diff --git a/Bio/AlignIO/MsfIO.py b/Bio/AlignIO/MsfIO.py
index d620f1b5b13..fe9957818bb 100644
--- a/Bio/AlignIO/MsfIO.py
+++ b/Bio/AlignIO/MsfIO.py
@@ -316,7 +316,7 @@ def __next__(self):
             )
 
         records = (
-            SeqRecord(Seq(s), id=i, name=i, description=i, annotations={"weight": w},)
+            SeqRecord(Seq(s), id=i, name=i, description=i, annotations={"weight": w})
             for (i, s, w) in zip(ids, seqs, weights)
         )
 
diff --git a/Bio/AlignIO/StockholmIO.py b/Bio/AlignIO/StockholmIO.py
index b98a36d6b34..582539a07c5 100644
--- a/Bio/AlignIO/StockholmIO.py
+++ b/Bio/AlignIO/StockholmIO.py
@@ -231,10 +231,7 @@ def _write_record(self, record):
         seq_name = seq_name.replace(" ", "_")
 
         if "start" in record.annotations and "end" in record.annotations:
-            suffix = "/%s-%s" % (
-                record.annotations["start"],
-                record.annotations["end"],
-            )
+            suffix = "/%s-%s" % (record.annotations["start"], record.annotations["end"])
             if seq_name[-len(suffix) :] != suffix:
                 seq_name = "%s/%s-%s" % (
                     seq_name,
diff --git a/Bio/Blast/Record.py b/Bio/Blast/Record.py
index de685651cf6..863324cc7c0 100644
--- a/Bio/Blast/Record.py
+++ b/Bio/Blast/Record.py
@@ -252,7 +252,7 @@ def __str__(self):
         else:
             lines.append(
                 "Query:%8s %s...%s %s"
-                % (self.query_start, self.query[:45], self.query[-3:], self.query_end,)
+                % (self.query_start, self.query[:45], self.query[-3:], self.query_end)
             )
             lines.append("               %s...%s" % (self.match[:45], self.match[-3:]))
             lines.append(
diff --git a/Bio/GenBank/Scanner.py b/Bio/GenBank/Scanner.py
index a62a01b25d3..db4bfd36394 100644
--- a/Bio/GenBank/Scanner.py
+++ b/Bio/GenBank/Scanner.py
@@ -529,7 +529,7 @@ def parse_records(self, handle, do_features=True):
                 yield record
 
     def parse_cds_features(
-        self, handle, alphabet=None, tags2id=("protein_id", "locus_tag", "product"),
+        self, handle, alphabet=None, tags2id=("protein_id", "locus_tag", "product")
     ):
         """Parse CDS features, return SeqRecord object iterator.
 
diff --git a/Bio/Nexus/Nexus.py b/Bio/Nexus/Nexus.py
index ea39bab9fb8..c40a8470bca 100644
--- a/Bio/Nexus/Nexus.py
+++ b/Bio/Nexus/Nexus.py
@@ -416,7 +416,7 @@ def combine(matrices):
             combined.matrix[t] += Seq(
                 str(m.matrix[t])
                 .replace(m.gap, combined.gap)
-                .replace(m.missing, combined.missing),
+                .replace(m.missing, combined.missing)
             )
         # replace date of missing taxa with symbol for missing data
         for t in combined_only:
@@ -425,7 +425,7 @@ def combine(matrices):
             combined.matrix[t] = Seq(combined.missing * combined.nchar) + Seq(
                 str(m.matrix[t])
                 .replace(m.gap, combined.gap)
-                .replace(m.missing, combined.missing),
+                .replace(m.missing, combined.missing)
             )
         combined.taxlabels.extend(m_only)  # new taxon list
         for cn, cs in m.charsets.items():  # adjust character sets for new matrix
@@ -1052,7 +1052,7 @@ def _matrix(self, options):
             # Reformat sequence for non-standard datatypes
             if self.datatype != "standard":
                 iupac_seq = Seq(
-                    _replace_parenthesized_ambigs(chars, self.rev_ambiguous_values),
+                    _replace_parenthesized_ambigs(chars, self.rev_ambiguous_values)
                 )
                 # first taxon has the reference sequence if matchhar is used
                 if taxcount == 1:
diff --git a/Bio/PDB/internal_coords.py b/Bio/PDB/internal_coords.py
index 7452a957313..f9c4938efa4 100644
--- a/Bio/PDB/internal_coords.py
+++ b/Bio/PDB/internal_coords.py
@@ -84,17 +84,7 @@
 from Bio.PDB.ic_data import ic_data_sidechain_extras, residue_atom_bond_state
 
 # for type checking only
-from typing import (
-    List,
-    Dict,
-    Set,
-    TextIO,
-    Union,
-    Tuple,
-    cast,
-    TYPE_CHECKING,
-    Optional,
-)
+from typing import List, Dict, Set, TextIO, Union, Tuple, cast, TYPE_CHECKING, Optional
 
 if TYPE_CHECKING:
     from Bio.PDB.Residue import Residue
@@ -606,7 +596,7 @@ def init_atom_coords(self) -> None:
         a4shift[udFwd] = self.hedraIC[self.dH2ndx, 0][mdFwd]  # len12
 
         self.a4_pre_rotation[:, 2][self.dAtoms_needs_update] = numpy.add(
-            self.a4_pre_rotation[:, 2][self.dAtoms_needs_update], a4shift,
+            self.a4_pre_rotation[:, 2][self.dAtoms_needs_update], a4shift
         )  # so a2 at origin
 
         # build rz rotation matrix for dihedral angle
@@ -1649,7 +1639,7 @@ def clear_transforms(self):
             d.rcst = None
 
     def assemble(
-        self, resetLocation: bool = False, verbose: bool = False,
+        self, resetLocation: bool = False, verbose: bool = False
     ) -> Union[Dict["AtomKey", numpy.array], Dict[HKT, numpy.array], None]:
         """Compute atom coordinates for this residue from internal coordinates.
 
@@ -2841,11 +2831,7 @@ def __init__(self, *args: Union[List["AtomKey"], HKT], **kwargs: str) -> None:
 
         if "len12" in kwargs:
             self.lal = numpy.array(
-                (
-                    float(kwargs["len12"]),
-                    float(kwargs["angle"]),
-                    float(kwargs["len23"]),
-                )
+                (float(kwargs["len12"]), float(kwargs["angle"]), float(kwargs["len23"]))
             )
         else:
             self.lal = numpy.zeros(3)
diff --git a/Bio/SeqIO/FastaIO.py b/Bio/SeqIO/FastaIO.py
index 73abcd484c4..879ce5bff2f 100644
--- a/Bio/SeqIO/FastaIO.py
+++ b/Bio/SeqIO/FastaIO.py
@@ -203,7 +203,7 @@ def iterate(self, handle):
                     # Should we use SeqRecord default for no ID?
                     first_word = ""
                 yield SeqRecord(
-                    Seq(sequence), id=first_word, name=first_word, description=title,
+                    Seq(sequence), id=first_word, name=first_word, description=title
                 )
 
 
@@ -239,7 +239,7 @@ def iterate(self, handle):
                 # Should we use SeqRecord default for no ID?
                 first_word = ""
             yield SeqRecord(
-                Seq(sequence), id=first_word, name=first_word, description=title,
+                Seq(sequence), id=first_word, name=first_word, description=title
             )
 
 
diff --git a/Bio/SeqIO/PirIO.py b/Bio/SeqIO/PirIO.py
index 7f3ae07a35b..1a916d42ad8 100644
--- a/Bio/SeqIO/PirIO.py
+++ b/Bio/SeqIO/PirIO.py
@@ -171,7 +171,7 @@ def iterate(self, handle):
 
             # Return the record and then continue...
             record = SeqRecord(
-                Seq(seq[:-1]), id=identifier, name=identifier, description=description,
+                Seq(seq[:-1]), id=identifier, name=identifier, description=description
             )
             record.annotations["PIR-type"] = pir_type
             if _pir_mol_type[pir_type]:
diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py
index 38f75dfcdff..867728995f1 100644
--- a/Bio/SeqIO/SffIO.py
+++ b/Bio/SeqIO/SffIO.py
@@ -1044,7 +1044,7 @@ def iterate(self, handle):
                 # the index_offset so we can skip extra handle.tell() calls:
                 index_offset = 0
             yield _sff_read_seq_record(
-                handle, number_of_flows_per_read, flow_chars, key_sequence, trim,
+                handle, number_of_flows_per_read, flow_chars, key_sequence, trim
             )
         _check_eof(handle, index_offset, index_length)
 
diff --git a/Bio/SeqIO/_index.py b/Bio/SeqIO/_index.py
index 560b1c2cefe..52b3066d70e 100644
--- a/Bio/SeqIO/_index.py
+++ b/Bio/SeqIO/_index.py
@@ -141,7 +141,7 @@ def get(self, offset):
         handle = self._handle
         handle.seek(offset)
         return SeqIO.SffIO._sff_read_seq_record(
-            handle, self._flows_per_read, self._flow_chars, self._key_sequence,
+            handle, self._flows_per_read, self._flow_chars, self._key_sequence
         )
 
     def get_raw(self, offset):
diff --git a/Bio/codonalign/__init__.py b/Bio/codonalign/__init__.py
index 7ed17005f0e..db3aa3ea472 100644
--- a/Bio/codonalign/__init__.py
+++ b/Bio/codonalign/__init__.py
@@ -246,7 +246,7 @@ def _get_aa_regex(codon_table, stop="*", unknown="X"):
 
 
 def _check_corr(
-    pro, nucl, gap_char, codon_table, complete_protein=False, anchor_len=10,
+    pro, nucl, gap_char, codon_table, complete_protein=False, anchor_len=10
 ):
     """Check if the nucleotide can be translated into the protein (PRIVATE).
 
@@ -571,7 +571,7 @@ def get_aa_from_codonre(re_aa):
 
 
 def _get_codon_rec(
-    pro, nucl, span_mode, gap_char, codon_table, complete_protein=False, max_score=10,
+    pro, nucl, span_mode, gap_char, codon_table, complete_protein=False, max_score=10
 ):
     """Generate codon alignment based on regular re match (PRIVATE).
 
diff --git a/Bio/codonalign/codonalignment.py b/Bio/codonalign/codonalignment.py
index f5570b6f1b6..38cf0e1c965 100644
--- a/Bio/codonalign/codonalignment.py
+++ b/Bio/codonalign/codonalignment.py
@@ -65,7 +65,7 @@ def __str__(self):
         rows = len(self._records)
         lines = [
             "CodonAlignment with %i rows and %i columns (%i codons)"
-            % (rows, self.get_alignment_length(), self.get_aln_length(),)
+            % (rows, self.get_alignment_length(), self.get_aln_length())
         ]
 
         if rows <= 60:
diff --git a/Bio/codonalign/codonseq.py b/Bio/codonalign/codonseq.py
index 725355a10bf..7f1dc57b34b 100644
--- a/Bio/codonalign/codonseq.py
+++ b/Bio/codonalign/codonseq.py
@@ -276,9 +276,7 @@ def _get_codon_list(codonseq):
     return codon_lst
 
 
-def cal_dn_ds(
-    codon_seq1, codon_seq2, method="NG86", codon_table=None, k=1, cfreq=None,
-):
+def cal_dn_ds(codon_seq1, codon_seq2, method="NG86", codon_table=None, k=1, cfreq=None):
     """Calculate dN and dS of the given two sequences.
 
     Available methods:
diff --git a/BioSQL/BioSeq.py b/BioSQL/BioSeq.py
index b9b105b342e..7555890262e 100644
--- a/BioSQL/BioSeq.py
+++ b/BioSQL/BioSeq.py
@@ -321,7 +321,7 @@ def _retrieve_annotations(adaptor, primary_id, taxon_id):
 
 def _retrieve_alphabet(adaptor, primary_id):
     results = adaptor.execute_and_fetchall(
-        "SELECT alphabet FROM biosequence WHERE bioentry_id = %s", (primary_id,),
+        "SELECT alphabet FROM biosequence WHERE bioentry_id = %s", (primary_id,)
     )
     assert len(results) == 1
     alphabets = results[0]
diff --git a/Scripts/PDB/hsexpo.py b/Scripts/PDB/hsexpo.py
index 3bf786cd7a9..5a075d5975f 100644
--- a/Scripts/PDB/hsexpo.py
+++ b/Scripts/PDB/hsexpo.py
@@ -43,7 +43,7 @@
     default="HSEb",
 )
 ap.add_argument(
-    "-o", "--out", dest="outfile", help="output to PDB file (B factor=exposure)",
+    "-o", "--out", dest="outfile", help="output to PDB file (B factor=exposure)"
 )
 ap.add_argument(
     "-r",
diff --git a/Tests/common_BioSQL.py b/Tests/common_BioSQL.py
index b7786cfd368..e4c1b9d6aa5 100644
--- a/Tests/common_BioSQL.py
+++ b/Tests/common_BioSQL.py
@@ -495,12 +495,7 @@ def test_convert(self):
     def test_addition(self):
         """Check can add Seq objects from BioSQL together."""
         test_seq = self.item.seq
-        for other in [
-            Seq("ACGT"),
-            MutableSeq("ACGT"),
-            "ACGT",
-            test_seq,
-        ]:
+        for other in [Seq("ACGT"), MutableSeq("ACGT"), "ACGT", test_seq]:
             test = test_seq + other
             self.assertEqual(test, str(test_seq) + str(other))
             self.assertIsInstance(test, Seq)
diff --git a/Tests/pairwise2_testCases.py b/Tests/pairwise2_testCases.py
index 629e215c342..48f0cb586f1 100755
--- a/Tests/pairwise2_testCases.py
+++ b/Tests/pairwise2_testCases.py
@@ -855,10 +855,7 @@ def test_clean_alignments(self):
             ("ACCGT", "AC-G-", 3.0, 0, 4),
             ("ACCGT", "A-CG-", 3.0, 0, 4),
         ]
-        expected = [
-            ("ACCGT", "AC-G-", 3.0, 0, 4),
-            ("ACCGT", "A-CG-", 3.0, 0, 4),
-        ]
+        expected = [("ACCGT", "AC-G-", 3.0, 0, 4), ("ACCGT", "A-CG-", 3.0, 0, 4)]
         result = pairwise2._clean_alignments(alns)
         self.assertEqual(expected, result)
 
diff --git a/Tests/test_AlignIO.py b/Tests/test_AlignIO.py
index 4cde4234c35..87cb366e62a 100644
--- a/Tests/test_AlignIO.py
+++ b/Tests/test_AlignIO.py
@@ -451,7 +451,7 @@ def test_reading_alignments_nexus2(self):
         self.check_alignment_rows(
             alignment,
             [
-                ("Aegotheles", "AAAAAGGCATTGTGGTGGGAAT",),
+                ("Aegotheles", "AAAAAGGCATTGTGGTGGGAAT"),
                 ("Aerodramus", "?????????TTGTGGTGGGAAT"),
             ],
         )
diff --git a/Tests/test_Align_emboss.py b/Tests/test_Align_emboss.py
index f75e464466e..c4a5056a669 100644
--- a/Tests/test_Align_emboss.py
+++ b/Tests/test_Align_emboss.py
@@ -960,21 +960,17 @@ def test_local_water2(self):
             repr(alignment.sequences[0].seq),
             "Seq({78: 'CGTTTGAGTCTGGGATG'}, length=95)",
         )
-        self.assertEqual(
-            alignment.sequences[0].seq[78:95], "CGTTTGAGTCTGGGATG",
-        )
-        self.assertEqual(
-            alignment.sequences[1].seq[0:18], "CGTTTGAGTACTGGGATG",
-        )
+        self.assertEqual(alignment.sequences[0].seq[78:95], "CGTTTGAGTCTGGGATG")
+        self.assertEqual(alignment.sequences[1].seq[0:18], "CGTTTGAGTACTGGGATG")
         self.assertTrue(
             numpy.array_equal(
-                alignment.coordinates, numpy.array([[78, 87, 87, 95], [0, 9, 10, 18]]),
+                alignment.coordinates, numpy.array([[78, 87, 87, 95], [0, 9, 10, 18]])
             )
         )
         self.assertEqual(alignment[0], "CGTTTGAGT-CTGGGATG")
         self.assertEqual(alignment[1], "CGTTTGAGTACTGGGATG")
         self.assertEqual(
-            alignment.column_annotations["emboss_consensus"], "||||||||| ||||||||",
+            alignment.column_annotations["emboss_consensus"], "||||||||| ||||||||"
         )
 
 
diff --git a/Tests/test_BioSQL_sqlite3.py b/Tests/test_BioSQL_sqlite3.py
index 45871e59662..77fb76337f8 100644
--- a/Tests/test_BioSQL_sqlite3.py
+++ b/Tests/test_BioSQL_sqlite3.py
@@ -16,11 +16,7 @@
 from common_BioSQL import *  # noqa: F403
 
 # Import these explicitly to avoid flake8 F405 below:
-from common_BioSQL import (
-    load_biosql_ini,
-    check_config,
-    temp_db_filename,
-)
+from common_BioSQL import load_biosql_ini, check_config, temp_db_filename
 
 # Constants for the database driver
 DBDRIVER = "sqlite3"
diff --git a/Tests/test_CAPS.py b/Tests/test_CAPS.py
index 9cf67f64d93..1d6d43c33af 100644
--- a/Tests/test_CAPS.py
+++ b/Tests/test_CAPS.py
@@ -20,7 +20,7 @@ def createAlignment(sequences):
         (
             SeqRecord(Seq(s), id="sequence%i" % (i + 1))
             for (i, s) in enumerate(sequences)
-        ),
+        )
     )
 
 
diff --git a/Tests/test_Emboss.py b/Tests/test_Emboss.py
index 0102fda6a3e..30df45c4855 100644
--- a/Tests/test_Emboss.py
+++ b/Tests/test_Emboss.py
@@ -305,7 +305,7 @@ def test_ig(self):
         # NOTE - EMBOSS considers "genbank" to be for nucleotides only,
         # and will turn "X" into "N" for GenBank output.
         self.check_SeqIO_to_EMBOSS(
-            "IntelliGenetics/VIF_mase-pro.txt", "ig", skip_formats=["genbank", "embl"],
+            "IntelliGenetics/VIF_mase-pro.txt", "ig", skip_formats=["genbank", "embl"]
         )
         # TODO - What does a % in an ig sequence mean?
         # e.g. "IntelliGenetics/vpu_nucaligned.txt"
@@ -457,13 +457,13 @@ def pairwise_alignment_check(self, query_seq, targets, alignments, local=True):
                 # Local alignment
                 self.assertIn(str(alignment[0].seq).replace("-", ""), query_seq)
                 self.assertIn(
-                    str(alignment[1].seq).replace("-", "").upper(), target.seq.upper(),
+                    str(alignment[1].seq).replace("-", "").upper(), target.seq.upper()
                 )
             else:
                 # Global alignment
                 self.assertEqual(query_seq, str(alignment[0].seq).replace("-", ""))
                 self.assertEqual(
-                    target.seq.upper(), str(alignment[1].seq).replace("-", "").upper(),
+                    target.seq.upper(), str(alignment[1].seq).replace("-", "").upper()
                 )
         return True
 
diff --git a/Tests/test_Entrez.py b/Tests/test_Entrez.py
index 5fd03fed0cb..59cff8c86c4 100644
--- a/Tests/test_Entrez.py
+++ b/Tests/test_Entrez.py
@@ -144,7 +144,7 @@ def test_construct_cgi_ecitmatch(self):
         self.assertEqual(get_base_url(parsed), URL_HEAD + "ecitmatch.cgi")
         query.pop("bdata")  # TODO
         self.assertDictEqual(
-            query, {"retmode": ["xml"], "db": [variables["db"]], **QUERY_DEFAULTS},
+            query, {"retmode": ["xml"], "db": [variables["db"]], **QUERY_DEFAULTS}
         )
 
     def test_construct_cgi_einfo(self):
@@ -170,7 +170,7 @@ def test_construct_cgi_epost1(self):
 
         self.assertEqual(result_url, URL_HEAD + "epost.fcgi")  # Params in POST data
         self.assertDictEqual(
-            query, {"db": [variables["db"]], "id": [variables["id"]], **QUERY_DEFAULTS},
+            query, {"db": [variables["db"]], "id": [variables["id"]], **QUERY_DEFAULTS}
         )
 
     def test_construct_cgi_epost2(self):
@@ -185,9 +185,7 @@ def test_construct_cgi_epost2(self):
         self.assertEqual(result_url, URL_HEAD + "epost.fcgi")  # Params in POST data
         # Compare IDs up to reordering:
         self.assertCountEqual(query.pop("id"), variables["id"])
-        self.assertDictEqual(
-            query, {"db": [variables["db"]], **QUERY_DEFAULTS},
-        )
+        self.assertDictEqual(query, {"db": [variables["db"]], **QUERY_DEFAULTS})
 
     def test_construct_cgi_elink1(self):
         variables = {
@@ -320,10 +318,10 @@ def test_custom_directory(self):
 
         # Confirm that the two temp directories are named what we want.
         self.assertEqual(
-            handler.local_dtd_dir, os.path.join(tmpdir, "Bio", "Entrez", "DTDs"),
+            handler.local_dtd_dir, os.path.join(tmpdir, "Bio", "Entrez", "DTDs")
         )
         self.assertEqual(
-            handler.local_xsd_dir, os.path.join(tmpdir, "Bio", "Entrez", "XSDs"),
+            handler.local_xsd_dir, os.path.join(tmpdir, "Bio", "Entrez", "XSDs")
         )
 
         # And that they were created.
diff --git a/Tests/test_GenBank.py b/Tests/test_GenBank.py
index f4715a15004..96722c211c4 100644
--- a/Tests/test_GenBank.py
+++ b/Tests/test_GenBank.py
@@ -7512,7 +7512,7 @@ def test_implicit_orign_wrap_extract_and_translate(self):
             "MPYKTQGCLGKGATPTPSSRGI*",
         )
         self.assertEqual(
-            seq_features[2].extract(seq_record).seq.translate(), "MPRLEGVGVAPFPRQPWVL*",
+            seq_features[2].extract(seq_record).seq.translate(), "MPRLEGVGVAPFPRQPWVL*"
         )
 
     def test_fuzzy_origin_wrap(self):
diff --git a/Tests/test_GenomeDiagram.py b/Tests/test_GenomeDiagram.py
index 377e0c49bfb..01d716681fb 100644
--- a/Tests/test_GenomeDiagram.py
+++ b/Tests/test_GenomeDiagram.py
@@ -303,7 +303,7 @@ def test_slicing(self):
 
         self.assertEqual(
             gd[4:16],
-            [(5, 15), (10, 20),],  # noqa 231
+            [(5, 15), (10, 20)],  # noqa 231
             "Unable to insert and retrieve points correctly",
         )
 
diff --git a/Tests/test_HMMGeneral.py b/Tests/test_HMMGeneral.py
index 08c132eb090..74d8d550d89 100644
--- a/Tests/test_HMMGeneral.py
+++ b/Tests/test_HMMGeneral.py
@@ -122,9 +122,7 @@ def test_set_equal_probabilities(self):
         self.mm_builder.allow_transition("2", "1", 0.95)
         self.mm_builder.set_equal_probabilities()
 
-        self.assertEqual(
-            self.mm_builder.initial_prob, {"1": 0.5, "2": 0.5},
-        )
+        self.assertEqual(self.mm_builder.initial_prob, {"1": 0.5, "2": 0.5})
         self.assertEqual(
             self.mm_builder.transition_prob, {("1", "2"): 0.5, ("2", "1"): 0.5}
         )
diff --git a/Tests/test_NCBI_qblast.py b/Tests/test_NCBI_qblast.py
index b688cb665fa..baaa77ca458 100644
--- a/Tests/test_NCBI_qblast.py
+++ b/Tests/test_NCBI_qblast.py
@@ -220,7 +220,7 @@ def test_discomegablast(self):
                CTTGTGTGCCACTGGTAAATCCACCCCCCCTAAGCCTCTAATAGGGAGACCTTAG""",
             0.0000001,
             None,
-            {"template_type": 0, "template_length": 18, "megablast": "on",},  # noqa 231
+            {"template_type": 0, "template_length": 18, "megablast": "on"},  # noqa 231
             ["XM_635681.1", "XM_008496783.1"],
         )
 
diff --git a/Tests/test_NaiveBayes.py b/Tests/test_NaiveBayes.py
index 93212615fdb..77c9544814d 100644
--- a/Tests/test_NaiveBayes.py
+++ b/Tests/test_NaiveBayes.py
@@ -47,18 +47,7 @@ def test_car_data(self):
             ["Red", "Sports", "Imported"],
         ]
 
-        ycar = [
-            "Yes",
-            "No",
-            "Yes",
-            "No",
-            "Yes",
-            "No",
-            "Yes",
-            "No",
-            "No",
-            "Yes",
-        ]
+        ycar = ["Yes", "No", "Yes", "No", "Yes", "No", "Yes", "No", "No", "Yes"]
 
         carmodel = NaiveBayes.train(xcar, ycar)
         self.assertEqual(
diff --git a/Tests/test_PDB_Polypeptide.py b/Tests/test_PDB_Polypeptide.py
index 2551fbe51eb..ea7133fba1d 100644
--- a/Tests/test_PDB_Polypeptide.py
+++ b/Tests/test_PDB_Polypeptide.py
@@ -66,7 +66,7 @@ def test_ppbuilder_real_nonstd(self):
         self.assertIsInstance(s, Seq)
         # Here non-standard MSE are shown as M
         self.assertEqual(
-            "MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQG", s,
+            "MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQG", s
         )
 
     def test_ppbuilder_torsion(self):
@@ -164,7 +164,7 @@ def test_cappbuilder_real_nonstd(self):
         self.assertIsInstance(s, Seq)
         # Here non-standard MSE are shown as M
         self.assertEqual(
-            "MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQG", s,
+            "MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQG", s
         )
 
     def test_cappbuilder_tau(self):
diff --git a/Tests/test_PDB_parse_pdb_header.py b/Tests/test_PDB_parse_pdb_header.py
index f970b434972..3445d08be99 100644
--- a/Tests/test_PDB_parse_pdb_header.py
+++ b/Tests/test_PDB_parse_pdb_header.py
@@ -136,13 +136,7 @@ def test_parse_remark_465(self):
         info = _parse_remark_465("1  DG B     9")
         self.assertEqual(
             info,
-            {
-                "model": 1,
-                "res_name": "DG",
-                "chain": "B",
-                "ssseq": 9,
-                "insertion": None,
-            },
+            {"model": 1, "res_name": "DG", "chain": "B", "ssseq": 9, "insertion": None},
         )
 
     def test_parse_header_line(self):
diff --git a/Tests/test_PhyloXML.py b/Tests/test_PhyloXML.py
index 0d9be3d1410..1c02cd82b7f 100644
--- a/Tests/test_PhyloXML.py
+++ b/Tests/test_PhyloXML.py
@@ -102,27 +102,27 @@ class ParseTests(unittest.TestCase):
     test_parse_dollo = _test_parse_factory(EX_DOLLO, 1)
 
     # lvl-2 clades, sub-clade counts, lvl-3 clades
-    test_shape_apaf = _test_shape_factory(EX_APAF, (((2, (2, 2)), (2, (2, 2)),),),)
-    test_shape_bcl2 = _test_shape_factory(EX_BCL2, (((2, (2, 2)), (2, (2, 2)),),),)
+    test_shape_apaf = _test_shape_factory(EX_APAF, (((2, (2, 2)), (2, (2, 2))),))
+    test_shape_bcl2 = _test_shape_factory(EX_BCL2, (((2, (2, 2)), (2, (2, 2))),))
     test_shape_phylo = _test_shape_factory(
         EX_PHYLO,
         (
-            ((2, (0, 0)), (0, ()),),
-            ((2, (0, 0)), (0, ()),),
-            ((2, (0, 0)), (0, ()),),
-            ((2, (0, 0)), (0, ()),),
-            ((2, (0, 0)), (0, ()),),
-            ((2, (0, 0)), (0, ()),),
-            ((2, (0, 0)), (0, ()),),
-            ((2, (0, 0)), (0, ()),),
-            ((2, (0, 0)), (0, ()),),
-            ((0, ()), (2, (0, 0)),),
-            ((3, (0, 0, 0)), (0, ()),),
-            ((2, (0, 0)), (0, ()),),
-            ((2, (0, 0)), (0, ()),),
+            ((2, (0, 0)), (0, ())),
+            ((2, (0, 0)), (0, ())),
+            ((2, (0, 0)), (0, ())),
+            ((2, (0, 0)), (0, ())),
+            ((2, (0, 0)), (0, ())),
+            ((2, (0, 0)), (0, ())),
+            ((2, (0, 0)), (0, ())),
+            ((2, (0, 0)), (0, ())),
+            ((2, (0, 0)), (0, ())),
+            ((0, ()), (2, (0, 0))),
+            ((3, (0, 0, 0)), (0, ())),
+            ((2, (0, 0)), (0, ())),
+            ((2, (0, 0)), (0, ())),
         ),
     )
-    test_shape_dollo = _test_shape_factory(EX_DOLLO, (((2, (2, 2)), (2, (2, 2)),),),)
+    test_shape_dollo = _test_shape_factory(EX_DOLLO, (((2, (2, 2)), (2, (2, 2))),))
 
 
 class TreeTests(unittest.TestCase):
diff --git a/Tests/test_Phylo_matplotlib.py b/Tests/test_Phylo_matplotlib.py
index aa9ec1632d4..14007cb4c39 100644
--- a/Tests/test_Phylo_matplotlib.py
+++ b/Tests/test_Phylo_matplotlib.py
@@ -64,14 +64,8 @@ def test_draw_with_label_colors_dict(self):
         pyplot.ioff()  # Turn off interactive display
         dollo = Phylo.read(EX_DOLLO, "phyloxml")
         apaf = Phylo.read(EX_APAF, "phyloxml")
-        label_colors_dollo = {
-            "f_50": "red",
-            "f_34": "blue",
-        }
-        label_colors_apaf = {
-            "22_MOUSE": "red",
-            "18_NEMVE": "blue",
-        }
+        label_colors_dollo = {"f_50": "red", "f_34": "blue"}
+        label_colors_apaf = {"22_MOUSE": "red", "18_NEMVE": "blue"}
         Phylo.draw(dollo, label_colors=label_colors_dollo, do_show=False)
         Phylo.draw(apaf, label_colors=label_colors_apaf, do_show=False)
 
diff --git a/Tests/test_SCOP_Raf.py b/Tests/test_SCOP_Raf.py
index 7b8b8f747fa..52de94044a0 100644
--- a/Tests/test_SCOP_Raf.py
+++ b/Tests/test_SCOP_Raf.py
@@ -78,9 +78,7 @@ def testSeqMapIndex(self):
         self.assertEqual(r.flags, "111011")
 
         r = index.getSeqMap("103m 1-10")
-        self.assertEqual(
-            r.pdbid, "103m",
-        )
+        self.assertEqual(r.pdbid, "103m")
         self.assertEqual(len(r.res), 10)
         self.assertEqual(r.pdb_datestamp, "010301")
         self.assertEqual(r.flags, "111011")
diff --git a/Tests/test_SearchIO_blast_tab.py b/Tests/test_SearchIO_blast_tab.py
index 5e1c66d3a08..e800263360b 100644
--- a/Tests/test_SearchIO_blast_tab.py
+++ b/Tests/test_SearchIO_blast_tab.py
@@ -771,11 +771,10 @@ def test_tab_2226_tblastn_011(self):
         self.assertEqual(1e-04, hsp.evalue)
         self.assertEqual(31.6, hsp.bitscore)
         self.assertEqual(
-            "GLADTHTIEVTVDNEPVSLDITEESTSDLDKFNSG--------DKVTITYEKNDEGQLL",
-            hsp.query.seq,
+            "GLADTHTIEVTVDNEPVSLDITEESTSDLDKFNSG--------DKVTITYEKNDEGQLL", hsp.query.seq
         )
         self.assertEqual(
-            "GLVPDHTLILPVGHYQSMLDLTEEVQTELDQFKSALRKYYLSKGKTCVIYERNFRTQHL", hsp.hit.seq,
+            "GLVPDHTLILPVGHYQSMLDLTEEVQTELDQFKSALRKYYLSKGKTCVIYERNFRTQHL", hsp.hit.seq
         )
         self.assertEqual(70.0, hsp.bitscore_raw)
         self.assertEqual(20, hsp.ident_num)
@@ -969,11 +968,10 @@ def test_tab_2226_tblastn_013(self):
         self.assertEqual(1e-04, hsp.evalue)
         self.assertEqual(31.6, hsp.bitscore)
         self.assertEqual(
-            "GLADTHTIEVTVDNEPVSLDITEESTSDLDKFNSG--------DKVTITYEKNDEGQLL",
-            hsp.query.seq,
+            "GLADTHTIEVTVDNEPVSLDITEESTSDLDKFNSG--------DKVTITYEKNDEGQLL", hsp.query.seq
         )
         self.assertEqual(
-            "GLVPDHTLILPVGHYQSMLDLTEEVQTELDQFKSALRKYYLSKGKTCVIYERNFRTQHL", hsp.hit.seq,
+            "GLVPDHTLILPVGHYQSMLDLTEEVQTELDQFKSALRKYYLSKGKTCVIYERNFRTQHL", hsp.hit.seq
         )
 
         # check if we've finished iteration over qresults
diff --git a/Tests/test_SearchIO_exonerate.py b/Tests/test_SearchIO_exonerate.py
index eb86fdb9fdf..df08a283c7b 100644
--- a/Tests/test_SearchIO_exonerate.py
+++ b/Tests/test_SearchIO_exonerate.py
@@ -2246,7 +2246,7 @@ def test_exn_22_m_protein2genome(self):
         self.assertEqual("AAT", hsp.aln_annotation_all[0]["hit_annotation"][0])
         self.assertEqual("TT", hsp.aln_annotation_all[0]["hit_annotation"][-1])
         self.assertEqual(
-            "XELLEQKDAQNKTTTDFLLCSLKSLLSEITKYRAKNSDDERILAFLDDLQE", hsp[-1].query.seq,
+            "XELLEQKDAQNKTTTDFLLCSLKSLLSEITKYRAKNSDDERILAFLDDLQE", hsp[-1].query.seq
         )
         self.assertEqual(
             "XNKILNRDPQFMSNSSFHQCVSLDSINTIEKDEEKNSDDDAGLQAATDARE", hsp[-1].hit.seq
diff --git a/Tests/test_SearchIO_fasta_m10.py b/Tests/test_SearchIO_fasta_m10.py
index dec5c60eda3..86a999eb137 100644
--- a/Tests/test_SearchIO_fasta_m10.py
+++ b/Tests/test_SearchIO_fasta_m10.py
@@ -330,7 +330,7 @@ def test_output003(self):
         self.assertEqual(86, hsp.query_start)
         self.assertEqual(141, hsp.query_end)
         self.assertEqual(
-            "ISISNNKDQYEELQKEQGERDLKTVDQLVRIAAAGGGLRLSASTKTVDQLVRIAA", hsp.query.seq,
+            "ISISNNKDQYEELQKEQGERDLKTVDQLVRIAAAGGGLRLSASTKTVDQLVRIAA", hsp.query.seq
         )
         self.assertEqual(17, hsp.hit_start)
         self.assertEqual(69, hsp.hit_end)
diff --git a/Tests/test_SearchIO_hmmer3_text.py b/Tests/test_SearchIO_hmmer3_text.py
index ac1b4fc37af..dc806fd2c95 100644
--- a/Tests/test_SearchIO_hmmer3_text.py
+++ b/Tests/test_SearchIO_hmmer3_text.py
@@ -549,10 +549,10 @@ def test_30_hmmscan_001(self):
             hsp.aln_annotation["CS"],
         )
         self.assertEqual(
-            "rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakekk", hsp.hit.seq,
+            "rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakekk", hsp.hit.seq
         )
         self.assertEqual(
-            "KRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR", hsp.query.seq,
+            "KRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR", hsp.query.seq
         )
         self.assertEqual(
             "79****************************************************997",
diff --git a/Tests/test_SeqIO.py b/Tests/test_SeqIO.py
index c3146f34acf..549a7a94d94 100644
--- a/Tests/test_SeqIO.py
+++ b/Tests/test_SeqIO.py
@@ -560,7 +560,7 @@ def perform_test(
                     for acc in accs:
                         self.assertTrue(acc, "Bad accession in annotations: %r" % acc)
                         self.assertEqual(
-                            acc, acc.strip(), "Bad accession in annotations: %r" % acc,
+                            acc, acc.strip(), "Bad accession in annotations: %r" % acc
                         )
                     self.assertEqual(
                         len(set(accs)),
@@ -570,7 +570,7 @@ def perform_test(
                 for ref in record.dbxrefs:
                     self.assertTrue(ref, "Bad cross reference in dbxrefs: %r" % ref)
                     self.assertEqual(
-                        ref, ref.strip(), "Bad cross reference in dbxrefs: %r" % ref,
+                        ref, ref.strip(), "Bad cross reference in dbxrefs: %r" % ref
                     )
                 self.assertEqual(
                     len(set(record.dbxrefs)),
@@ -3743,10 +3743,7 @@ def test_stockholm2(self):
             "363253|refseq_protein.50.proto_past_mitoc_micro_vira|gi|94986659|ref|YP_594592.1|awsonia_intraceuaris_PHE/MN1-00",
         ]
         lengths = [43, 43, 43, 43]
-        molecule_types = {
-            "seqxml": "protein",
-            "nexus": "protein",
-        }
+        molecule_types = {"seqxml": "protein", "nexus": "protein"}
         alignment = """\
  MMMEEE alignment column 0
  TQIVVV alignment column 1
@@ -4359,9 +4356,7 @@ def test_phd4(self):
         names = ["EBE03TV04IHLTF.77-243"]
         lengths = [30]
         alignment = None
-        messages = {
-            "sff": "Missing SFF flow information",
-        }
+        messages = {"sff": "Missing SFF flow information"}
         self.perform_test(
             "phd",
             False,
@@ -5063,9 +5058,7 @@ def test_fastq4(self):
             "nexus": "DNA",
         }
         alignment = None
-        messages = {
-            "sff": "Missing SFF flow information",
-        }
+        messages = {"sff": "Missing SFF flow information"}
         self.perform_test(
             "fastq",
             False,
@@ -5093,9 +5086,7 @@ def test_fastq5(self):
             "nexus": "DNA",
         }
         alignment = None
-        messages = {
-            "sff": "Missing SFF flow information",
-        }
+        messages = {"sff": "Missing SFF flow information"}
         self.perform_test(
             "fastq",
             False,
@@ -5123,9 +5114,7 @@ def test_fastq_illumina1(self):
             "nexus": "DNA",
         }
         alignment = None
-        messages = {
-            "sff": "Missing SFF flow information",
-        }
+        messages = {"sff": "Missing SFF flow information"}
         self.perform_test(
             "fastq-illumina",
             False,
@@ -5153,9 +5142,7 @@ def test_fastq_solexa1(self):
             "nexus": "DNA",
         }
         alignment = None
-        messages = {
-            "sff": "Missing SFF flow information",
-        }
+        messages = {"sff": "Missing SFF flow information"}
         self.perform_test(
             "fastq-solexa",
             False,
@@ -5357,9 +5344,7 @@ def test_abi2(self):
         names = ["3100"]
         lengths = [795]
         alignment = None
-        messages = {
-            "sff": "Missing SFF flow information",
-        }
+        messages = {"sff": "Missing SFF flow information"}
         self.perform_test(
             "abi",
             False,
diff --git a/Tests/test_SeqIO_TwoBitIO.py b/Tests/test_SeqIO_TwoBitIO.py
index 5cd08255a7d..262afea0c24 100644
--- a/Tests/test_SeqIO_TwoBitIO.py
+++ b/Tests/test_SeqIO_TwoBitIO.py
@@ -362,7 +362,7 @@ def test_find(self):
             self.seq1_twobit.find("CT", 75), self.seq1_fasta.find("CT", 75)
         )
         self.assertEqual(
-            self.seq1_twobit.find("CT", 75, 100), self.seq1_fasta.find("CT", 75, 100),
+            self.seq1_twobit.find("CT", 75, 100), self.seq1_fasta.find("CT", 75, 100)
         )
         self.assertEqual(
             self.seq1_twobit.find("CT", None, 100),
diff --git a/Tests/test_SeqIO_index.py b/Tests/test_SeqIO_index.py
index 2a0bd18d76e..c46e91ef1bf 100644
--- a/Tests/test_SeqIO_index.py
+++ b/Tests/test_SeqIO_index.py
@@ -590,13 +590,13 @@ def get_raw_check(self, filename, fmt, comp):
                 rec_dict = SeqIO.index(filename, fmt, key_function=str.lower)
                 if sqlite3:
                     rec_dict_db = SeqIO.index_db(
-                        ":memory:", filename, fmt, key_function=str.lower,
+                        ":memory:", filename, fmt, key_function=str.lower
                     )
         else:
             rec_dict = SeqIO.index(filename, fmt, key_function=str.lower)
             if sqlite3:
                 rec_dict_db = SeqIO.index_db(
-                    ":memory:", filename, fmt, key_function=str.lower,
+                    ":memory:", filename, fmt, key_function=str.lower
                 )
 
         self.assertCountEqual(id_list, rec_dict.keys(), msg=msg)
diff --git a/Tests/test_SeqIO_online.py b/Tests/test_SeqIO_online.py
index f74ca22c8a9..43a096804af 100644
--- a/Tests/test_SeqIO_online.py
+++ b/Tests/test_SeqIO_online.py
@@ -59,10 +59,7 @@ def simple(self, database, formats, entry, length, checksum):
             record = SeqIO.read(handle, f)
             handle.close()
             # NCBI still takes GI on input, but phasing it out in output
-            gi_to_acc = {
-                "6273291": "AF191665.1",
-                "16130152": "NP_416719.1",
-            }
+            gi_to_acc = {"6273291": "AF191665.1", "16130152": "NP_416719.1"}
             if entry in gi_to_acc:
                 entry = gi_to_acc[entry]
             self.assertTrue(
diff --git a/Tests/test_Seq_objs.py b/Tests/test_Seq_objs.py
index 921a3e210cd..a368d29ff23 100644
--- a/Tests/test_Seq_objs.py
+++ b/Tests/test_Seq_objs.py
@@ -1065,9 +1065,7 @@ def test_join_MutableSeq_TypeError_iter(self):
     def test_join_Seq(self):
         """Checks if Seq join correctly concatenates sequence with the spacer."""
         spacer = Seq("NNNNN")
-        self.assertEqual(
-            "N" * 15, spacer.join([Seq("NNNNN"), Seq("NNNNN")]),
-        )
+        self.assertEqual("N" * 15, spacer.join([Seq("NNNNN"), Seq("NNNNN")]))
 
         spacer1 = Seq("")
         spacers = [spacer1, Seq("NNNNN"), Seq("GGG")]
@@ -1128,11 +1126,9 @@ def test_join_MutableSeq_mixed(self):
         """Check MutableSeq objects can be joined."""
         spacer = MutableSeq("NNNNN")
         self.assertEqual(
-            "N" * 15, spacer.join([MutableSeq("NNNNN"), MutableSeq("NNNNN")]),
-        )
-        self.assertRaises(
-            TypeError, spacer.join([Seq("NNNNN"), MutableSeq("NNNNN")]),
+            "N" * 15, spacer.join([MutableSeq("NNNNN"), MutableSeq("NNNNN")])
         )
+        self.assertRaises(TypeError, spacer.join([Seq("NNNNN"), MutableSeq("NNNNN")]))
 
     def test_join_Seq_with_file(self):
         """Checks if Seq join correctly concatenates sequence from a file with the spacer."""
@@ -1185,11 +1181,7 @@ def test_join_MutableSeq(self):
         # Only expect it to take Seq objects and/or strings in an iterable!
 
         spacer1 = MutableSeq("")
-        spacers = [
-            spacer1,
-            MutableSeq("NNNNN"),
-            MutableSeq("GGG"),
-        ]
+        spacers = [spacer1, MutableSeq("NNNNN"), MutableSeq("GGG")]
         example_strings = ["ATG", "ATG", "ATG", "ATG"]
         example_strings_seqs = ["ATG", "ATG", Seq("ATG"), "ATG"]
 
@@ -1931,7 +1923,7 @@ def test_addition(self):
             "Seq({3: 'KLM', 11: 'XYZ', 17: 'PQRST', 25: 'HIJ'}, length=30)",
         )
         self.assertEqual(
-            repr(p1 + t), "Seq({3: 'KLM', 11: 'XYZ', 17: 'ACGTacgtNNNNnn'}, length=31)",
+            repr(p1 + t), "Seq({3: 'KLM', 11: 'XYZ', 17: 'ACGTacgtNNNNnn'}, length=31)"
         )
         self.assertEqual(
             repr(p2 + s1), "Seq({0: 'PQRST', 8: 'HIJ', 13: 'ABCD'}, length=17)"
@@ -1950,8 +1942,7 @@ def test_addition(self):
             "Seq({0: 'PQRST', 8: 'HIJ', 13: 'PQRST', 21: 'HIJ'}, length=26)",
         )
         self.assertEqual(
-            repr(p2 + t),
-            "Seq({0: 'PQRST', 8: 'HIJ', 13: 'ACGTacgtNNNNnn'}, length=27)",
+            repr(p2 + t), "Seq({0: 'PQRST', 8: 'HIJ', 13: 'ACGTacgtNNNNnn'}, length=27)"
         )
         self.assertEqual(t + s1, Seq("ACGTacgtNNNNnnABCD"))
         self.assertEqual(t + s2, Seq("ACGTacgtNNNNnnEFG"))
diff --git a/Tests/test_SwissProt.py b/Tests/test_SwissProt.py
index dcee284ff03..6d461c481c7 100644
--- a/Tests/test_SwissProt.py
+++ b/Tests/test_SwissProt.py
@@ -3323,7 +3323,7 @@ def test_P60137(self):
             "RecName: Full=Photosystem II reaction center protein L {ECO:0000255|HAMAP-Rule:MF_01317}; Short=PSII-L {ECO:0000255|HAMAP-Rule:MF_01317};",
         )
         self.assertEqual(
-            repr(seq_record.seq), "Seq('MTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN')",
+            repr(seq_record.seq), "Seq('MTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN')"
         )
 
         with open(datafile) as test_handle:
diff --git a/Tests/test_TogoWS.py b/Tests/test_TogoWS.py
index 4a6182494bd..98e024a1d71 100644
--- a/Tests/test_TogoWS.py
+++ b/Tests/test_TogoWS.py
@@ -163,7 +163,7 @@ def test_pubmed_16381885(self):
         data = Medline.read(handle)
         handle.close()
         self.assertEqual(
-            data["TI"], "From genomics to chemical genomics: new developments in KEGG.",
+            data["TI"], "From genomics to chemical genomics: new developments in KEGG."
         )
         self.assertEqual(
             data["AU"],
diff --git a/Tests/test_UniProt_GOA.py b/Tests/test_UniProt_GOA.py
index 1a84aa48681..610814d7ba8 100644
--- a/Tests/test_UniProt_GOA.py
+++ b/Tests/test_UniProt_GOA.py
@@ -120,9 +120,7 @@ def test_gpi_iterator_one_two(self):
         self.assertEqual(recs[0]["DB"], "UniProtKB")
         self.assertEqual(recs[0]["DB_Object_ID"], "A0A024R1R8")
         self.assertEqual(recs[0]["DB_Object_Symbol"], "hCG_2014768")
-        self.assertEqual(
-            recs[0]["DB_Object_Name"], ["HCG2014768, isoform CRA_a"],
-        )
+        self.assertEqual(recs[0]["DB_Object_Name"], ["HCG2014768, isoform CRA_a"])
         self.assertEqual(recs[0]["DB_Object_Synonym"], ["hCG_2014768"])
         self.assertEqual(recs[0]["DB_Object_Type"], "protein")
         self.assertEqual(recs[0]["Taxon"], "taxon:9606")
diff --git a/Tests/test_cellosaurus.py b/Tests/test_cellosaurus.py
index 1fabc115f9b..d6fdbb2ac0d 100644
--- a/Tests/test_cellosaurus.py
+++ b/Tests/test_cellosaurus.py
@@ -23,7 +23,7 @@ def test_read(self):
         self.assertEqual(record["DR"][2], ("IHW", "IHW9326"))
         self.assertEqual(record["DR"][3], ("IMGT/HLA", "10074"))
         self.assertEqual(
-            record["WW"][0], "http://bioinformatics.hsanmartino.it/ecbr/cl326.html",
+            record["WW"][0], "http://bioinformatics.hsanmartino.it/ecbr/cl326.html"
         )
         self.assertEqual(
             record["CC"][0],
diff --git a/Tests/test_codonalign.py b/Tests/test_codonalign.py
index e0ae3a7c3c9..a56b8b68312 100644
--- a/Tests/test_codonalign.py
+++ b/Tests/test_codonalign.py
@@ -184,14 +184,12 @@ def setUp(self):
         # Test set 1
         seq1 = SeqRecord(
             Seq(
-                "TCAGGGACTGCGAGAACCAAGCTACTGCTGCTGCTGGCTGCGCTCTGCGCCGCAGGTGGGGCGCTGGAG",
+                "TCAGGGACTGCGAGAACCAAGCTACTGCTGCTGCTGGCTGCGCTCTGCGCCGCAGGTGGGGCGCTGGAG"
             ),
             id="pro1",
         )
         seq2 = SeqRecord(
-            Seq(
-                "TCAGGGACTTCGAGAACCAAGCGCTCCTGCTGCTGGCTGCGCTCGGCGCCGCAGGTGGAGCACTGGAG",
-            ),
+            Seq("TCAGGGACTTCGAGAACCAAGCGCTCCTGCTGCTGGCTGCGCTCGGCGCCGCAGGTGGAGCACTGGAG"),
             id="pro2",
         )
         pro1 = SeqRecord(Seq("SGTARTKLLLLLAALCAAGGALE"), id="pro1")
diff --git a/Tests/test_pairwise_aligner.py b/Tests/test_pairwise_aligner.py
index c5abba6945f..28670d1fb67 100644
--- a/Tests/test_pairwise_aligner.py
+++ b/Tests/test_pairwise_aligner.py
@@ -2860,7 +2860,7 @@ def gap_score(i, n):
             numpy.array_equal(
                 alignment.aligned,
                 numpy.array([[[0, 2], [3, 4], [4, 6]], [[6, 4], [4, 3], [2, 0]]]),
-            ),
+            )
         )
         alignment = alignments[3]
         self.assertAlmostEqual(alignment.score, -8.0)
@@ -3785,8 +3785,7 @@ def test_pickle_aligner_match_mismatch(self):
             pickled_aligner.query_internal_extend_gap_score,
         )
         self.assertAlmostEqual(
-            aligner.query_left_open_gap_score,
-            pickled_aligner.query_left_open_gap_score,
+            aligner.query_left_open_gap_score, pickled_aligner.query_left_open_gap_score
         )
         self.assertAlmostEqual(
             aligner.query_left_extend_gap_score,
@@ -3870,8 +3869,7 @@ def test_pickle_aligner_substitution_matrix(self):
             pickled_aligner.query_internal_extend_gap_score,
         )
         self.assertAlmostEqual(
-            aligner.query_left_open_gap_score,
-            pickled_aligner.query_left_open_gap_score,
+            aligner.query_left_open_gap_score, pickled_aligner.query_left_open_gap_score
         )
         self.assertAlmostEqual(
             aligner.query_left_extend_gap_score,
diff --git a/Tests/test_prodoc.py b/Tests/test_prodoc.py
index 7a6943cd0c2..b98d2eff8cc 100644
--- a/Tests/test_prodoc.py
+++ b/Tests/test_prodoc.py
@@ -554,7 +554,7 @@ def test_read_pdoc00340(self):
 
     def test_read_pdoc00424(self):
         """Reading Prodoc record PDOC00424."""
-        filename = os.path.join("Prosite", "Doc", "pdoc00424.txt",)
+        filename = os.path.join("Prosite", "Doc", "pdoc00424.txt")
         with open(filename) as handle:
             record = Prodoc.read(handle)
 
@@ -761,7 +761,7 @@ def test_read_pdoc00472(self):
 
     def test_read_pdoc00640(self):
         """Reading Prodoc record PDOC00640."""
-        filename = os.path.join("Prosite", "Doc", "pdoc00640.txt",)
+        filename = os.path.join("Prosite", "Doc", "pdoc00640.txt")
         with open(filename) as handle:
             record = Prodoc.read(handle)
 
diff --git a/Tests/test_seq.py b/Tests/test_seq.py
index 912b9c16ffb..1c978e60ec3 100644
--- a/Tests/test_seq.py
+++ b/Tests/test_seq.py
@@ -318,10 +318,7 @@ def setUp(self):
             Seq.Seq("U.CAG"),
             "UGCAU",
         ]
-        self.nuc = [
-            Seq.Seq("ATCG"),
-            "UUUTTTACG",
-        ]
+        self.nuc = [Seq.Seq("ATCG"), "UUUTTTACG"]
         self.protein = [
             Seq.Seq("ATCGPK"),
             Seq.Seq("atcGPK"),
@@ -621,7 +618,7 @@ def test_first_nucleotide(self):
 
     def test_setting_slices(self):
         self.assertEqual(
-            Seq.MutableSeq("CAAA"), self.mutable_s[1:5], "Slice mutable seq",
+            Seq.MutableSeq("CAAA"), self.mutable_s[1:5], "Slice mutable seq"
         )
 
         self.mutable_s[1:3] = "GAT"
@@ -640,7 +637,7 @@ def test_setting_slices(self):
         if numpy is not None:
             one, three, five, seven = numpy.array([1, 3, 5, 7])  # numpy integers
             self.assertEqual(
-                Seq.MutableSeq("AATA"), self.mutable_s[one:five], "Slice mutable seq",
+                Seq.MutableSeq("AATA"), self.mutable_s[one:five], "Slice mutable seq"
             )
 
             self.mutable_s[one:three] = "GAT"