[med-svn] [Git][med-team/libslow5lib][master] 16 commits: New upstream version 1.3.1+dfsg

Wed Nov 5 21:12:03 GMT 2025

Étienne Mollier pushed to branch master at Debian Med / libslow5lib

Commits:
f1f60f4f by Étienne Mollier at 2025-11-05T19:49:06+01:00
New upstream version 1.3.1+dfsg
- - - - -
85fdd057 by Étienne Mollier at 2025-11-05T19:49:11+01:00
Update upstream source from tag 'upstream/1.3.1+dfsg'

Update to upstream version '1.3.1+dfsg'
with Debian dir fb2ee6146e5d306efa35b57b2db6947512f62eac
- - - - -
62f445a1 by Étienne Mollier at 2025-11-05T19:54:39+01:00
use_debian_packaged_streamvbyte.patch: refresh.

- - - - -
be53835f by Étienne Mollier at 2025-11-05T19:59:27+01:00
enable_shared_and_static.patch: refresh.

- - - - -
5963dd2b by Étienne Mollier at 2025-11-05T20:02:31+01:00
fix-baseline.patch: refresh.

- - - - -
a1fae695 by Étienne Mollier at 2025-11-05T20:10:16+01:00
use_debian_packaged_streamvbyte.patch: complement.

There were a few __slow5_streamvbyte calls to convert to plain
streamvbyte.

Gbp-Dch: ignore

- - - - -
c386a570 by Étienne Mollier at 2025-11-05T20:14:10+01:00
d/libslow5-0t64.symbols: append new symbols.

- - - - -
3728bf78 by Étienne Mollier at 2025-11-05T20:51:07+01:00
d/control: declare compliance to standards version 4.7.2.

- - - - -
098a6b85 by Étienne Mollier at 2025-11-05T20:51:31+01:00
d/control: drop redundant Rules-Requires-Root: no.

- - - - -
7f5b468c by Étienne Mollier at 2025-11-05T20:54:45+01:00
d/control: build depends on python3-numpy-dev.

- - - - -
67e42cf4 by Étienne Mollier at 2025-11-05T21:37:02+01:00
use_debian_packaged_streamvbyte.patch: last adjustment.

This change was needed in order to fix a heap corruption detected on
free(2) invocation and crashing the autopkgtest with:

	free(): corrupted unsorted chunks

It is worth noting that upstream stores debug techniques based on the
address sanitizer in the file python/pydebug.sh.  Taking inspiration
on this script to invoke the address sanitizer was invaluable to
determine what the issue was exactly.

This change is part of the patch refresh to align with the new
upstream version.

Gbp-Dch: ignore

- - - - -
5dc2da85 by Étienne Mollier at 2025-11-05T21:37:27+01:00
d/rules: install all examples.

- - - - -
42b21ef5 by Étienne Mollier at 2025-11-05T21:50:33+01:00
d/clean: cleanup extra files.

Closes: #1048497

- - - - -
d4e8b436 by Étienne Mollier at 2025-11-05T21:58:33+01:00
d/rules: protect include/ directory from mishaps.

Closes: #1049769

- - - - -
f6c6f45c by Étienne Mollier at 2025-11-05T22:09:03+01:00
unshuffle-makefile.patch: new: fix make --reverse.

Closes: #1105533

- - - - -
a844fab7 by Étienne Mollier at 2025-11-05T22:11:31+01:00
d/changelog: initialise the changelog.

- - - - -

73 changed files:

- .travis.yml
- CMakeLists.txt
- README.md
- debian/changelog
- debian/clean
- debian/control
- debian/libslow5-0t64.symbols
- debian/patches/enable_shared_and_static.patch
- debian/patches/fix-baseline.patch
- debian/patches/series
- + debian/patches/unshuffle-makefile.patch
- debian/patches/use_debian_packaged_streamvbyte.patch
- debian/rules
- docs/getting_started.md
- docs/index.md
- docs/pyslow5_api/pyslow5.md
- + docs/slow5_api/low_level_api/slow5_aux_add_enum.md
- + docs/slow5_api/low_level_api/slow5_idx_load_with.md
- + docs/slow5_api/low_level_api/slow5_set_skip_rid.md
- + docs/slow5_api/mt_api/slow5_free_batch.md
- + docs/slow5_api/mt_api/slow5_free_mt.md
- + docs/slow5_api/mt_api/slow5_get_batch.md
- + docs/slow5_api/mt_api/slow5_get_next_batch.md
- + docs/slow5_api/mt_api/slow5_init_batch.md
- + docs/slow5_api/mt_api/slow5_init_mt.md
- + docs/slow5_api/mt_api/slow5_write_batch.md
- docs/slow5_api/slow5.md
- docs/slow5_api/slow5_internal.md
- docs/slow5_api/slow5_low_level_api.md
- + docs/slow5_api/slow5_mt_api.md
- docs/slow5_api/slow5_set_press.md
- examples/adv/README.md
- + examples/adv/auxiliary_field_enum_write.c
- examples/adv/build.sh
- + examples/mt/README.md
- + examples/mt/build.sh
- + examples/mt/lazymt.c
- + examples/mt/mt.c
- include/slow5/slow5.h
- include/slow5/slow5_defs.h
- + include/slow5/slow5_mt.h
- include/slow5/slow5_press.h
- python/README.md
- python/example.py
- python/pydebug.sh
- python/pyslow5.h
- python/pyslow5.pxd
- python/pyslow5.pyx
- + python/pytest.sh
- − python/slow5threads.h
- python/test.py
- python/valgrind-python.supp
- setup.py
- src/slow5.c
- + src/slow5_byte.h
- src/slow5_extra.h
- src/slow5_idx.c
- src/slow5_idx.h
- python/slow5threads.c → src/slow5_mt.c
- src/slow5_press.c
- test/bench/build.sh
- test/bench/convert_to_pa.c
- test/bench/convert_to_pa_rand.c
- test/bench/get_all.c
- test/bench/get_all_read_ids.c → test/bench/get_read_ids.c
- test/bench/get_selected_read_ids_read_number.c → test/bench/get_read_number_rand.c
- test/bench/get_selected_read_ids_sample_count.c → test/bench/get_sample_count_rand.c
- test/bench/get_all_samples.c → test/bench/get_samples.c
- test/bench/get_all_samples_no_pipelining.c → test/bench/get_samples_no_pipelining.c
- test/bench/get_selected_read_ids_samples.c → test/bench/get_samples_rand.c
- + test/bench/readme.md
- test/unit_test_helpers.c
- test/unit_test_press.c

The diff was not included because it is too large.

View it on GitLab: https://salsa.debian.org/med-team/libslow5lib/-/compare/2f58d9e3c4047d5761daad9f14fd38ede0341aca...a844fab76b1aca0947fd1e0394ed0986881df7aa

-- 
View it on GitLab: https://salsa.debian.org/med-team/libslow5lib/-/compare/2f58d9e3c4047d5761daad9f14fd38ede0341aca...a844fab76b1aca0947fd1e0394ed0986881df7aa
You're receiving this email because of your account on salsa.debian.org.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20251105/18e26a74/attachment-0001.htm>