third-party/cqf/gqf.c | 187 11 + 176 - 0 !
third-party/cqf/gqf.h | 3 0 + 3 - 0 !
2 files changed, 11 insertions(+), 179 deletions(-)

---

tests/test_assembly.py | 2 1 + 1 - 0 !
tests/test_countgraph.py | 4 2 + 2 - 0 !
tests/test_counting_single.py | 4 2 + 2 - 0 !
tests/test_cython_parsing.py | 2 1 + 1 - 0 !
tests/test_graph.py | 6 3 + 3 - 0 !
tests/test_hll.py | 2 1 + 1 - 0 !
tests/test_labelhash.py | 2 1 + 1 - 0 !
tests/test_nodegraph.py | 2 1 + 1 - 0 !
tests/test_sandbox_scripts.py | 2 1 + 1 - 0 !
tests/test_scripts.py | 2 1 + 1 - 0 !
tests/test_subset_graph.py | 2 1 + 1 - 0 !
11 files changed, 15 insertions(+), 15 deletions(-)

 add pytest 8 compat

third-party/cqf/Makefile | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 enable building on aarch64 and other non-x86 systems

third-party/cqf/Makefile | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 restore standard build flags into third-party/cqf

Improves build hardening for Debian

MANIFEST.in | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 contributing.md has moved and isn't installed anymore

setup.py | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 use /usr/bin/env python3 as the crunchbang interpreter in setup.py

setup.cfg | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 use debian packaged libraries

setup.py | 2 0 + 2 - 0 !
1 file changed, 2 deletions(-)

 allow any version of setuptools

doc/_templates/page.html | 2 2 + 0 - 0 !
doc/conf.py | 2 1 + 1 - 0 !
2 files changed, 3 insertions(+), 1 deletion(-)

 turn off google analytics as per lintian warning

doc/conf.py | 10 7 + 3 - 0 !
1 file changed, 7 insertions(+), 3 deletions(-)

 use debian package version instead of git version

Makefile | 2 1 + 1 - 0 !
src/oxli/Makefile | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 use correct library version etc. (fixed by upstream #1240, remove for 2.0)

tests/test_read_parsers.py | 15 12 + 3 - 0 !
1 file changed, 12 insertions(+), 3 deletions(-)

 work around a suspected cpython bug

Occurs when exception strings are empty. See upstream issues #885, #1190.

scripts/extract-paired-reads.py | 2 1 + 1 - 0 !
tests/khmer_tst_utils.py | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 fix fatal pytest.skip usage

Makefile | 22 11 + 11 - 0 !
1 file changed, 11 insertions(+), 11 deletions(-)

 s/python/python3/ as appropriate

src/oxli/test-compile.cc | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 fix liboxli sanity check test

src/oxli/kmer_hash.cc | 1 1 + 0 - 0 !
1 file changed, 1 insertion(+)

 fix gcc-11 ftbfs with including limits header

khmer/kfile.py | 4 2 + 2 - 0 !
setup.py | 2 1 + 1 - 0 !
2 files changed, 3 insertions(+), 3 deletions(-)

 use stdlib bz2 instead of bz2file
Bug-Debian: https://bugs.debian.org/987287

khmer/kfile.py | 6 6 + 0 - 0 !
khmer/khmer_args.py | 6 4 + 2 - 0 !
scripts/trim-low-abund.py | 2 1 + 1 - 0 !
tests/khmer_tst_utils.py | 31 22 + 9 - 0 !
4 files changed, 33 insertions(+), 12 deletions(-)

 cope with https://bugs.python.org/issue14156 being fixed

setup.py | 9 6 + 3 - 0 !
1 file changed, 6 insertions(+), 3 deletions(-)

 rerun cython to support python 3.10+

setup.py | 11 10 + 1 - 0 !
1 file changed, 10 insertions(+), 1 deletion(-)

 the location for compiler cpy binaries changed, reflect the change in setup.py

tests/test_sandbox_scripts.py | 5 3 + 2 - 0 !
versioneer.py | 4 2 + 2 - 0 !
2 files changed, 5 insertions(+), 4 deletions(-)

 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
 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.

khmer/kfile.py | 35 35 + 0 - 0 !
scripts/abundance-dist-single.py | 4 4 + 0 - 0 !
scripts/abundance-dist.py | 35 19 + 16 - 0 !
scripts/do-partition.py | 4 2 + 2 - 0 !
scripts/extract-long-sequences.py | 14 7 + 7 - 0 !
scripts/extract-paired-reads.py | 56 29 + 27 - 0 !
scripts/extract-partitions.py | 21 16 + 5 - 0 !
scripts/fastq-to-fasta.py | 30 15 + 15 - 0 !
scripts/filter-abund-single.py | 33 17 + 16 - 0 !
scripts/filter-abund.py | 58 33 + 25 - 0 !
scripts/filter-stoptags.py | 7 3 + 4 - 0 !
scripts/interleave-reads.py | 67 33 + 34 - 0 !
scripts/normalize-by-median.py | 59 32 + 27 - 0 !
scripts/partition-graph.py | 3 2 + 1 - 0 !
scripts/sample-reads-randomly.py | 35 18 + 17 - 0 !
scripts/split-paired-reads.py | 56 31 + 25 - 0 !
scripts/trim-low-abund.py | 206 105 + 101 - 0 !
17 files changed, 401 insertions(+), 322 deletions(-)

 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.