Make fast forward from 0.22.1+ds-1

[dgit --quilt=gbp]

fix test failure with htslib 1.20.

This data file contains invalid data, which is diagnosed by
improvements in bam_parse_basemod2() in HTSlib 1.20. Updating these
base modification data files to the versions in htslib and hts-specs
corrects the problem.
Author: John Marshall
Origin: upstream, https://github.com/pysam-developers/pysam/issues/1291#issuecomment-2131146211
Bug: https://github.com/pysam-developers/pysam/issues/1291
Reviewed-by: Étienne Mollier <emollier@debian.org>
Last-Update: 2024-05-29

Gbp-Pq: Name htslib-1.20.patch

Attempt skipping failing test on 32-bit

Forwarded: not-needed
Last-Update: 2021-10-15

Last-Update: 2021-10-15
Gbp-Pq: Name skip-test-on-32-bit.patch

Do not clean *.bam files

Last-Update: 2020-01-23 14:31:06 +0100
Forwarded: not-needed

Gbp-Pq: Name clean_less

Skip tests trying to access remote site

Last-Update: Tue, 11 Sep 2018 14:12:55 +0200
Forwarded: not-needed

Gbp-Pq: Name skip_test_remote.patch

ready to upload to unstable.

htslib-1.20.patch: new: anticipate test failure.

Upcoming upload of htslib 1.20 comes with improvements causing a test
failure in pysam.  This change anticipates the correction without
introduction of regressions with existing releases of htslib.

Thanks: John Marshall

ready to upload to unstable.

Declare fast forward from 0.22.0+ds-1

[dgit --quilt=gbp --overwrite]

Attempt skipping failing test on 32-bit

Forwarded: not-needed
Last-Update: 2021-10-15

Last-Update: 2021-10-15
Gbp-Pq: Name skip-test-on-32-bit.patch

Do not clean *.bam files

Last-Update: 2020-01-23 14:31:06 +0100
Forwarded: not-needed

Gbp-Pq: Name clean_less

Skip tests trying to access remote site

Last-Update: Tue, 11 Sep 2018 14:12:55 +0200
Forwarded: not-needed

Gbp-Pq: Name skip_test_remote.patch

skip-test-on-32-bit.patch: refresh.

skip_test_remote.patch: unfuzz.

d/control: remove dh-exec: it is not in use anymore.

d/python-pysam.links: delete: now irrelevant.

This file set symbolic links up to help with Python 2.7, which is
obsolete and should not be used anymore, so these links are not useful
anymore.

d/control: declare compliance to standards version 4.7.0.

d/copyright: update copyright year.

Update upstream source from tag 'upstream/0.22.1+ds'

Update to upstream version '0.22.1+ds'
with Debian dir 2ee2db91e5d45c01ef09c42c6e401fa04adb59ca

New upstream version 0.22.1+ds

Create new changelog entry

Upload to unstable

Record python-pysam (0.22.0+ds-1) in archive suite sid

Attempt skipping failing test on 32-bit

Forwarded: not-needed
Last-Update: 2021-10-15

Last-Update: 2021-10-15
Gbp-Pq: Name skip-test-on-32-bit.patch

Do not clean *.bam files

Last-Update: 2020-01-23 14:31:06 +0100
Forwarded: not-needed

Gbp-Pq: Name clean_less

Skip tests trying to access remote site

Last-Update: Tue, 11 Sep 2018 14:12:55 +0200
Forwarded: not-needed

Gbp-Pq: Name skip_test_remote.patch

python-pysam (0.22.0+ds-1) unstable; urgency=medium

  * New upstream version
Closes: #1055505
  * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
  * Fix clean target
Closes: #1047165
[dgit import unpatched python-pysam 0.22.0+ds-1]

Import python-pysam_0.22.0+ds.orig.tar.xz

[dgit import orig python-pysam_0.22.0+ds.orig.tar.xz]

Import python-pysam_0.22.0+ds-1.debian.tar.xz

[dgit import tarball python-pysam 0.22.0+ds-1 python-pysam_0.22.0+ds-1.debian.tar.xz]

Fix clean target

Close bug

Drop patch accepted upstream

routine-update: Build-Depends: s/dh-python/dh-sequence-python3/

Update upstream source from tag 'upstream/0.22.0+ds'

Update to upstream version '0.22.0+ds'
with Debian dir 36d5c28baf2be2d1426cabd3e9cd67d92768a431

New upstream version 0.22.0+ds

routine-update: New upstream version

ready to upload to unstable.

Declare fast forward from 0.20.0+ds-3

[dgit --quilt=gbp --overwrite]

fix typos caught by lintian.

Forwarded: https://github.com/pysam-developers/pysam/pull/1198
Last-Update: 2023-06-23

Last-Update: 2023-06-23
Gbp-Pq: Name typos.patch

Attempt skipping failing test on 32-bit

Forwarded: not-needed
Last-Update: 2021-10-15

Last-Update: 2021-10-15
Gbp-Pq: Name skip-test-on-32-bit.patch

Do not clean *.bam files

Last-Update: 2020-01-23 14:31:06 +0100
Forwarded: not-needed

Gbp-Pq: Name clean_less

Skip tests trying to access remote site

Last-Update: Tue, 11 Sep 2018 14:12:55 +0200
Forwarded: not-needed

Gbp-Pq: Name skip_test_remote.patch

typos.patch: add; fix typos caught by lintian.

d/rules: delete extra license files.

d/copyright: bump copyright year.

remove todo item.

d/changelog: fix version in TODO item.

update changelog (with TODO item)

clean_less patch: forwarding not-needed

skip-test-on-32-bit.patch: provide dep3 header

skip_test_remote.patch: forwarding not-needed

python3.11.patch removed

The patch is applied upstream.

disable-tests-python3.11.patch removed

The patch has been applied upstream.

Update upstream source from tag 'upstream/0.21.0+ds'

Update to upstream version '0.21.0+ds'
with Debian dir 326ee67c670e3e34d69697644bdaf07727690840

New upstream version 0.21.0+ds

routine-update: New upstream version

Upload to unstable

Record python-pysam (0.20.0+ds-3) in archive suite sid

Add patch to return proper sysconf so for current python

Last-Update: 2022-12-30

Gbp-Pq: Name python3.11.patch

skip tests bound to fail past python3.11.

Bug: https://github.com/pysam-developers/pysam/issues/1151
Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1024425
Last-Update: 2022-12-27

Thanks John Marshall and Graham Inggs for the independent suggestion.
Last-Update: 2022-12-27
Gbp-Pq: Name disable-tests-python3.11.patch

skip-test-on-32-bit

Gbp-Pq: Name skip-test-on-32-bit.patch

Do not clean *.bam files

Last-Update: 2020-01-23 14:31:06 +0100

Gbp-Pq: Name clean_less

Skip tests trying to access remote site

Last-Update: Tue, 11 Sep 2018 14:12:55 +0200

Gbp-Pq: Name skip_test_remote.patch

python-pysam (0.20.0+ds-3) unstable; urgency=medium

  * Team Upload.
  * Add patch to fix proper "SO" extension.

[dgit import unpatched python-pysam 0.20.0+ds-3]

Import python-pysam_0.20.0+ds-3.debian.tar.xz

[dgit import tarball python-pysam 0.20.0+ds-3 python-pysam_0.20.0+ds-3.debian.tar.xz]

Add patch to fix proper so ext

routine-update: Ready to upload to unstable

Make fast forward from 0.20.0+ds-1

[dgit --quilt=gbp]

skip tests bound to fail past python3.11.

Bug: https://github.com/pysam-developers/pysam/issues/1151
Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1024425
Last-Update: 2022-12-27

Thanks John Marshall and Graham Inggs for the independent suggestion.
Last-Update: 2022-12-27
Gbp-Pq: Name disable-tests-python3.11.patch

skip-test-on-32-bit

Gbp-Pq: Name skip-test-on-32-bit.patch

Do not clean *.bam files

Last-Update: 2020-01-23 14:31:06 +0100

Gbp-Pq: Name clean_less

Skip tests trying to access remote site

Last-Update: Tue, 11 Sep 2018 14:12:55 +0200

Gbp-Pq: Name skip_test_remote.patch

routine-update: Standards-Version: 4.6.2

update changelog

d/control: restore autodep8-python autopkgtest.

d/control: restore dependency on python3-all-dev.

disable-tests-python3.11.patch: add; work around test failure.

Thanks: John Marshall and Graham Inggs
Closes: #1024425

ready to upload to unstable.

Import python-pysam_0.20.0+ds.orig.tar.xz

[dgit import orig python-pysam_0.20.0+ds.orig.tar.xz]

Make fast forward from 0.19.1+ds-1

[dgit --quilt=gbp]

skip-test-on-32-bit

Gbp-Pq: Name skip-test-on-32-bit.patch

Do not clean *.bam files

Last-Update: 2020-01-23 14:31:06 +0100

Gbp-Pq: Name clean_less

Skip tests trying to access remote site

Last-Update: Tue, 11 Sep 2018 14:12:55 +0200

Gbp-Pq: Name skip_test_remote.patch

d/control: disable autopkgtest-pkg-python.

This only disables the superficial test which raises the missing
python3.11 support.  Classical autopkgtest is still there.

unrelease: autopkgtest needs adjustment.

ready to upload to unstable.

d/control: make build only depend on python3-dev.

Currently python3.11 support is missing, this is a temporary measure
to make sure the package can be shipped for bookworm.

test-truncated-bam.patch: delete; applied upstream.

skip_test_remote.patch: refresh.

Update lintian override info format in d/python-pysam.lintian-overrides on line 4.

Changes-By: lintian-brush
Fixes: lintian: mismatched-override
See-also: https://lintian.debian.org/tags/mismatched-override.html

Update upstream source from tag 'upstream/0.20.0+ds'

Update to upstream version '0.20.0+ds'
with Debian dir 2c2bff2e77fc8502275a657cbd46232dcf7c1767

New upstream version 0.20.0+ds

routine-update: New upstream version

ready to upload to unstable.

Declare fast forward from 0.17.0+ds-2

[dgit --quilt=gbp --overwrite]

Truncate ex2.bam irrespective of its size

Bug: https://github.com/pysam-developers/pysam/issues/1128
Applied-Upstream: 56b1624c21b02762fdcea3aa5f657a4152ca178e
Reviewed-by: Étienne Mollier <emollier@debian.org>
Last-Update: 2022-10-02

The Makefile also builds ex2.bam from ex2.sam via `samtools view`.
Samtools as traditionally built using zlib typically generates a
124703-byte file, whereas when built using libdeflate it typically
generates a 122804-byte file -- but `head -c 124000` leaves that unchanged
and the test cases fail because ex2_truncated.bam is unexpectedly valid.

Rewrite the truncation rule to remove the final 512 bytes, irrespective
of ex2.bam's length. (No practical compression will reduce it to less
than 512 bytes in total, so this is safe.) Fixes #1128.
Last-Update: 2022-10-02
Gbp-Pq: Name test-truncated-bam.patch

skip-test-on-32-bit

Gbp-Pq: Name skip-test-on-32-bit.patch

Do not clean *.bam files

Last-Update: 2020-01-23 14:31:06 +0100

Gbp-Pq: Name clean_less

Skip tests trying to access remote site

Last-Update: Tue, 11 Sep 2018 14:12:55 +0200

Gbp-Pq: Name skip_test_remote.patch

d/*.lintian-overrides: remove unused overrides.