import Chain
     from Bio.PDB.Structure import Structure

Bio/PDB/NACCESS.py

@@ -20,15 +20,14 @@ use naccess -y, naccess -h or naccess -w to include HETATM records
 """
 
 import os
-import tempfile
 import shutil
 import subprocess
+import tempfile
 import warnings
+
+from Bio.PDB.AbstractPropertyMap import AbstractAtomPropertyMap
+from Bio.PDB.AbstractPropertyMap import AbstractResiduePropertyMap
 from Bio.PDB.PDBIO import PDBIO
-from Bio.PDB.AbstractPropertyMap import (
-    AbstractResiduePropertyMap,
-    AbstractAtomPropertyMap,
-)
 
 
 def run_naccess(
@@ -199,6 +198,7 @@ class NACCESS_atomic(AbstractAtomPropertyMap):
 
 if __name__ == "__main__":
     import sys
+
     from Bio.PDB.PDBParser import PDBParser
 
     p = PDBParser()

Bio/PDB/NeighborSearch.py

@@ -11,7 +11,9 @@
 import numpy as np
 
 from Bio.PDB.PDBExceptions import PDBException
-from Bio.PDB.Selection import unfold_entities, entity_levels, uniqueify
+from Bio.PDB.Selection import entity_levels
+from Bio.PDB.Selection import unfold_entities
+from Bio.PDB.Selection import uniqueify
 
 
 class NeighborSearch:

Bio/PDB/PDBIO.py

@@ -10,15 +10,14 @@ import warnings
 
 # Exceptions and Warnings
 from Bio import BiopythonWarning
+
+# Allowed Elements
+from Bio.Data.IUPACData import atom_weights
 from Bio.PDB.PDBExceptions import PDBIOException
 
 # To allow saving of chains, residues, etc..
 from Bio.PDB.StructureBuilder import StructureBuilder
 
-# Allowed Elements
-from Bio.Data.IUPACData import atom_weights
-
-
 _ATOM_FORMAT_STRING = (
     "%s%5i %-4s%c%3s %c%4i%c   %8.3f%8.3f%8.3f%s%6.2f      %4s%2s%2s\n"
 )

Bio/PDB/PDBList.py

@@ -44,7 +44,9 @@ import re
 import shutil
 import sys
 from concurrent.futures import ThreadPoolExecutor
-from typing import List, Optional, Tuple
+from typing import List
+from typing import Optional
+from typing import Tuple
 from urllib.request import Request
 from urllib.request import urlcleanup
 from urllib.request import urlopen

Bio/PDB/PDBMLParser.py

@@ -10,7 +10,10 @@ See https://pdbml.wwpdb.org/.
 """
 
 from os import PathLike
-from typing import Dict, Union, Tuple, TextIO
+from typing import Dict
+from typing import TextIO
+from typing import Tuple
+from typing import Union
 from xml.etree import ElementTree
 from xml.etree.ElementTree import Element
 

Bio/PDB/PDBParser.py

@@ -10,13 +10,10 @@ import warnings
 import numpy as np
 
 from Bio.File import as_handle
-
+from Bio.PDB.parse_pdb_header import _parse_pdb_header_list
 from Bio.PDB.PDBExceptions import PDBConstructionException
 from Bio.PDB.PDBExceptions import PDBConstructionWarning
-
 from Bio.PDB.StructureBuilder import StructureBuilder
-from Bio.PDB.parse_pdb_header import _parse_pdb_header_list
-
 
 # If PDB spec says "COLUMNS 18-20" this means line[17:20]
 

Bio/PDB/PICIO.py

@@ -9,38 +9,35 @@
 import re
 from datetime import date
 from io import StringIO
+from typing import List
+from typing import Optional
+from typing import Set
+from typing import TextIO
+from typing import Tuple
+from typing import Union
 
 import numpy as np
 
+from Bio import SeqIO
+from Bio.Data.PDBData import protein_letters_1to3
 from Bio.File import as_handle
-from Bio.PDB.StructureBuilder import StructureBuilder
+from Bio.PDB.ic_data import dihedra_primary_defaults
+from Bio.PDB.ic_data import dihedra_secondary_defaults
+from Bio.PDB.ic_data import dihedra_secondary_xoxt_defaults
+from Bio.PDB.ic_data import hedra_defaults
+from Bio.PDB.ic_data import ic_data_backbone
+from Bio.PDB.ic_data import ic_data_sidechains
+from Bio.PDB.internal_coords import AtomKey
+from Bio.PDB.internal_coords import Dihedron
+from Bio.PDB.internal_coords import Edron
+from Bio.PDB.internal_coords import Hedron
+from Bio.PDB.internal_coords import IC_Chain
+from Bio.PDB.internal_coords import IC_Residue
 from Bio.PDB.parse_pdb_header import _parse_pdb_header_list
 from Bio.PDB.PDBExceptions import PDBException
-
-from Bio.Data.PDBData import protein_letters_1to3
-
-from Bio.PDB.internal_coords import (
-    IC_Residue,
-    IC_Chain,
-    Edron,
-    Hedron,
-    Dihedron,
-    AtomKey,
-)
-
-from Bio.PDB.ic_data import (
-    ic_data_backbone,
-    ic_data_sidechains,
-    hedra_defaults,
-    dihedra_primary_defaults,
-    dihedra_secondary_defaults,
-    dihedra_secondary_xoxt_defaults,
-)
-
-from typing import TextIO, Set, List, Tuple, Union, Optional
-from Bio.PDB.Structure import Structure
 from Bio.PDB.Residue import Residue
-from Bio import SeqIO
+from Bio.PDB.Structure import Structure
+from Bio.PDB.StructureBuilder import StructureBuilder
 
 
 # @profile

Bio/PDB/PSEA.py

@@ -16,8 +16,8 @@ Comput Appl Biosci 1997 , 13:291-295
 ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/
 """
 
-import subprocess
 import os
+import subprocess
 
 from Bio.PDB.Polypeptide import is_aa
 

Bio/PDB/Polypeptide.py

@@ -52,16 +52,15 @@ last residues) have been shown as M (methionine) by the get_sequence method.
 
 import warnings
 
-
 from Bio.Data.PDBData import nucleic_letters_3to1
 from Bio.Data.PDBData import nucleic_letters_3to1_extended
 from Bio.Data.PDBData import protein_letters_3to1
 from Bio.Data.PDBData import protein_letters_3to1_extended
 from Bio.PDB.PDBExceptions import PDBException
-from Bio.PDB.vectors import calc_dihedral, calc_angle
+from Bio.PDB.vectors import calc_angle
+from Bio.PDB.vectors import calc_dihedral
 from Bio.Seq import Seq
 
-
 # Sorted by 1-letter code
 aa3, aa1 = zip(*sorted(protein_letters_3to1.items(), key=lambda x: x[1]))
 standard_aa_names = aa3

Bio/PDB/Residue.py

@@ -7,10 +7,12 @@
 
 """Residue class, used by Structure objects."""
 
-from Bio.PDB.PDBExceptions import PDBConstructionException
-from Bio.PDB.Entity import Entity, DisorderedEntityWrapper
+from typing import TYPE_CHECKING
+from typing import TypeVar
 
-from typing import TYPE_CHECKING, TypeVar
+from Bio.PDB.Entity import DisorderedEntityWrapper
+from Bio.PDB.Entity import Entity
+from Bio.PDB.PDBExceptions import PDBConstructionException
 
 if TYPE_CHECKING:
     from Bio.PDB.Atom import Atom

Bio/PDB/ResidueDepth.py

@@ -57,13 +57,12 @@ import warnings
 
 import numpy as np
 
+from Bio import BiopythonWarning
 from Bio.PDB import PDBParser
 from Bio.PDB import Selection
 from Bio.PDB.AbstractPropertyMap import AbstractPropertyMap
 from Bio.PDB.Polypeptide import is_aa
 
-from Bio import BiopythonWarning
-
 # Table 1: Atom Type to radius
 _atomic_radii = {
     #   atom num dist  Rexplicit Runited-atom

Bio/PDB/SCADIO.py

@@ -36,17 +36,17 @@ hydrogen bonds is at <https://www.thingiverse.com/thing:3957471>.
 """
 # import re
 
-from Bio.File import as_handle
-from Bio.PDB.PDBExceptions import PDBException
+import numpy as np  # type: ignore
 
-from Bio.PDB.internal_coords import IC_Residue, IC_Chain
+from Bio.File import as_handle
+from Bio.PDB.internal_coords import IC_Chain
+from Bio.PDB.internal_coords import IC_Residue
+from Bio.PDB.PDBExceptions import PDBException
 
 # from Bio.PDB.Structure import Structure
 # from Bio.PDB.Residue import Residue
 from Bio.PDB.vectors import homog_scale_mtx
 
-import numpy as np  # type: ignore
-
 
 def _scale_residue(res, scale, scaleMtx):
     if res.internal_coord: