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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 <tille@debian.org>
Reviewed-By: Étienne Mollier <emollier@debian.org>
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
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