Merge python-pysam (0.22.1+ds-2+rpi1) import into refs/heads/workingbranch

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

python-pysam (0.22.1+ds-2+rpi1) trixie-staging; urgency=medium

  [changes brought forward from 0.20.0+ds-3+rpi1 by Peter Michael Green <plugwash@raspbian.org> at Sun, 29 Jan 2023 22:32:22 +0000]
  * Disable testsuite.

[dgit import unpatched python-pysam 0.22.1+ds-2+rpi1]

Import python-pysam_0.22.1+ds-2+rpi1.debian.tar.xz

[dgit import tarball python-pysam 0.22.1+ds-2+rpi1 python-pysam_0.22.1+ds-2+rpi1.debian.tar.xz]

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.

Import python-pysam_0.22.1+ds.orig.tar.xz

[dgit import orig python-pysam_0.22.1+ds.orig.tar.xz]

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