Merge python-pysam (0.22.0+ds-1) import into refs/heads/workingbranch

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]

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

ready to upload to unstable.

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

routine-update: New upstream version

New upstream version 0.21.0+ds

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.

d/control: add myself to uploaders.

d/*.lintian-overrides: refresh mismatches.

test-truncated-bam.patch: added; fix test truncated BAM failure.

Thanks: John Marshall

Remove unused license definitions for LGPL-2.1+, BSD-3-clause.

Changes-By: lintian-brush
Fixes: lintian: unused-license-paragraph-in-dep5-copyright
See-also: https://lintian.debian.org/tags/unused-license-paragraph-in-dep5-copyright.html

routine-update: Standards-Version: 4.6.1

Update upstream source from tag 'upstream/0.19.1+ds'

Update to upstream version '0.19.1+ds'
with Debian dir 8d6067cf8e6433e7474d1bfcaaa7dc7205ee6434

New upstream version 0.19.1+ds

routine-update: New upstream version

Upload to experimental

Bump Build-Depends: libhts-dev (>= 1.14~)

Remove superflous file patterns from debian/copyright

Upload to experimental

Update upstream source from tag 'upstream/0.18.0+ds'

Update to upstream version '0.18.0+ds'
with Debian dir fbe513c606d10f93e294607f45f5cce098219fe3

New upstream version 0.18.0+ds

Remove also win32 dir from upstream code (and when beeing at it also .github and .gitignore)

Drop outdated and unused tests

Remove constraints unnecessary since buster

* Build-Depends: Drop versioned constraint on bcftools, libhts-dev and samtools.

Changes-By: deb-scrub-obsolete

Avoid explicitly specifying -Wl,--as-needed linker flag.

Changes-By: lintian-brush
Fixes: lintian: debian-rules-uses-as-needed-linker-flag
See-also: https://lintian.debian.org/tags/debian-rules-uses-as-needed-linker-flag.html

Update renamed lintian tag names in lintian overrides.

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

routine-update: No tab in license text

Update upstream source from tag 'upstream/0.18.0+ds'

Update to upstream version '0.18.0+ds'
with Debian dir 56361846805f33ba070134821867efdb2fd1768a

New upstream version 0.18.0+ds

routine-update: New upstream version

Upload to unstable

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 (0.17.0+ds-2) unstable; urgency=medium

  * Team Upload.
  * Move from experimental to unstable
  * Skip failing test on 32-bit

[dgit import unpatched python-pysam 0.17.0+ds-2]

Import python-pysam_0.17.0+ds-2.debian.tar.xz

[dgit import tarball python-pysam 0.17.0+ds-2 python-pysam_0.17.0+ds-2.debian.tar.xz]