diff --git a/Bio/ExPASy/ScanProsite.py b/Bio/ExPASy/ScanProsite.py index 7299c5419..8b4ec10b1 100644 --- a/Bio/ExPASy/ScanProsite.py +++ b/Bio/ExPASy/ScanProsite.py @@ -5,7 +5,6 @@ """Code for calling and parsing ScanProsite from ExPASy.""" -# Importing these functions with leading underscore as not intended for reuse from urllib.parse import urlencode from urllib.request import urlopen from xml.sax import handler diff --git a/Bio/GenBank/__init__.py b/Bio/GenBank/__init__.py index 3119a0b1c..fd1627dd8 100644 --- a/Bio/GenBank/__init__.py +++ b/Bio/GenBank/__init__.py @@ -49,8 +49,6 @@ from Bio.SeqFeature import SeqFeature from Bio.SeqFeature import SimpleLocation from .Scanner import GenBankScanner - -# other Bio.GenBank stuff from .utils import FeatureValueCleaner # Constants used to parse GenBank header lines diff --git a/Bio/Graphics/BasicChromosome.py b/Bio/Graphics/BasicChromosome.py index f25a31382..3db3186d6 100644 --- a/Bio/Graphics/BasicChromosome.py +++ b/Bio/Graphics/BasicChromosome.py @@ -33,7 +33,6 @@ This provides nice output in PDF, SVG and postscript. If you have 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 diff --git a/Bio/Graphics/ColorSpiral.py b/Bio/Graphics/ColorSpiral.py index bcf8a4400..5af74773b 100644 --- a/Bio/Graphics/ColorSpiral.py +++ b/Bio/Graphics/ColorSpiral.py @@ -19,7 +19,6 @@ a dictionary of colours (if passed an iterable containing the names of categories to be coloured). """ -# standard library import colorsys # colour format conversions import random # for jitter values from math import exp diff --git a/Bio/Graphics/Comparative.py b/Bio/Graphics/Comparative.py index 8b9c1ade4..22dccaa8f 100644 --- a/Bio/Graphics/Comparative.py +++ b/Bio/Graphics/Comparative.py @@ -11,7 +11,6 @@ compare different types of information. The most basic example is comparing two variables in a traditional scatter plot. """ -# reportlab from reportlab.graphics.charts.lineplots import LinePlot from reportlab.graphics.charts.markers import makeEmptyCircle from reportlab.graphics.charts.markers import makeEmptySquare diff --git a/Bio/Graphics/DisplayRepresentation.py b/Bio/Graphics/DisplayRepresentation.py index de4de6135..8135ebb8b 100644 --- a/Bio/Graphics/DisplayRepresentation.py +++ b/Bio/Graphics/DisplayRepresentation.py @@ -10,10 +10,8 @@ Classes in this module are designed to hold information in a way that makes it easy to draw graphical figures. """ -# reportlab from reportlab.lib import colors -# local stuff from Bio.Graphics.BasicChromosome import ChromosomeSegment from Bio.Graphics.BasicChromosome import TelomereSegment diff --git a/Bio/Graphics/Distribution.py b/Bio/Graphics/Distribution.py index b74a83172..70842ce6d 100644 --- a/Bio/Graphics/Distribution.py +++ b/Bio/Graphics/Distribution.py @@ -14,7 +14,6 @@ or anything similar. Reportlab is used for producing the graphical output. """ -# standard library import math from reportlab.graphics.charts.barcharts import BarChartProperties @@ -23,8 +22,6 @@ 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 diff --git a/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py b/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py index 8fcb5bb15..40d14be58 100644 --- a/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py +++ b/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py @@ -32,8 +32,6 @@ For dealing with biological information, the package expects Biopython objects like SeqFeatures. """ -# ReportLab imports - from itertools import islice from math import cos from math import pi diff --git a/Bio/Graphics/GenomeDiagram/_CircularDrawer.py b/Bio/Graphics/GenomeDiagram/_CircularDrawer.py index 59d4f564f..1ea177574 100644 --- a/Bio/Graphics/GenomeDiagram/_CircularDrawer.py +++ b/Bio/Graphics/GenomeDiagram/_CircularDrawer.py @@ -13,8 +13,6 @@ """CircularDrawer module for GenomeDiagram.""" -# ReportLab imports - from math import cos from math import pi from math import sin @@ -29,8 +27,6 @@ from reportlab.graphics.shapes import String from reportlab.lib import colors from ._AbstractDrawer import _stroke_and_fill_colors - -# GenomeDiagram imports from ._AbstractDrawer import AbstractDrawer from ._AbstractDrawer import draw_polygon from ._AbstractDrawer import intermediate_points diff --git a/Bio/Graphics/GenomeDiagram/_FeatureSet.py b/Bio/Graphics/GenomeDiagram/_FeatureSet.py index 02aef5343..8b0168cb9 100644 --- a/Bio/Graphics/GenomeDiagram/_FeatureSet.py +++ b/Bio/Graphics/GenomeDiagram/_FeatureSet.py @@ -24,8 +24,6 @@ For drawing capabilities, this module uses reportlab to draw and write the diagram: http://www.reportlab.com """ -# GenomeDiagram -# Builtins import re from ._Feature import Feature diff --git a/Bio/Graphics/GenomeDiagram/_Graph.py b/Bio/Graphics/GenomeDiagram/_Graph.py index 97f94b334..bda541613 100644 --- a/Bio/Graphics/GenomeDiagram/_Graph.py +++ b/Bio/Graphics/GenomeDiagram/_Graph.py @@ -21,8 +21,6 @@ For drawing capabilities, this module uses reportlab to draw and write the diagram: http://www.reportlab.com """ -# ReportLab imports - from math import sqrt from reportlab.lib import colors diff --git a/Bio/Graphics/GenomeDiagram/_LinearDrawer.py b/Bio/Graphics/GenomeDiagram/_LinearDrawer.py index 27fdbc212..39da87964 100644 --- a/Bio/Graphics/GenomeDiagram/_LinearDrawer.py +++ b/Bio/Graphics/GenomeDiagram/_LinearDrawer.py @@ -20,8 +20,6 @@ For drawing capabilities, this module uses reportlab to draw and write the diagram: http://www.reportlab.com """ -# ReportLab imports - from math import ceil from reportlab.graphics.shapes import Drawing @@ -32,8 +30,6 @@ from reportlab.graphics.shapes import String from reportlab.lib import colors from ._AbstractDrawer import _stroke_and_fill_colors - -# GenomeDiagram imports from ._AbstractDrawer import AbstractDrawer from ._AbstractDrawer import angle2trig from ._AbstractDrawer import deduplicate diff --git a/Bio/HMM/MarkovModel.py b/Bio/HMM/MarkovModel.py index 93fdece59..07957638b 100644 --- a/Bio/HMM/MarkovModel.py +++ b/Bio/HMM/MarkovModel.py @@ -7,7 +7,6 @@ """Deal with representations of Markov Models.""" -# standard modules import copy import math import random diff --git a/Bio/HMM/Trainer.py b/Bio/HMM/Trainer.py index 5bc4ad85a..47f6d4c47 100644 --- a/Bio/HMM/Trainer.py +++ b/Bio/HMM/Trainer.py @@ -20,13 +20,11 @@ This aims to estimate two parameters: """ -# standard modules import math import warnings from Bio import BiopythonDeprecationWarning -# local stuff from .DynamicProgramming import ScaledDPAlgorithms warnings.warn( diff --git a/Bio/PDB/PDBIO.py b/Bio/PDB/PDBIO.py index 35fc37d4a..69c526df1 100644 --- a/Bio/PDB/PDBIO.py +++ b/Bio/PDB/PDBIO.py @@ -8,14 +8,9 @@ import os 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 _ATOM_FORMAT_STRING = ( diff --git a/Bio/PDB/ic_rebuild.py b/Bio/PDB/ic_rebuild.py index cae4e5187..c4f705af4 100644 --- a/Bio/PDB/ic_rebuild.py +++ b/Bio/PDB/ic_rebuild.py @@ -10,8 +10,6 @@ import re from io import StringIO from itertools import zip_longest from typing import Any - -# for typing from typing import Dict from typing import Tuple from typing import Union diff --git a/Bio/PDB/internal_coords.py b/Bio/PDB/internal_coords.py index 755575dd3..c9ca3bc10 100644 --- a/Bio/PDB/internal_coords.py +++ b/Bio/PDB/internal_coords.py @@ -271,13 +271,9 @@ import copy import re from collections import deque from collections import namedtuple - -# from numpy import floor, ndarray from numbers import Integral from typing import cast from typing import Dict - -# for type checking only from typing import List from typing import Optional from typing import Set