Description: Port to Python3.12 by removing vendored six.py Since most part of the fix involve unvendoring six.py, forwarding does not seem too relevant. Forwarded: not-needed Bug-Debian: https://bugs.debian.org/#1061797 Author: Andreas Tille Reviewed-By: Étienne Mollier Last-Update: 2024-02-02 --- flye.orig/flye/assembly/scaffolder.py +++ flye/flye/assembly/scaffolder.py @@ -12,7 +12,7 @@ import flye.utils.fasta_parser as fp import flye.config.py_cfg as cfg -from flye.six import iteritems +from six import iteritems logger = logging.getLogger() --- flye.orig/flye/config/configurator.py +++ flye/flye/config/configurator.py @@ -12,7 +12,7 @@ import flye.utils.fasta_parser as fp import flye.config.py_cfg as cfg -from flye.six import iteritems +from six import iteritems logger = logging.getLogger() --- flye.orig/flye/main.py +++ flye/flye/main.py @@ -33,7 +33,7 @@ #import flye.trestle.trestle as tres #import flye.trestle.graph_resolver as tres_graph from flye.repeat_graph.repeat_graph import RepeatGraph -from flye.six.moves import range +from six.moves import range if sys.version_info[0] == 2: raise Exception("Python 2 is unsupported") --- flye.orig/flye/polishing/alignment.py +++ flye/flye/polishing/alignment.py @@ -18,8 +18,8 @@ import flye.utils.fasta_parser as fp from flye.utils.utils import which, get_median from flye.utils.sam_parser import AlignmentException -from flye.six import iteritems -from flye.six.moves import range +from six import iteritems +from six.moves import range logger = logging.getLogger() --- flye.orig/flye/polishing/bubbles.py +++ flye/flye/polishing/bubbles.py @@ -10,7 +10,7 @@ from __future__ import division import logging from bisect import bisect -from flye.six.moves import range +from six.moves import range from collections import defaultdict from queue import Queue @@ -22,7 +22,7 @@ from flye.polishing.alignment import shift_gaps, get_uniform_alignments from flye.utils.sam_parser import SynchronizedSamReader, SynchonizedChunkManager from flye.utils.utils import process_in_parallel, get_median -from flye.six.moves import zip +from six.moves import zip logger = logging.getLogger() --- flye.orig/flye/polishing/consensus.py +++ flye/flye/polishing/consensus.py @@ -10,8 +10,8 @@ from __future__ import division import logging from collections import defaultdict -from flye.six.moves import range -from flye.six import itervalues +from six.moves import range +from six import itervalues import multiprocessing import traceback @@ -21,7 +21,7 @@ import flye.config.py_cfg as cfg import flye.utils.fasta_parser as fp from flye.utils.utils import process_in_parallel -from flye.six.moves import zip +from six.moves import zip logger = logging.getLogger() --- flye.orig/flye/polishing/polish.py +++ flye/flye/polishing/polish.py @@ -21,8 +21,8 @@ import flye.utils.fasta_parser as fp from flye.utils.utils import which import flye.config.py_cfg as cfg -from flye.six import iteritems -from flye.six.moves import range +from six import iteritems +from six.moves import range POLISH_BIN = "flye-modules" --- flye.orig/flye/short_plasmids/circular_sequences.py +++ flye/flye/short_plasmids/circular_sequences.py @@ -9,8 +9,8 @@ import flye.utils.fasta_parser as fp from flye.utils.sam_parser import read_paf, read_paf_grouped import logging -from flye.six import iteritems -from flye.six.moves import range +from six import iteritems +from six.moves import range logger = logging.getLogger() --- flye.orig/flye/short_plasmids/unmapped_reads.py +++ flye/flye/short_plasmids/unmapped_reads.py @@ -9,8 +9,8 @@ from flye.utils.sam_parser import read_paf_grouped import logging from collections import defaultdict -from flye.six import iteritems -from flye.six.moves import range +from six import iteritems +from six.moves import range logger = logging.getLogger() --- flye.orig/flye/short_plasmids/utils.py +++ flye/flye/short_plasmids/utils.py @@ -2,7 +2,7 @@ #This file is a part of Flye program. #Released under the BSD license (see LICENSE file) -from flye.six.moves import range +from six.moves import range def find_connected_components(graph): def dfs(start_vertex, connected_components_counter): --- flye.orig/flye/trestle/divergence.py +++ flye/flye/trestle/divergence.py @@ -12,7 +12,7 @@ from __future__ import division import logging from collections import defaultdict -from flye.six.moves import range +from six.moves import range import multiprocessing import os.path @@ -22,7 +22,7 @@ import flye.utils.fasta_parser as fp from flye.utils.utils import process_in_parallel import flye.config.py_cfg as config -from flye.six.moves import zip +from six.moves import zip logger = logging.getLogger() --- flye.orig/flye/trestle/graph_resolver.py +++ flye/flye/trestle/graph_resolver.py @@ -13,8 +13,8 @@ import flye.utils.fasta_parser as fp from flye.repeat_graph.graph_alignment import iter_alignments -from flye.six import iteritems -from flye.six.moves import zip +from six import iteritems +from six.moves import zip logger = logging.getLogger() --- flye.orig/flye/trestle/trestle.py +++ flye/flye/trestle/trestle.py @@ -25,8 +25,8 @@ import flye.trestle.divergence as div import flye.trestle.trestle_config as trestle_config -from flye.six.moves import range -from flye.six.moves import zip +from six.moves import range +from six.moves import zip logger = logging.getLogger() --- flye.orig/flye/utils/fasta_parser.py +++ flye/flye/utils/fasta_parser.py @@ -23,7 +23,7 @@ _STR = bytes.decode _BYTES = str.encode -from flye.six.moves import range +from six.moves import range logger = logging.getLogger() --- flye.orig/flye/utils/sam_parser.py +++ flye/flye/utils/sam_parser.py @@ -32,8 +32,8 @@ _STR = bytes.decode _BYTES = str.encode -from flye.six.moves import range -from flye.six import iteritems +from six.moves import range +from six import iteritems import flye.utils.fasta_parser as fp from flye.utils.utils import get_median