ruff fix PIE790 Unnecessary pass statement

$ ruff --fix --select PIE790 BioSQL/ Bio/ Doc/examples/ Tests/ Scripts/
Found 62 errors (62 fixed, 0 remaining).

Then re-ran black.

Bio/AlignIO/Interfaces.py

@@ -137,7 +137,6 @@ class SequentialAlignmentWriter(AlignmentWriter):
         This method should be replaced by any derived class to do something
         useful.
         """
-        pass
 
     def write_footer(self):
         """Use this to write any footer.
@@ -145,7 +144,6 @@ class SequentialAlignmentWriter(AlignmentWriter):
         This method should be replaced by any derived class to do something
         useful.
         """
-        pass
 
     def write_alignment(self, alignment):
         """Use this to write a single alignment.

Bio/CAPS/__init__.py

@@ -48,8 +48,6 @@ class DifferentialCutsite:
 class AlignmentHasDifferentLengthsError(Exception):
     """Exception where sequences in alignment have different lengths."""
 
-    pass
-
 
 class CAPSMap:
     """A map of an alignment showing all possible dcuts.

Bio/Data/CodonTable.py

@@ -44,8 +44,6 @@ standard_rna_table = None
 class TranslationError(Exception):
     """Container for translation specific exceptions."""
 
-    pass
-
 
 class CodonTable:
     """A codon-table, or genetic code."""

Bio/GenBank/Scanner.py

@@ -399,7 +399,6 @@ class InsdcScanner:
 
         Used by the parse_records() and parse() methods.
         """
-        pass
 
     def _feed_header_lines(self, consumer, lines):
         """Handle the header lines (list of strings), passing data to the consumer (PRIVATE).
@@ -408,7 +407,6 @@ class InsdcScanner:
 
         Used by the parse_records() and parse() methods.
         """
-        pass
 
     @staticmethod
     def _feed_feature_table(consumer, feature_tuples):
@@ -433,7 +431,6 @@ class InsdcScanner:
 
         Used by the parse_records() and parse() methods.
         """
-        pass
 
     def feed(self, handle, consumer, do_features=True):
         """Feed a set of data into the consumer.

Bio/GenBank/__init__.py

@@ -112,8 +112,6 @@ class Iterator:
 class ParserFailureError(ValueError):
     """Failure caused by some kind of problem in the parser."""
 
-    pass
-
 
 _cleaner = FeatureValueCleaner()
 

Bio/Graphics/BasicChromosome.py

@@ -178,7 +178,6 @@ class Organism(_ChromosomeComponent):
         Subclasses should implement this (see also self._legend_height) to
         provide specialized legends.
         """
-        pass
 
 
 class Chromosome(_ChromosomeComponent):
@@ -445,7 +444,6 @@ class ChromosomeSegment(_ChromosomeComponent):
         This should be overridden in derived classes if there are
         subcomponents to be drawn.
         """
-        pass
 
     def _draw_segment(self, cur_drawing):
         """Draw the current chromosome segment (PRIVATE)."""
@@ -484,7 +482,6 @@ class ChromosomeSegment(_ChromosomeComponent):
         This should be overridden in derived classes if there are
         subcomponents to be drawn.
         """
-        pass
 
     def _draw_label(self, cur_drawing):
         """Add a label to the chromosome segment (PRIVATE).
@@ -817,4 +814,3 @@ class SpacerSegment(ChromosomeSegment):
         so this method therefore does nothing, but is defined
         to match the expected API of the other segment objects.
         """
-        pass

Bio/Graphics/Distribution.py

@@ -134,7 +134,6 @@ class DistributionPage:
 
         Subclasses can implement to provide a specialized legend.
         """
-        pass
 
 
 class BarChartDistribution:
@@ -249,8 +248,6 @@ class LineDistribution:
 
     def __init__(self):
         """Initialize the class."""
-        pass
 
     def draw(self, cur_drawing, start_x, start_y, end_x, end_y):
         """Draw a line distribution into the current drawing."""
-        pass

Bio/Nexus/Nexus.py

@@ -64,8 +64,6 @@ DEFAULTNEXUS = (
 class NexusError(Exception):
     """Provision for the management of Nexus exceptions."""
 
-    pass
-
 
 class CharBuffer:
     """Helps reading NEXUS-words and characters from a buffer (semi-PRIVATE).
@@ -905,7 +903,6 @@ class Nexus:
         Thus, we ignore the taxlabels command to make handling of duplicate
         taxon names easier.
         """
-        pass
         # self.taxlabels = []
         # opts = CharBuffer(options)
         # while True:

Bio/Nexus/Nodes.py

@@ -22,14 +22,10 @@ from typing import Dict, List, Optional
 class ChainException(Exception):
     """Provision for the management of Chain exceptions."""
 
-    pass
-
 
 class NodeException(Exception):
     """Provision for the management of Node exceptions."""
 
-    pass
-
 
 class Chain:
     """Stores a list of nodes that are linked together."""

Bio/Nexus/StandardData.py

@@ -13,8 +13,6 @@
 class NexusError(Exception):
     """Provision for the management of Nexus exceptions."""
 
-    pass
-
 
 class StandardData:
     """Create a StandardData iterable object.

Bio/Nexus/Trees.py

@@ -28,8 +28,6 @@ NODECOMMENT_END = "]"
 class TreeError(Exception):
     """Provision for the management of Tree exceptions."""
 
-    pass
-
 
 class NodeData:
     """Store tree-relevant data associated with nodes (e.g. branches or otus)."""

Bio/PDB/PDBExceptions.py

@@ -14,25 +14,17 @@ from Bio import BiopythonWarning
 class PDBException(Exception):
     """Define class PDBException."""
 
-    pass
-
 
 # The PDB file cannot be unambiguously represented in the SMCRA
 # data structure
 class PDBConstructionException(Exception):
     """Define class PDBConstructionException."""
 
-    pass
-
 
 class PDBConstructionWarning(BiopythonWarning):
     """Define class PDBConstructionWarning."""
 
-    pass
-
 
 # The SMCRA structure could not be written to file
 class PDBIOException(Exception):
     """Define class PDBIOException."""
-
-    pass

Bio/PDB/PDBIO.py

@@ -67,7 +67,6 @@ class StructureIO:
 
     def __init__(self):
         """Initialise."""
-        pass
 
     def set_structure(self, pdb_object):
         """Check what the user is providing and build a structure."""

Bio/PDB/StructureBuilder.py

@@ -310,4 +310,3 @@ class StructureBuilder:
 
     def set_symmetry(self, spacegroup, cell):
         """Set symmetry."""
-        pass

Bio/PDB/internal_coords.py

@@ -4963,10 +4963,6 @@ def set_accuracy_95(num: float) -> float:
 class HedronMatchError(Exception):
     """Cannot find hedron in residue for given key."""
 
-    pass
-
 
 class MissingAtomError(Exception):
     """Missing atom coordinates for hedron or dihedron."""
-
-    pass

Bio/PDB/mmcifio.py

@@ -67,7 +67,6 @@ class MMCIFIO(StructureIO):
 
     def __init__(self):
         """Initialise."""
-        pass
 
     def set_dict(self, dic):
         """Set the mmCIF dictionary to be written out."""

Bio/PDB/mmtf/DefaultParser.py

@@ -196,7 +196,6 @@ class StructureDecoder:
         :param experimnetal_methods: the list of experimental methods in the structure
 
         """
-        pass
 
     def set_bio_assembly_trans(
         self, bio_assembly_index, input_chain_indices, input_transform
@@ -208,11 +207,9 @@ class StructureDecoder:
         :param input_transform: the list of doubles for  the transform of this bioassmbly transform.
 
         """
-        pass
 
     def finalize_structure(self):
         """Any functions needed to cleanup the structure."""
-        pass
 
     def set_group_bond(self, atom_index_one, atom_index_two, bond_order):
         """Add bonds within a group.
@@ -222,7 +219,6 @@ class StructureDecoder:
         :param bond_order: the integer bond order
 
         """
-        pass
 
     def set_inter_group_bond(self, atom_index_one, atom_index_two, bond_order):
         """Add bonds between groups.
@@ -232,4 +228,3 @@ class StructureDecoder:
         :param bond_order: the bond order
 
         """
-        pass

Bio/PDB/mmtf/mmtfio.py

@@ -38,7 +38,6 @@ class MMTFIO(StructureIO):
 
     def __init__(self):
         """Initialise."""
-        pass
 
     def save(self, filepath, select=_select):
         """Save the structure to a file.

Bio/Phylo/NeXMLIO.py

@@ -60,8 +60,6 @@ def matches(s):
 class NeXMLError(Exception):
     """Exception raised when NeXML object construction cannot continue."""
 
-    pass
-
 
 # ---------------------------------------------------------
 # Public API

Bio/Phylo/NewickIO.py

@@ -21,8 +21,6 @@ from Bio.Phylo import Newick
 class NewickError(Exception):
     """Exception raised when Newick object construction cannot continue."""
 
-    pass
-
 
 tokens = [
     (r"\(", "open parens"),

Bio/Phylo/PAML/_paml.py

@@ -37,11 +37,9 @@ class Paml:
 
     def write_ctl_file(self):
         """Write control file."""
-        pass
 
     def read_ctl_file(self):
         """Read control file."""
-        pass
 
     def print_options(self):
         """Print out all of the options and their current settings."""

Bio/Phylo/PhyloXML.py

@@ -31,8 +31,6 @@ from Bio.Phylo import BaseTree
 class PhyloXMLWarning(BiopythonWarning):
     """Warning for non-compliance with the phyloXML specification."""
 
-    pass
-
 
 def _check_str(text, testfunc):
     """Check a string using testfunc, and warn if there's no match (PRIVATE)."""

Bio/Phylo/PhyloXMLIO.py

@@ -45,8 +45,6 @@ class PhyloXMLError(Exception):
     specification.
     """
 
-    pass
-
 
 # ---------------------------------------------------------
 # Public API

Bio/SearchIO/_legacy/NCBIStandalone.py

@@ -53,8 +53,6 @@ class LowQualityBlastError(Exception):
     in this case.
     """
 
-    pass
-
 
 class ShortQueryBlastError(Exception):
     """Error caused by running a short query sequence through BLAST.
@@ -69,8 +67,6 @@ class ShortQueryBlastError(Exception):
     This exception is raised when that condition is detected.
     """
 
-    pass
-
 
 class _Scanner:
     """Scan BLAST output from blastall or blastpgp.

Bio/SeqFeature.py

@@ -163,8 +163,6 @@ _re_location_category = re.compile(
 class LocationParserError(ValueError):
     """Could not parse a feature location string."""
 
-    pass
-
 
 class SeqFeature:
     """Represent a Sequence Feature on an object.
@@ -2120,8 +2118,6 @@ class UncertainPosition(ExactPosition):
     XML format explicitly marked as uncertain. Does not apply to GenBank/EMBL.
     """
 
-    pass
-
 
 class UnknownPosition(Position):
     """Specify a specific position which is unknown (has no position).

Bio/SeqIO/Interfaces.py

@@ -183,7 +183,6 @@ class SequenceWriter:
 
     def write_header(self):
         """Write the file header to the output file."""
-        pass
         ##################################################
         # You MUST implement this method in the subclass #
         # if the file format defines a file header.      #
@@ -191,7 +190,6 @@ class SequenceWriter:
 
     def write_footer(self):
         """Write the file footer to the output file."""
-        pass
         ##################################################
         # You MUST implement this method in the subclass #
         # if the file format defines a file footer.      #

Bio/Wise/__init__.py

@@ -145,7 +145,6 @@ def all_pairs(singles):
 
 def main():
     """Provision for command line testing."""
-    pass
 
 
 def _test(*args, **keywds):

Bio/Wise/psw.py

@@ -32,8 +32,6 @@ _OPTION_SCORES = "-m"
 class AlignmentColumnFullException(Exception):
     """Manage exception in the alignment output."""
 
-    pass
-
 
 class Alignment(list):
     """Define a container for all alignment Columns, output from running psw."""

BioSQL/DBUtils.py

@@ -24,7 +24,6 @@ class Generic_dbutils:
 
     def __init__(self):
         """Create a Generic_dbutils object."""
-        pass
 
     def tname(self, table):
         """Return the name of the table."""
@@ -53,7 +52,6 @@ class Generic_dbutils:
     def autocommit(self, conn, y=1):
         """Set autocommit on the database connection."""
         # Let's hope it was not really needed
-        pass
 
 
 class Sqlite_dbutils(Generic_dbutils):

Scripts/Restriction/ranacompiler.py

@@ -140,8 +140,6 @@ def double_quote_repr(value):  # TODO similar not to produce long horizontal lis
 class OverhangError(ValueError):
     """Exception for dealing with overhang."""
 
-    pass
-
 
 def regex(site):
     """Construct a regular expression (string) from a DNA sequence.
@@ -327,7 +325,6 @@ class TypeCompiler:
 
     def __init__(self):
         """TypeCompiler() -> new TypeCompiler instance."""
-        pass
 
     def buildtype(self):
         """Build new types that will be needed for constructing the enzymes."""

Scripts/xbbtools/xbb_translations.py

@@ -23,7 +23,6 @@ class xbb_translations:
 
     def __init__(self):
         """Initialize the class."""
-        pass
 
     def frame1(self, seq, translation_table=1):
         """Translate first reading frame."""

Tests/common_BioSQL.py

@@ -204,7 +204,6 @@ def create_database():
                     # Seen this with PyPy 2.1 (and older) on Windows -
                     # which suggests an open handle still exists?
                     print(f"Could not remove {TESTDB!r}")
-                    pass
         # Now pick a new filename - just in case there is a stale handle
         # (which might be happening under Windows...)
         TESTDB = temp_db_filename()

Tests/test_GraphicsBitmaps.py

@@ -130,7 +130,6 @@ class ComparativeTest(unittest.TestCase):
     def test_simple_scatter_plot(self):
         """Test creation of a simple PNG scatter plot."""
         # Dummy method to show up via run_tests.py
-        pass
 
 
 if __name__ == "__main__":

Tests/test_LogisticRegression.py

@@ -54,7 +54,6 @@ ys = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0]
 
 def show_progress(iteration, loglikelihood):
     """No action callback function, used when training the model."""
-    pass
 
 
 class TestLogisticRegression(unittest.TestCase):

Tests/test_SeqIO_PdbIO.py

@@ -89,14 +89,10 @@ def SeqresTestGenerator(extension, parser):
 class TestPdbSeqres(SeqresTestGenerator("pdb", "pdb-seqres")):
     """Test pdb-seqres SeqIO driver."""
 
-    pass
-
 
 class TestCifSeqres(SeqresTestGenerator("cif", "cif-seqres")):
     """Test cif-seqres SeqIO driver."""
 
-    pass
-
 
 def AtomTestGenerator(extension, parser):
     """Test factory for tests reading ATOM (or similar) records.

Tests/test_Tutorial.py

@@ -174,8 +174,6 @@ def extract_doctests(latex_filename):
 class TutorialDocTestHolder:
     """Python doctests extracted from the Biopython Tutorial."""
 
-    pass
-
 
 def check_deps(dependencies):
     """Check 'lib:XXX' and 'internet' dependencies are met."""

Tests/test_motifs.py

@@ -4940,7 +4940,6 @@ class TestMEME(unittest.TestCase):
 
     def test_meme_parser_rna(self):
         """Test if Bio.motifs can parse MEME output files using RNA."""
-        pass
 
 
 class TestMAST(unittest.TestCase):