[Debian-med-packaging] Bug#1055687: khmer ftbfs with Python 3.12
Olivier Gayot
olivier.gayot at canonical.com
Sun Nov 26 20:06:39 GMT 2023
Package: khmer
Followup-For: Bug #1055687
User: ubuntu-devel at lists.ubuntu.com
Usertags: origin-ubuntu noble ubuntu-patch
Control: tags -1 patch
Dear Maintainer,
My previous patch was unfortunately very incomplete. I am submitting
another patch that fixes the remaining issues when building with Python
3.12. Both debdiffs should be applied for the build to succeed.
Additional fixes that were needed for the build to succeed:
* Python 3.12 dropped the "imp" module. Updated to use importlib
instead.
* Python 3.12 is much less forgiving when a script opens a file for
writing and forgets to close it. Most Python scripts in scripts/ failed
to do so or did so inconsistently. This resulted in the test suite
either hanging or failing. I went through all invocations of open() /
get_file_writer() and ensured that the resources are cleaned up. The
resulting patch is sadly difficult to read though.
I submitted all changes upstream, although I doubt somebody will pick
them up:
https://github.com/dib-lab/khmer/pull/1922
In Ubuntu, the attached patch was applied to achieve the following:
* Fix build against Python 3.12 (LP: #2044383).
Thanks for considering the patch.
-- System Information:
Debian Release: trixie/sid
APT prefers mantic-updates
APT policy: (500, 'mantic-updates'), (500, 'mantic-security'), (500, 'mantic')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 6.1.0-16-generic (SMP w/8 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
-------------- next part --------------
diff -Nru khmer-3.0.0~a3+dfsg/debian/control khmer-3.0.0~a3+dfsg/debian/control
--- khmer-3.0.0~a3+dfsg/debian/control 2023-11-25 17:44:28.000000000 +0100
+++ khmer-3.0.0~a3+dfsg/debian/control 2023-11-26 02:28:32.000000000 +0100
@@ -1,6 +1,5 @@
Source: khmer
-Maintainer: Ubuntu Developers <ubuntu-devel-discuss at lists.ubuntu.com>
-XSBC-Original-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Michael R. Crusoe <crusoe at debian.org>,
Kevin Murray <spam at kdmurray.id.au>
Section: science
diff -Nru khmer-3.0.0~a3+dfsg/debian/patches/close-opened-files.patch khmer-3.0.0~a3+dfsg/debian/patches/close-opened-files.patch
--- khmer-3.0.0~a3+dfsg/debian/patches/close-opened-files.patch 1970-01-01 01:00:00.000000000 +0100
+++ khmer-3.0.0~a3+dfsg/debian/patches/close-opened-files.patch 2023-11-26 02:28:32.000000000 +0100
@@ -0,0 +1,1124 @@
+Description: ensure that Python scripts close files that they open for writing
+ Python scripts under scripts/ in the source tree do not consistently close
+ files that they open for writing. While some of the scripts use context
+ managers, most of them do not (or do so inconsistently).
+ In previous releases of Ubuntu, this apparently was not much of a concern.
+ However, Python 3.12 seems to be much less forgiving when files are not
+ properly closed. When running the test suite, many of the files that are not
+ explicitly closed appear truncated. This leads to various tests failing or
+ hanging and causing FTBFS when the test suite runs at build time.
+ .
+ Furthermore, khmer defines the get_file_writer() function, but it cannot be
+ consistently used as a context manager because it sometimes closes the
+ underlying file descriptor ; and sometimes does not depending on the
+ arguments.
+ .
+ Fixed by defining a new FileWriter context manager and ensuring that
+ each call to open() / get_file_writer() frees up resources properly.
+Author: Olivier Gayot <olivier.gayot at canonical.com>
+Bug-Ubuntu: https://launchpad.net/bugs/2044383
+Bug-Debian: https://bugs.debian.org/1055687
+Forwarded: https://github.com/dib-lab/khmer/pull/1922
+Last-Update: 2023-11-26
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+Index: khmer-3.0.0~a3+dfsg/scripts/abundance-dist.py
+===================================================================
+--- khmer-3.0.0~a3+dfsg.orig/scripts/abundance-dist.py 2023-11-26 20:23:39.915485717 +0100
++++ khmer-3.0.0~a3+dfsg/scripts/abundance-dist.py 2023-11-26 20:23:39.911485747 +0100
+@@ -42,6 +42,7 @@
+ Use '-h' for parameter help.
+ """
+
++import contextlib
+ import sys
+ import csv
+ import khmer
+@@ -143,26 +144,28 @@
+ sys.exit(1)
+
+ if args.output_histogram_filename in ('-', '/dev/stdout'):
+- countgraph_fp = sys.stdout
++ countgraph_ctx = contextlib.nullcontext(enter_result=sys.stdout)
+ else:
+- countgraph_fp = open(args.output_histogram_filename, 'w')
+- countgraph_fp_csv = csv.writer(countgraph_fp)
+- # write headers:
+- countgraph_fp_csv.writerow(['abundance', 'count', 'cumulative',
+- 'cumulative_fraction'])
+-
+- sofar = 0
+- for _, i in enumerate(abundances):
+- if i == 0 and not args.output_zero:
+- continue
++ countgraph_ctx = open(args.output_histogram_filename, 'w')
+
+- sofar += i
+- frac = sofar / float(total)
++ with countgraph_ctx as countgraph_fp:
++ countgraph_fp_csv = csv.writer(countgraph_fp)
++ # write headers:
++ countgraph_fp_csv.writerow(['abundance', 'count', 'cumulative',
++ 'cumulative_fraction'])
++
++ sofar = 0
++ for _, i in enumerate(abundances):
++ if i == 0 and not args.output_zero:
++ continue
+
+- countgraph_fp_csv.writerow([_, i, sofar, round(frac, 3)])
++ sofar += i
++ frac = sofar / float(total)
+
+- if sofar == total:
+- break
++ countgraph_fp_csv.writerow([_, i, sofar, round(frac, 3)])
++
++ if sofar == total:
++ break
+
+
+ if __name__ == '__main__':
+Index: khmer-3.0.0~a3+dfsg/scripts/abundance-dist-single.py
+===================================================================
+--- khmer-3.0.0~a3+dfsg.orig/scripts/abundance-dist-single.py 2023-11-26 20:23:39.915485717 +0100
++++ khmer-3.0.0~a3+dfsg/scripts/abundance-dist-single.py 2023-11-26 20:23:39.911485747 +0100
+@@ -218,6 +218,10 @@
+
+ log_info('wrote to: {output}', output=args.output_histogram_filename)
+
++ # Ensure that the output files are properly written. Python 3.12 seems to
++ # be less forgiving here ..
++ hist_fp.close()
++
+
+ if __name__ == '__main__':
+ main()
+Index: khmer-3.0.0~a3+dfsg/scripts/do-partition.py
+===================================================================
+--- khmer-3.0.0~a3+dfsg.orig/scripts/do-partition.py 2023-11-26 20:23:39.915485717 +0100
++++ khmer-3.0.0~a3+dfsg/scripts/do-partition.py 2023-11-26 20:23:39.911485747 +0100
+@@ -168,8 +168,8 @@
+ worker_q.put((nodegraph, _, start, end))
+
+ print('enqueued %d subset tasks' % n_subsets, file=sys.stderr)
+- open('%s.info' % args.graphbase, 'w').write('%d subsets total\n'
+- % (n_subsets))
++ with open('%s.info' % args.graphbase, 'w') as info_fp:
++ info_fp.write('%d subsets total\n' % (n_subsets))
+
+ if n_subsets < args.threads:
+ args.threads = n_subsets
+Index: khmer-3.0.0~a3+dfsg/scripts/extract-long-sequences.py
+===================================================================
+--- khmer-3.0.0~a3+dfsg.orig/scripts/extract-long-sequences.py 2023-11-26 20:23:39.915485717 +0100
++++ khmer-3.0.0~a3+dfsg/scripts/extract-long-sequences.py 2023-11-26 20:23:39.911485747 +0100
+@@ -52,7 +52,7 @@
+ import sys
+ from khmer import __version__
+ from khmer.utils import write_record
+-from khmer.kfile import add_output_compression_type, get_file_writer
++from khmer.kfile import add_output_compression_type, FileWriter
+ from khmer.khmer_args import sanitize_help, KhmerArgumentParser
+
+
+@@ -81,12 +81,12 @@
+
+ def main():
+ args = sanitize_help(get_parser()).parse_args()
+- outfp = get_file_writer(args.output, args.gzip, args.bzip)
+- for filename in args.input_filenames:
+- for record in screed.open(filename):
+- if len(record['sequence']) >= args.length:
+- write_record(record, outfp)
+- print('wrote to: ' + args.output.name, file=sys.stderr)
++ with FileWriter(args.output, args.gzip, args.bzip) as outfp:
++ for filename in args.input_filenames:
++ for record in screed.open(filename):
++ if len(record['sequence']) >= args.length:
++ write_record(record, outfp)
++ print('wrote to: ' + args.output.name, file=sys.stderr)
+
+
+ if __name__ == '__main__':
+Index: khmer-3.0.0~a3+dfsg/khmer/kfile.py
+===================================================================
+--- khmer-3.0.0~a3+dfsg.orig/khmer/kfile.py 2023-11-26 20:23:39.915485717 +0100
++++ khmer-3.0.0~a3+dfsg/khmer/kfile.py 2023-11-26 20:23:39.911485747 +0100
+@@ -35,6 +35,7 @@
+ """File handling/checking utilities for command-line scripts."""
+
+
++import contextlib
+ import os
+ import sys
+ import errno
+@@ -252,3 +253,37 @@
+ ofile = file_handle
+
+ return ofile
++
++
++ at contextlib.contextmanager
++def FileWriter(file_handle, do_gzip, do_bzip, *, steal_ownership=False):
++ """Alternative to get_file_writer that requires the use of a with block.
++ The intent is to address an inherent problem with get_file_writer() that
++ makes it difficult to use as a context manager. When get_file_writer() is
++ called with both gzip=False and bzip=False, the underlying file handle is
++ returned. As a consequence, doing:
++ > with get_file_writer(sys.stdout, bzip=False, gzip=False) as fh:
++ > pass
++ ends up closing sys.stdout when the with block is exited. Using the
++ function without a context manager avoids the issue, but then it results in
++ leaked open files when either bzip=True or gzip=True.
++ FileWriter must be used as a context manager, but it ensures that resources
++ are closed upon exiting the with block. Furthermore, it can be explicitly
++ requested to close the underlying file_handle."""
++ ofile = None
++
++ if do_gzip and do_bzip:
++ raise ValueError("Cannot specify both bzip and gzip compression!")
++
++ if do_gzip:
++ ofile = gzip.GzipFile(fileobj=file_handle, mode='w')
++ elif do_bzip:
++ ofile = bz2.open(file_handle, mode='w')
++ else:
++ ofile = contextlib.nullcontext(enter_result=file_handle)
++
++ with ofile as x:
++ yield x
++
++ if steal_ownership:
++ file_handle.close()
+Index: khmer-3.0.0~a3+dfsg/scripts/extract-paired-reads.py
+===================================================================
+--- khmer-3.0.0~a3+dfsg.orig/scripts/extract-paired-reads.py 2023-11-26 20:23:39.915485717 +0100
++++ khmer-3.0.0~a3+dfsg/scripts/extract-paired-reads.py 2023-11-26 20:23:39.911485747 +0100
+@@ -44,6 +44,7 @@
+
+ Reads FASTQ and FASTA input, retains format for output.
+ """
++from contextlib import nullcontext
+ import sys
+ import os.path
+ import textwrap
+@@ -53,7 +54,7 @@
+ from khmer.khmer_args import sanitize_help, KhmerArgumentParser
+ from khmer.khmer_args import FileType as khFileType
+ from khmer.kfile import add_output_compression_type
+-from khmer.kfile import get_file_writer
++from khmer.kfile import FileWriter
+
+ from khmer.utils import broken_paired_reader, write_record, write_record_pair
+
+@@ -132,39 +133,40 @@
+
+ # OVERRIDE default output file locations with -p, -s
+ if args.output_paired:
+- paired_fp = get_file_writer(args.output_paired, args.gzip, args.bzip)
+- out2 = paired_fp.name
++ paired_ctx = FileWriter(args.output_paired, args.gzip, args.bzip)
++ out2 = args.output_paired.name
+ else:
+ # Don't override, just open the default filename from above
+- paired_fp = get_file_writer(open(out2, 'wb'), args.gzip, args.bzip)
++ paired_ctx = FileWriter(open(out2, 'wb'), args.gzip, args.bzip,
++ steal_ownership=True)
+ if args.output_single:
+- single_fp = get_file_writer(args.output_single, args.gzip, args.bzip)
++ single_ctx = FileWriter(args.output_single, args.gzip, args.bzip)
+ out1 = args.output_single.name
+ else:
+ # Don't override, just open the default filename from above
+- single_fp = get_file_writer(open(out1, 'wb'), args.gzip, args.bzip)
++ single_ctx = FileWriter(open(out1, 'wb'), args.gzip, args.bzip,
++ steal_ownership=True)
+
+- print('reading file "%s"' % infile, file=sys.stderr)
+- print('outputting interleaved pairs to "%s"' % out2, file=sys.stderr)
+- print('outputting orphans to "%s"' % out1, file=sys.stderr)
+-
+- n_pe = 0
+- n_se = 0
+-
+- reads = ReadParser(infile)
+- for index, is_pair, read1, read2 in broken_paired_reader(reads):
+- if index % 100000 == 0 and index > 0:
+- print('...', index, file=sys.stderr)
+-
+- if is_pair:
+- write_record_pair(read1, read2, paired_fp)
+- n_pe += 1
+- else:
+- write_record(read1, single_fp)
+- n_se += 1
+-
+- single_fp.close()
+- paired_fp.close()
++ with paired_ctx as paired_fp, single_ctx as single_fp:
++ print('reading file "%s"' % infile, file=sys.stderr)
++ print('outputting interleaved pairs to "%s"' % out2,
++ file=sys.stderr)
++ print('outputting orphans to "%s"' % out1, file=sys.stderr)
++
++ n_pe = 0
++ n_se = 0
++
++ reads = ReadParser(infile)
++ for index, is_pair, read1, read2 in broken_paired_reader(reads):
++ if index % 100000 == 0 and index > 0:
++ print('...', index, file=sys.stderr)
++
++ if is_pair:
++ write_record_pair(read1, read2, paired_fp)
++ n_pe += 1
++ else:
++ write_record(read1, single_fp)
++ n_se += 1
+
+ if n_pe == 0:
+ raise TypeError("no paired reads!? check file formats...")
+Index: khmer-3.0.0~a3+dfsg/scripts/extract-partitions.py
+===================================================================
+--- khmer-3.0.0~a3+dfsg.orig/scripts/extract-partitions.py 2023-11-26 20:23:39.915485717 +0100
++++ khmer-3.0.0~a3+dfsg/scripts/extract-partitions.py 2023-11-26 20:23:39.911485747 +0100
+@@ -301,10 +301,10 @@
+ args.max_size)
+
+ if args.output_unassigned:
+- ofile = open('%s.unassigned.%s' % (args.prefix, suffix), 'wb')
+- unassigned_fp = get_file_writer(ofile, args.gzip, args.bzip)
+- extractor.process_unassigned(unassigned_fp)
+- unassigned_fp.close()
++ with open('%s.unassigned.%s' % (args.prefix, suffix), 'wb') as ofile:
++ unassigned_fp = get_file_writer(ofile, args.gzip, args.bzip)
++ extractor.process_unassigned(unassigned_fp)
++ unassigned_fp.close()
+ else:
+ extractor.process_unassigned()
+
+@@ -320,13 +320,21 @@
+ print('nothing to output; exiting!', file=sys.stderr)
+ return
+
++ to_close = []
+ # open a bunch of output files for the different groups
+ group_fps = {}
+ for index in range(extractor.group_n):
+ fname = '%s.group%04d.%s' % (args.prefix, index, suffix)
+- group_fp = get_file_writer(open(fname, 'wb'), args.gzip,
++ back_fp = open(fname, 'wb')
++ group_fp = get_file_writer(back_fp, args.gzip,
+ args.bzip)
+ group_fps[index] = group_fp
++ # It feels more natural to close the writer before closing the
++ # underlying file. fp.close() is theoretically idempotent, so it should
++ # be fine even though sometimes get_file_writer "steals" ownership of
++ # the underlying stream.
++ to_close.append(group_fp)
++ to_close.append(back_fp)
+
+ # write 'em all out!
+ # refresh the generator
+@@ -351,6 +359,9 @@
+ args.prefix,
+ suffix), file=sys.stderr)
+
++ for fp in to_close:
++ fp.close()
++
+
+ if __name__ == '__main__':
+ main()
+Index: khmer-3.0.0~a3+dfsg/scripts/fastq-to-fasta.py
+===================================================================
+--- khmer-3.0.0~a3+dfsg.orig/scripts/fastq-to-fasta.py 2023-11-26 20:23:39.915485717 +0100
++++ khmer-3.0.0~a3+dfsg/scripts/fastq-to-fasta.py 2023-11-26 20:23:39.911485747 +0100
+@@ -45,7 +45,7 @@
+ import sys
+ import screed
+ from khmer import __version__
+-from khmer.kfile import (add_output_compression_type, get_file_writer,
++from khmer.kfile import (add_output_compression_type, FileWriter,
+ describe_file_handle)
+ from khmer.utils import write_record
+ from khmer.khmer_args import sanitize_help, KhmerArgumentParser
+@@ -74,21 +74,21 @@
+ args = sanitize_help(get_parser()).parse_args()
+
+ print('fastq from ', args.input_sequence, file=sys.stderr)
+- outfp = get_file_writer(args.output, args.gzip, args.bzip)
+- n_count = 0
+- for n, record in enumerate(screed.open(args.input_sequence)):
+- if n % 10000 == 0:
+- print('...', n, file=sys.stderr)
+-
+- sequence = record['sequence']
+-
+- if 'N' in sequence:
+- if not args.n_keep:
+- n_count += 1
+- continue
++ with FileWriter(args.output, args.gzip, args.bzip) as outfp:
++ n_count = 0
++ for n, record in enumerate(screed.open(args.input_sequence)):
++ if n % 10000 == 0:
++ print('...', n, file=sys.stderr)
++
++ sequence = record['sequence']
++
++ if 'N' in sequence:
++ if not args.n_keep:
++ n_count += 1
++ continue
+
+- del record['quality']
+- write_record(record, outfp)
++ del record['quality']
++ write_record(record, outfp)
+
+ print('\n' + 'lines from ' + args.input_sequence, file=sys.stderr)
+
+Index: khmer-3.0.0~a3+dfsg/scripts/filter-abund.py
+===================================================================
+--- khmer-3.0.0~a3+dfsg.orig/scripts/filter-abund.py 2023-11-26 20:23:39.915485717 +0100
++++ khmer-3.0.0~a3+dfsg/scripts/filter-abund.py 2023-11-26 20:23:39.911485747 +0100
+@@ -44,6 +44,7 @@
+
+ Use '-h' for parameter help.
+ """
++from contextlib import nullcontext
+ import sys
+ import os
+ import textwrap
+@@ -56,7 +57,7 @@
+ sanitize_help, check_argument_range)
+ from khmer.khmer_args import FileType as khFileType
+ from khmer.kfile import (check_input_files, check_space,
+- add_output_compression_type, get_file_writer)
++ add_output_compression_type, FileWriter)
+ from khmer.khmer_logger import (configure_logging, log_info, log_error,
+ log_warn)
+ from khmer.trimming import (trim_record)
+@@ -137,31 +138,38 @@
+
+ if args.single_output_file:
+ outfile = args.single_output_file.name
+- outfp = get_file_writer(args.single_output_file, args.gzip, args.bzip)
++ out_single_ctx = FileWriter(args.single_output_file, args.gzip,
++ args.bzip)
++ else:
++ out_single_ctx = nullcontext()
++
++ with out_single_ctx as out_single_fp:
++ # the filtering loop
++ for infile in infiles:
++ log_info('filtering {infile}', infile=infile)
++ if not args.single_output_file:
++ outfile = os.path.basename(infile) + '.abundfilt'
++ out_ctx = FileWriter(open(outfile, 'wb'), args.gzip,
++ args.bzip, steal_ownership=True)
++ else:
++ out_ctx = nullcontext(enter_result=out_single_fp)
++
++ paired_iter = broken_paired_reader(ReadParser(infile),
++ min_length=ksize,
++ force_single=True)
++
++ with out_ctx as outfp:
++ for n, is_pair, read1, read2 in paired_iter:
++ assert not is_pair
++ assert read2 is None
++
++ trimmed_record, _ = trim_record(countgraph, read1, args.cutoff,
++ args.variable_coverage,
++ args.normalize_to)
++ if trimmed_record:
++ write_record(trimmed_record, outfp)
+
+- # the filtering loop
+- for infile in infiles:
+- log_info('filtering {infile}', infile=infile)
+- if not args.single_output_file:
+- outfile = os.path.basename(infile) + '.abundfilt'
+- outfp = open(outfile, 'wb')
+- outfp = get_file_writer(outfp, args.gzip, args.bzip)
+-
+- paired_iter = broken_paired_reader(ReadParser(infile),
+- min_length=ksize,
+- force_single=True)
+-
+- for n, is_pair, read1, read2 in paired_iter:
+- assert not is_pair
+- assert read2 is None
+-
+- trimmed_record, _ = trim_record(countgraph, read1, args.cutoff,
+- args.variable_coverage,
+- args.normalize_to)
+- if trimmed_record:
+- write_record(trimmed_record, outfp)
+-
+- log_info('output in {outfile}', outfile=outfile)
++ log_info('output in {outfile}', outfile=outfile)
+
+
+ if __name__ == '__main__':
+Index: khmer-3.0.0~a3+dfsg/scripts/filter-abund-single.py
+===================================================================
+--- khmer-3.0.0~a3+dfsg.orig/scripts/filter-abund-single.py 2023-11-26 20:23:39.915485717 +0100
++++ khmer-3.0.0~a3+dfsg/scripts/filter-abund-single.py 2023-11-26 20:23:39.911485747 +0100
+@@ -60,7 +60,7 @@
+ from khmer.kfile import (check_input_files, check_space,
+ check_space_for_graph,
+ add_output_compression_type,
+- get_file_writer)
++ FileWriter)
+ from khmer.khmer_logger import (configure_logging, log_info, log_error,
+ log_warn)
+ from khmer.trimming import (trim_record)
+@@ -160,22 +160,23 @@
+ outfile = os.path.basename(args.datafile) + '.abundfilt'
+ else:
+ outfile = args.outfile
+- outfp = open(outfile, 'wb')
+- outfp = get_file_writer(outfp, args.gzip, args.bzip)
+
+- paired_iter = broken_paired_reader(ReadParser(args.datafile),
+- min_length=graph.ksize(),
+- force_single=True)
+-
+- for n, is_pair, read1, read2 in paired_iter:
+- assert not is_pair
+- assert read2 is None
+-
+- trimmed_record, _ = trim_record(graph, read1, args.cutoff,
+- args.variable_coverage,
+- args.normalize_to)
+- if trimmed_record:
+- write_record(trimmed_record, outfp)
++ with FileWriter(open(outfile, 'wb'), args.gzip, args.bzip,
++ steal_ownership=True) as outfp:
++
++ paired_iter = broken_paired_reader(ReadParser(args.datafile),
++ min_length=graph.ksize(),
++ force_single=True)
++
++ for n, is_pair, read1, read2 in paired_iter:
++ assert not is_pair
++ assert read2 is None
++
++ trimmed_record, _ = trim_record(graph, read1, args.cutoff,
++ args.variable_coverage,
++ args.normalize_to)
++ if trimmed_record:
++ write_record(trimmed_record, outfp)
+
+ log_info('output in {outfile}', outfile=outfile)
+
+Index: khmer-3.0.0~a3+dfsg/scripts/filter-stoptags.py
+===================================================================
+--- khmer-3.0.0~a3+dfsg.orig/scripts/filter-stoptags.py 2023-11-26 20:23:39.915485717 +0100
++++ khmer-3.0.0~a3+dfsg/scripts/filter-stoptags.py 2023-11-26 20:23:39.911485747 +0100
+@@ -108,10 +108,9 @@
+ print('filtering', infile, file=sys.stderr)
+ outfile = os.path.basename(infile) + '.stopfilt'
+
+- outfp = open(outfile, 'w')
+-
+- tsp = ThreadedSequenceProcessor(process_fn)
+- tsp.start(verbose_loader(infile), outfp)
++ with open(outfile, 'w') as outfp:
++ tsp = ThreadedSequenceProcessor(process_fn)
++ tsp.start(verbose_loader(infile), outfp)
+
+ print('output in', outfile, file=sys.stderr)
+
+Index: khmer-3.0.0~a3+dfsg/scripts/interleave-reads.py
+===================================================================
+--- khmer-3.0.0~a3+dfsg.orig/scripts/interleave-reads.py 2023-11-26 20:23:39.915485717 +0100
++++ khmer-3.0.0~a3+dfsg/scripts/interleave-reads.py 2023-11-26 20:23:39.911485747 +0100
+@@ -52,7 +52,7 @@
+ from khmer.kfile import check_input_files, check_space
+ from khmer.khmer_args import sanitize_help, KhmerArgumentParser
+ from khmer.khmer_args import FileType as khFileType
+-from khmer.kfile import (add_output_compression_type, get_file_writer,
++from khmer.kfile import (add_output_compression_type, FileWriter,
+ describe_file_handle)
+ from khmer.utils import (write_record_pair, check_is_left, check_is_right,
+ check_is_pair)
+@@ -109,42 +109,41 @@
+
+ print("Interleaving:\n\t%s\n\t%s" % (s1_file, s2_file), file=sys.stderr)
+
+- outfp = get_file_writer(args.output, args.gzip, args.bzip)
+-
+- counter = 0
+- screed_iter_1 = screed.open(s1_file)
+- screed_iter_2 = screed.open(s2_file)
+- for read1, read2 in zip_longest(screed_iter_1, screed_iter_2):
+- if read1 is None or read2 is None:
+- print(("ERROR: Input files contain different number"
+- " of records."), file=sys.stderr)
+- sys.exit(1)
+-
+- if counter % 100000 == 0:
+- print('...', counter, 'pairs', file=sys.stderr)
+- counter += 1
+-
+- name1 = read1.name
+- name2 = read2.name
+-
+- if not args.no_reformat:
+- if not check_is_left(name1):
+- name1 += '/1'
+- if not check_is_right(name2):
+- name2 += '/2'
+-
+- read1.name = name1
+- read2.name = name2
+-
+- if not check_is_pair(read1, read2):
+- print("ERROR: This doesn't look like paired data! "
+- "%s %s" % (read1.name, read2.name), file=sys.stderr)
++ with FileWriter(args.output, args.gzip, args.bzip) as outfp:
++ counter = 0
++ screed_iter_1 = screed.open(s1_file)
++ screed_iter_2 = screed.open(s2_file)
++ for read1, read2 in zip_longest(screed_iter_1, screed_iter_2):
++ if read1 is None or read2 is None:
++ print(("ERROR: Input files contain different number"
++ " of records."), file=sys.stderr)
+ sys.exit(1)
+
+- write_record_pair(read1, read2, outfp)
++ if counter % 100000 == 0:
++ print('...', counter, 'pairs', file=sys.stderr)
++ counter += 1
++
++ name1 = read1.name
++ name2 = read2.name
++
++ if not args.no_reformat:
++ if not check_is_left(name1):
++ name1 += '/1'
++ if not check_is_right(name2):
++ name2 += '/2'
++
++ read1.name = name1
++ read2.name = name2
++
++ if not check_is_pair(read1, read2):
++ print("ERROR: This doesn't look like paired data! "
++ "%s %s" % (read1.name, read2.name), file=sys.stderr)
++ sys.exit(1)
++
++ write_record_pair(read1, read2, outfp)
+
+- print('final: interleaved %d pairs' % counter, file=sys.stderr)
+- print('output written to', describe_file_handle(outfp), file=sys.stderr)
++ print('final: interleaved %d pairs' % counter, file=sys.stderr)
++ print('output written to', describe_file_handle(outfp), file=sys.stderr)
+
+
+ if __name__ == '__main__':
+Index: khmer-3.0.0~a3+dfsg/scripts/normalize-by-median.py
+===================================================================
+--- khmer-3.0.0~a3+dfsg.orig/scripts/normalize-by-median.py 2023-11-26 20:23:39.915485717 +0100
++++ khmer-3.0.0~a3+dfsg/scripts/normalize-by-median.py 2023-11-26 20:23:39.911485747 +0100
+@@ -46,6 +46,7 @@
+ Use '-h' for parameter help.
+ """
+
++from contextlib import nullcontext
+ import sys
+ import screed
+ import os
+@@ -60,7 +61,7 @@
+ import argparse
+ from khmer.kfile import (check_space, check_space_for_graph,
+ check_valid_file_exists, add_output_compression_type,
+- get_file_writer, describe_file_handle)
++ FileWriter, describe_file_handle)
+ from khmer.utils import (write_record, broken_paired_reader, ReadBundle,
+ clean_input_reads)
+ from khmer.khmer_logger import (configure_logging, log_info, log_error)
+@@ -360,39 +361,43 @@
+ output_name = None
+
+ if args.single_output_file:
+- outfp = get_file_writer(args.single_output_file, args.gzip, args.bzip)
++ out_single_ctx = FileWriter(args.single_output_file, args.gzip, args.bzip)
+ else:
++ out_single_ctx = nullcontext()
+ if '-' in filenames or '/dev/stdin' in filenames:
+ print("Accepting input from stdin; output filename must "
+ "be provided with '-o'.", file=sys.stderr)
+ sys.exit(1)
+
+- #
+- # main loop: iterate over all files given, do diginorm.
+- #
+-
+- for filename, require_paired in files:
+- if not args.single_output_file:
+- output_name = os.path.basename(filename) + '.keep'
+- outfp = open(output_name, 'wb')
+- outfp = get_file_writer(outfp, args.gzip, args.bzip)
+-
+- # failsafe context manager in case an input file breaks
+- with catch_io_errors(filename, outfp, args.single_output_file,
+- args.force, corrupt_files):
+- screed_iter = clean_input_reads(screed.open(filename))
+- reader = broken_paired_reader(screed_iter, min_length=args.ksize,
+- force_single=force_single,
+- require_paired=require_paired)
+-
+- # actually do diginorm
+- for record in with_diagnostics(reader, filename):
+- if record is not None:
+- write_record(record, outfp)
+-
+- log_info('output in {name}', name=describe_file_handle(outfp))
++ with out_single_ctx as out_single_fp:
++ #
++ # main loop: iterate over all files given, do diginorm.
++ #
++ for filename, require_paired in files:
+ if not args.single_output_file:
+- outfp.close()
++ output_name = os.path.basename(filename) + '.keep'
++ out_ctx = FileWriter(open(output_name, 'wb'), args.gzip,
++ args.bzip, steal_ownership=True)
++ else:
++ out_ctx = nullcontext(enter_result=out_single_fp)
++
++ with out_ctx as outfp:
++ # failsafe context manager in case an input file breaks
++ with catch_io_errors(filename, outfp, args.single_output_file,
++ args.force, corrupt_files):
++ screed_iter = clean_input_reads(screed.open(filename))
++ reader = broken_paired_reader(screed_iter,
++ min_length=args.ksize,
++ force_single=force_single,
++ require_paired=require_paired)
++
++ # actually do diginorm
++ for record in with_diagnostics(reader, filename):
++ if record is not None:
++ write_record(record, outfp)
++
++ log_info('output in {name}',
++ name=describe_file_handle(outfp))
+
+ # finished - print out some diagnostics.
+
+Index: khmer-3.0.0~a3+dfsg/scripts/partition-graph.py
+===================================================================
+--- khmer-3.0.0~a3+dfsg.orig/scripts/partition-graph.py 2023-11-26 20:23:39.915485717 +0100
++++ khmer-3.0.0~a3+dfsg/scripts/partition-graph.py 2023-11-26 20:23:39.911485747 +0100
+@@ -143,7 +143,8 @@
+ worker_q.put((nodegraph, _, start, end))
+
+ print('enqueued %d subset tasks' % n_subsets, file=sys.stderr)
+- open('%s.info' % basename, 'w').write('%d subsets total\n' % (n_subsets))
++ with open('%s.info' % basename, 'w') as info_fp:
++ info_fp.write('%d subsets total\n' % (n_subsets))
+
+ n_threads = args.threads
+ if n_subsets < n_threads:
+Index: khmer-3.0.0~a3+dfsg/scripts/sample-reads-randomly.py
+===================================================================
+--- khmer-3.0.0~a3+dfsg.orig/scripts/sample-reads-randomly.py 2023-11-26 20:23:39.915485717 +0100
++++ khmer-3.0.0~a3+dfsg/scripts/sample-reads-randomly.py 2023-11-26 20:23:39.911485747 +0100
+@@ -47,6 +47,7 @@
+ """
+
+ import argparse
++from contextlib import nullcontext
+ import os.path
+ import random
+ import textwrap
+@@ -55,7 +56,7 @@
+ from khmer import __version__
+ from khmer import ReadParser
+ from khmer.kfile import (check_input_files, add_output_compression_type,
+- get_file_writer)
++ FileWriter)
+ from khmer.khmer_args import sanitize_help, KhmerArgumentParser
+ from khmer.utils import write_record, broken_paired_reader
+
+@@ -201,27 +202,27 @@
+ print('Writing %d sequences to %s' %
+ (len(reads[0]), output_filename), file=sys.stderr)
+
+- output_file = args.output_file
+- if not output_file:
+- output_file = open(output_filename, 'wb')
+-
+- output_file = get_file_writer(output_file, args.gzip, args.bzip)
+-
+- for records in reads[0]:
+- write_record(records[0], output_file)
+- if records[1] is not None:
+- write_record(records[1], output_file)
++ output_back_ctx = nullcontext(args.output_file)
++ if not args.output_file:
++ output_back_ctx = open(output_filename, 'wb')
++
++ with output_back_ctx as output_back_fp:
++ with FileWriter(output_back_fp, args.gzip, args.bzip) as output_fp:
++ for records in reads[0]:
++ write_record(records[0], output_fp)
++ if records[1] is not None:
++ write_record(records[1], output_fp)
+ else:
+ for n in range(num_samples):
+ n_filename = output_filename + '.%d' % n
+ print('Writing %d sequences to %s' %
+ (len(reads[n]), n_filename), file=sys.stderr)
+- output_file = get_file_writer(open(n_filename, 'wb'), args.gzip,
+- args.bzip)
+- for records in reads[n]:
+- write_record(records[0], output_file)
+- if records[1] is not None:
+- write_record(records[1], output_file)
++ with FileWriter(open(n_filename, 'wb'), args.gzip, args.bzip,
++ steal_ownership=True) as output_fp:
++ for records in reads[n]:
++ write_record(records[0], output_fp)
++ if records[1] is not None:
++ write_record(records[1], output_fp)
+
+
+ if __name__ == '__main__':
+Index: khmer-3.0.0~a3+dfsg/scripts/split-paired-reads.py
+===================================================================
+--- khmer-3.0.0~a3+dfsg.orig/scripts/split-paired-reads.py 2023-11-26 20:23:39.915485717 +0100
++++ khmer-3.0.0~a3+dfsg/scripts/split-paired-reads.py 2023-11-26 20:23:39.911485747 +0100
+@@ -44,6 +44,7 @@
+
+ Reads FASTQ and FASTA input, retains format for output.
+ """
++from contextlib import nullcontext
+ import sys
+ import os
+ import textwrap
+@@ -56,7 +57,7 @@
+ UnpairedReadsError)
+ from khmer.kfile import (check_input_files, check_space,
+ add_output_compression_type,
+- get_file_writer, describe_file_handle)
++ FileWriter, describe_file_handle)
+
+
+ def get_parser():
+@@ -145,22 +146,26 @@
+
+ # OVERRIDE output file locations with -1, -2
+ if args.output_first:
+- fp_out1 = get_file_writer(args.output_first, args.gzip, args.bzip)
+- out1 = fp_out1.name
++ out1_ctx = FileWriter(args.output_first, args.gzip, args.bzip)
++ out1 = args.output_first.name
+ else:
+ # Use default filename created above
+- fp_out1 = get_file_writer(open(out1, 'wb'), args.gzip, args.bzip)
++ out1_ctx = FileWriter(open(out1, 'wb'), args.gzip, args.bzip,
++ steal_ownership=True)
+ if args.output_second:
+- fp_out2 = get_file_writer(args.output_second, args.gzip, args.bzip)
+- out2 = fp_out2.name
++ out2_ctx = FileWriter(args.output_second, args.gzip, args.bzip)
++ out2 = args.output_second.name
+ else:
+ # Use default filename created above
+- fp_out2 = get_file_writer(open(out2, 'wb'), args.gzip, args.bzip)
++ out2_ctx = FileWriter(open(out2, 'wb'), args.gzip, args.bzip,
++ steal_ownership=True)
+
+ # put orphaned reads here, if -0!
+ if args.output_orphaned:
+- fp_out0 = get_file_writer(args.output_orphaned, args.gzip, args.bzip)
++ out0_ctx = FileWriter(args.output_orphaned, args.gzip, args.bzip)
+ out0 = describe_file_handle(args.output_orphaned)
++ else:
++ out0_ctx = nullcontext()
+
+ counter1 = 0
+ counter2 = 0
+@@ -171,23 +176,24 @@
+ paired_iter = broken_paired_reader(ReadParser(infile),
+ require_paired=not args.output_orphaned)
+
+- try:
+- for index, is_pair, record1, record2 in paired_iter:
+- if index % 10000 == 0:
+- print('...', index, file=sys.stderr)
+-
+- if is_pair:
+- write_record(record1, fp_out1)
+- counter1 += 1
+- write_record(record2, fp_out2)
+- counter2 += 1
+- elif args.output_orphaned:
+- write_record(record1, fp_out0)
+- counter3 += 1
+- except UnpairedReadsError as e:
+- print("Unpaired reads found starting at {name}; exiting".format(
+- name=e.read1.name), file=sys.stderr)
+- sys.exit(1)
++ with out0_ctx as fp_out0, out1_ctx as fp_out1, out2_ctx as fp_out2:
++ try:
++ for index, is_pair, record1, record2 in paired_iter:
++ if index % 10000 == 0:
++ print('...', index, file=sys.stderr)
++
++ if is_pair:
++ write_record(record1, fp_out1)
++ counter1 += 1
++ write_record(record2, fp_out2)
++ counter2 += 1
++ elif args.output_orphaned:
++ write_record(record1, fp_out0)
++ counter3 += 1
++ except UnpairedReadsError as e:
++ print("Unpaired reads found starting at {name}; exiting".format(
++ name=e.read1.name), file=sys.stderr)
++ sys.exit(1)
+
+ print("DONE; split %d sequences (%d left, %d right, %d orphans)" %
+ (counter1 + counter2, counter1, counter2, counter3), file=sys.stderr)
+Index: khmer-3.0.0~a3+dfsg/scripts/trim-low-abund.py
+===================================================================
+--- khmer-3.0.0~a3+dfsg.orig/scripts/trim-low-abund.py 2023-11-26 20:23:39.915485717 +0100
++++ khmer-3.0.0~a3+dfsg/scripts/trim-low-abund.py 2023-11-26 20:28:16.389478687 +0100
+@@ -43,6 +43,7 @@
+
+ Use -h for parameter help.
+ """
++from contextlib import nullcontext
+ import csv
+ import sys
+ import os
+@@ -63,7 +64,7 @@
+ from khmer.utils import write_record, broken_paired_reader, ReadBundle
+ from khmer.kfile import (check_space, check_space_for_graph,
+ check_valid_file_exists, add_output_compression_type,
+- get_file_writer)
++ get_file_writer, FileWriter)
+ from khmer.khmer_logger import configure_logging, log_info, log_error
+ from khmer.trimming import trim_record
+
+@@ -374,108 +375,111 @@
+ # only create the file writer once if outfp is specified; otherwise,
+ # create it for each file.
+ if args.output:
+- trimfp = get_file_writer(args.output, args.gzip, args.bzip)
++ trim_ctx = FileWriter(args.output, args.gzip, args.bzip)
++ else:
++ trim_ctx = nullcontext()
+
+ pass2list = []
+- for filename in args.input_filenames:
+- # figure out temporary filename for 2nd pass
+- pass2filename = filename.replace(os.path.sep, '-') + '.pass2'
+- pass2filename = os.path.join(tempdir, pass2filename)
+- pass2fp = open(pass2filename, 'w')
+-
+- # construct output filenames
+- if args.output is None:
+- # note: this will be saved in trimfp.
+- outfp = open(os.path.basename(filename) + '.abundtrim', 'wb')
+-
+- # get file handle w/gzip, bzip
+- trimfp = get_file_writer(outfp, args.gzip, args.bzip)
+-
+- # record all this info
+- pass2list.append((filename, pass2filename, trimfp))
+-
+- # input file stuff: get a broken_paired reader.
+- paired_iter = broken_paired_reader(ReadParser(filename), min_length=K,
+- force_single=args.ignore_pairs)
+-
+- # main loop through the file.
+- n_start = trimmer.n_reads
+- save_start = trimmer.n_saved
+-
+- watermark = REPORT_EVERY_N_READS
+- for read in trimmer.pass1(paired_iter, pass2fp):
+- if (trimmer.n_reads - n_start) > watermark:
+- log_info("... {filename} {n_saved} {n_reads} {n_bp} "
+- "{w_reads} {w_bp}", filename=filename,
+- n_saved=trimmer.n_saved, n_reads=trimmer.n_reads,
+- n_bp=trimmer.n_bp, w_reads=written_reads,
+- w_bp=written_bp)
+- watermark += REPORT_EVERY_N_READS
+-
+- # write out the trimmed/etc sequences that AREN'T going to be
+- # revisited in a 2nd pass.
+- write_record(read, trimfp)
+- written_bp += len(read)
+- written_reads += 1
+- pass2fp.close()
+-
+- log_info("{filename}: kept aside {kept} of {total} from first pass",
+- filename=filename, kept=trimmer.n_saved - save_start,
+- total=trimmer.n_reads - n_start)
+-
+- # first pass goes across all the data, so record relevant stats...
+- n_reads = trimmer.n_reads
+- n_bp = trimmer.n_bp
+- n_skipped = trimmer.n_skipped
+- bp_skipped = trimmer.bp_skipped
+- save_pass2_total = trimmer.n_saved
+-
+- # ### SECOND PASS. ###
+-
+- # nothing should have been skipped yet!
+- assert trimmer.n_skipped == 0
+- assert trimmer.bp_skipped == 0
+-
+- if args.single_pass:
+- pass2list = []
+-
+- # go back through all the files again.
+- for _, pass2filename, trimfp in pass2list:
+- log_info('second pass: looking at sequences kept aside in {pass2}',
+- pass2=pass2filename)
+-
+- # note that for this second pass, we don't care about paired
+- # reads - they will be output in the same order they're read in,
+- # so pairs will stay together if not orphaned. This is in contrast
+- # to the first loop. Hence, force_single=True below.
+-
+- read_parser = ReadParser(pass2filename)
+- paired_iter = broken_paired_reader(read_parser,
+- min_length=K,
+- force_single=True)
+-
+- watermark = REPORT_EVERY_N_READS
+- for read in trimmer.pass2(paired_iter):
+- if (trimmer.n_reads - n_start) > watermark:
+- log_info('... x 2 {a} {b} {c} {d} {e} {f} {g}',
+- a=trimmer.n_reads - n_start,
+- b=pass2filename, c=trimmer.n_saved,
+- d=trimmer.n_reads, e=trimmer.n_bp,
+- f=written_reads, g=written_bp)
+- watermark += REPORT_EVERY_N_READS
+-
+- write_record(read, trimfp)
+- written_reads += 1
+- written_bp += len(read)
+-
+- read_parser.close()
+-
+- log_info('removing {pass2}', pass2=pass2filename)
+- os.unlink(pass2filename)
+-
+- # if we created our own trimfps, close 'em.
+- if not args.output:
+- trimfp.close()
++ with trim_ctx as trimfp:
++ for filename in args.input_filenames:
++ # figure out temporary filename for 2nd pass
++ pass2filename = filename.replace(os.path.sep, '-') + '.pass2'
++ pass2filename = os.path.join(tempdir, pass2filename)
++ pass2fp = open(pass2filename, 'w')
++
++ # construct output filenames
++ if args.output is None:
++ # note: this will be saved in trimfp.
++ outfp = open(os.path.basename(filename) + '.abundtrim', 'wb')
++
++ # get file handle w/gzip, bzip
++ trimfp = get_file_writer(outfp, args.gzip, args.bzip)
++
++ # record all this info
++ pass2list.append((filename, pass2filename, trimfp))
++
++ # input file stuff: get a broken_paired reader.
++ paired_iter = broken_paired_reader(ReadParser(filename), min_length=K,
++ force_single=args.ignore_pairs)
++
++ # main loop through the file.
++ n_start = trimmer.n_reads
++ save_start = trimmer.n_saved
++
++ watermark = REPORT_EVERY_N_READS
++ for read in trimmer.pass1(paired_iter, pass2fp):
++ if (trimmer.n_reads - n_start) > watermark:
++ log_info("... {filename} {n_saved} {n_reads} {n_bp} "
++ "{w_reads} {w_bp}", filename=filename,
++ n_saved=trimmer.n_saved, n_reads=trimmer.n_reads,
++ n_bp=trimmer.n_bp, w_reads=written_reads,
++ w_bp=written_bp)
++ watermark += REPORT_EVERY_N_READS
++
++ # write out the trimmed/etc sequences that AREN'T going to be
++ # revisited in a 2nd pass.
++ write_record(read, trimfp)
++ written_bp += len(read)
++ written_reads += 1
++ pass2fp.close()
++
++ log_info("{filename}: kept aside {kept} of {total} from first pass",
++ filename=filename, kept=trimmer.n_saved - save_start,
++ total=trimmer.n_reads - n_start)
++
++ # first pass goes across all the data, so record relevant stats...
++ n_reads = trimmer.n_reads
++ n_bp = trimmer.n_bp
++ n_skipped = trimmer.n_skipped
++ bp_skipped = trimmer.bp_skipped
++ save_pass2_total = trimmer.n_saved
++
++ # ### SECOND PASS. ###
++
++ # nothing should have been skipped yet!
++ assert trimmer.n_skipped == 0
++ assert trimmer.bp_skipped == 0
++
++ if args.single_pass:
++ pass2list = []
++
++ # go back through all the files again.
++ for _, pass2filename, trimfp in pass2list:
++ log_info('second pass: looking at sequences kept aside in {pass2}',
++ pass2=pass2filename)
++
++ # note that for this second pass, we don't care about paired
++ # reads - they will be output in the same order they're read in,
++ # so pairs will stay together if not orphaned. This is in contrast
++ # to the first loop. Hence, force_single=True below.
++
++ read_parser = ReadParser(pass2filename)
++ paired_iter = broken_paired_reader(read_parser,
++ min_length=K,
++ force_single=True)
++
++ watermark = REPORT_EVERY_N_READS
++ for read in trimmer.pass2(paired_iter):
++ if (trimmer.n_reads - n_start) > watermark:
++ log_info('... x 2 {a} {b} {c} {d} {e} {f} {g}',
++ a=trimmer.n_reads - n_start,
++ b=pass2filename, c=trimmer.n_saved,
++ d=trimmer.n_reads, e=trimmer.n_bp,
++ f=written_reads, g=written_bp)
++ watermark += REPORT_EVERY_N_READS
++
++ write_record(read, trimfp)
++ written_reads += 1
++ written_bp += len(read)
++
++ read_parser.close()
++
++ log_info('removing {pass2}', pass2=pass2filename)
++ os.unlink(pass2filename)
++
++ # if we created our own trimfps, close 'em.
++ if not args.output:
++ trimfp.close()
+
+ try:
+ log_info('removing temp directory & contents ({temp})', temp=tempdir)
diff -Nru khmer-3.0.0~a3+dfsg/debian/patches/python3.12-support.patch khmer-3.0.0~a3+dfsg/debian/patches/python3.12-support.patch
--- khmer-3.0.0~a3+dfsg/debian/patches/python3.12-support.patch 2023-11-25 18:11:03.000000000 +0100
+++ khmer-3.0.0~a3+dfsg/debian/patches/python3.12-support.patch 2023-11-26 02:28:32.000000000 +0100
@@ -1,18 +1,25 @@
Description: Add support for Python 3.12
Ever since Python 3.2, configparser.SafeConfigParser has been deprecated in
- favor of configparser.ConfigParser. An alias existed for backward compability
- but the alias was dropped from Python 3.12.
+ favor of configparser.ConfigParser. An alias existed for backward
+ compatibility but the alias was dropped from Python 3.12. Let us now use
+ ConfigParser explicitly, and use .read_file() instead of .readfp() which was
+ dropped too.
+ .
+ The imp module has also been dropped, but a similar behavior can be achieved
+ using importlib.
Author: Olivier Gayot <olivier.gayot at canonical.com>
Author: Simon Quigley <tsimonq2 at ubuntu.com>
Bug-Ubuntu: https://launchpad.net/bugs/2044383
Bug-Debian: https://bugs.debian.org/1055687
Forwarded: https://github.com/dib-lab/khmer/pull/1922
-Last-Update: 2023-11-23
+Last-Update: 2023-11-26
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- a/versioneer.py
-+++ b/versioneer.py
-@@ -339,9 +339,9 @@ def get_config_from_root(root):
+Index: khmer-3.0.0~a3+dfsg/versioneer.py
+===================================================================
+--- khmer-3.0.0~a3+dfsg.orig/versioneer.py 2023-11-26 15:33:13.654983243 +0100
++++ khmer-3.0.0~a3+dfsg/versioneer.py 2023-11-26 15:33:13.650983273 +0100
+@@ -339,9 +339,9 @@
# configparser.NoOptionError (if it lacks "VCS="). See the docstring at
# the top of versioneer.py for instructions on writing your setup.cfg .
setup_cfg = os.path.join(root, "setup.cfg")
@@ -24,3 +31,26 @@
VCS = parser.get("versioneer", "VCS") # mandatory
def get(parser, name):
+Index: khmer-3.0.0~a3+dfsg/tests/test_sandbox_scripts.py
+===================================================================
+--- khmer-3.0.0~a3+dfsg.orig/tests/test_sandbox_scripts.py 2023-11-26 15:33:13.654983243 +0100
++++ khmer-3.0.0~a3+dfsg/tests/test_sandbox_scripts.py 2023-11-26 15:33:13.650983273 +0100
+@@ -42,7 +42,7 @@
+ from io import StringIO
+ import traceback
+ import glob
+-import imp
++import importlib
+
+ import pytest
+
+@@ -77,7 +77,8 @@
+ @pytest.mark.parametrize("filename", _sandbox_scripts())
+ def test_import_succeeds(filename, tmpdir, capsys):
+ try:
+- mod = imp.load_source('__zzz', filename)
++ loader = importlib.machinery.SourceFileLoader('__zzz', filename)
++ mod = loader.load_module()
+ except:
+ print(traceback.format_exc())
+ raise AssertionError("%s cannot be imported" % (filename,))
diff -Nru khmer-3.0.0~a3+dfsg/debian/patches/series khmer-3.0.0~a3+dfsg/debian/patches/series
--- khmer-3.0.0~a3+dfsg/debian/patches/series 2023-11-25 17:44:28.000000000 +0100
+++ khmer-3.0.0~a3+dfsg/debian/patches/series 2023-11-26 02:28:32.000000000 +0100
@@ -18,3 +18,4 @@
refresh_cython
find_object_files_at_right_loc.patch
python3.12-support.patch
+close-opened-files.patch
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