frozenleaves/biopython
1
0
Fork 0
mirror of https://github.com/biopython/biopython.git synced 2025-10-20 13:43:47 +08:00
Code Issues Packages Projects Releases Wiki Activity

ruff fix PIE790 Unnecessary pass statement

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

Then re-ran black.
This commit is contained in:
Peter Cock
2023-11-01 15:05:12 +00:00
parent c0663bd6f6
commit 68e3c989d9
37 changed files with 0 additions and 89 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
Bio/AlignIO/Interfaces.py
View File

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

2
Bio/CAPS/__init__.py
View File

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

2
Bio/Data/CodonTable.py
View File

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

3
Bio/GenBank/Scanner.py
View File

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

2
Bio/GenBank/__init__.py
View File

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

4
Bio/Graphics/BasicChromosome.py
View File

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

3
Bio/Graphics/Distribution.py
View File

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

3
Bio/Nexus/Nexus.py
View File

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

4
Bio/Nexus/Nodes.py
View File

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

2
Bio/Nexus/StandardData.py
View File

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

2
Bio/Nexus/Trees.py
View File

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

8
Bio/PDB/PDBExceptions.py
View File

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

1
Bio/PDB/PDBIO.py
View File

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

1
Bio/PDB/StructureBuilder.py
View File

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

4
Bio/PDB/internal_coords.py
View File

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

1
Bio/PDB/mmcifio.py
View File

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

5
Bio/PDB/mmtf/DefaultParser.py
View File

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

1
Bio/PDB/mmtf/mmtfio.py
View File

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

2
Bio/Phylo/NeXMLIO.py
View File

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

2
Bio/Phylo/NewickIO.py
View File

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

2
Bio/Phylo/PAML/_paml.py
View File

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

2
Bio/Phylo/PhyloXML.py
View File

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

2
Bio/Phylo/PhyloXMLIO.py
View File

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

4
Bio/SearchIO/_legacy/NCBIStandalone.py
View File

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

4
Bio/SeqFeature.py
View File

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

2
Bio/SeqIO/Interfaces.py
View File

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

1
Bio/Wise/__init__.py
View File

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

2
Bio/Wise/psw.py
View File

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

2
BioSQL/DBUtils.py
View File

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

3
Scripts/Restriction/ranacompiler.py
View File

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

1
Scripts/xbbtools/xbb_translations.py
View File

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

1
Tests/common_BioSQL.py
View File

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

1
Tests/test_GraphicsBitmaps.py
View File

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

1
Tests/test_LogisticRegression.py
View File

@ -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): def show_progress(iteration, loglikelihood):
"""No action callback function, used when training the model.""" """No action callback function, used when training the model."""
pass
class TestLogisticRegression(unittest.TestCase): class TestLogisticRegression(unittest.TestCase):

4
Tests/test_SeqIO_PdbIO.py
View File

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

2
Tests/test_Tutorial.py
View File

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

1
Tests/test_motifs.py
View File

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