Debian Patches

Status for ariba/2.14.7+ds-14

Patch Description Author Forwarded Bugs Origin Last update
use_debian_packaged_libs_for_extension.patch use Debian packages dependencies for extension build Sascha Steinbiss <satta@debian.org> no
use_bwa_compatible_fermi-lite.patch Adapt to fermi-lite which does not conflict with bwa An issue on fermi-lite upstream tracker
https://github.com/lh3/fermi-lite/issues/5
suggests to take over a patch for the Debian package which would
enable making it co-usable with libbwa-dev (which is needed in
libseqlib). This patch adapts ariba to the potential change in
fermi-lite.		 Andreas Tille <tille@debian.org> no 2017-02-04
add-testdata.patch include testdata in package Sascha Steinbiss <satta@debian.org> no 2019-09-09
disable-tests-with-internet-access.patch disable tests that need Internet access Sascha Steinbiss <satta@debian.org> not-needed 2019-09-09
support-pymummer-0.11.patch adapt test cases for new PyMUMmer version pymummer 0.11 uses a different internal format which is incompatible
with the one assumed by Ariba. Note that ariba hard-requires an earlier
version than the one in Debian. However, since Debian has updated
pymummer now, we need to catch up even though upstream does not.		 Sascha Steinbiss <satta@debian.org> no 2020-06-30
run-debian-spades-wrapper.patch run Debian SPAdes wrapper Debian's /usr/bin/spades.py is not a Python script, but a wrapper
around a common executable only provided for compatibility reasons.
Ariba is trying to execute it explicitly as a Python script.
This patch just calls the executable without forcing it through the
Python interpreter.		 Sascha Steinbiss <satta@debian.org> no 2020-06-30
python3.12.patch Fix autopkgtest by replacing distutils Andreas Tille <tille@debian.org> no debian 2024-02-01
python3.12_syntax_warning.patch Fix Python3.12 syntax warnings Andreas Tille <tille@debian.org> no debian 2024-12-04
py3.13.patch "exec" and "eval" changed semantic in Python 3.13 "exec" and "eval" changed semantic of the default locals namespace in
Python 3.13, this patch addresses this change ("exec" and "eval" usage
can be avoided, but the maintainer seems to be far away).		 s3v <c0llapsed@yahoo.it> no debian 2025-01-14
remove_pkg_resources.patch no
multiprocessing-py3.14.patch adapt to new multiprocessing code Adapts the code to Python 3.14's change from fork to forkserver as the default
multiprocessing start method, which causes ConnectionResetError when using
multiprocessing.Manager() in certain environments (chroots, containers).		 Sascha Steinbiss <satta@debian.org> no 2026-07-05
faidx-pysam-0.24.patch Fix write_fa_subset with pysam >= 0.24 pysam 0.24.x rewrote the samtools stdout redirection. As a result
pysam.faidx(infile, region) no longer returns the fetched sequence as
a string (it returns an empty string while the sequence is written to
the process' real stdout), which made write_fa_subset write empty
output files and broke ariba/tests/faidx_test.py::test_write_fa_subset.
Fetch sequences via pysam.FastaFile instead, which works with all
supported pysam versions.		 no 2026-09-21

All known versions for source package 'ariba'

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