[med-svn] [Git][med-team/python-pysam][master] 5 commits: test-truncated-bam.patch: added; fix test truncated BAM failure.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Oct 2 10:47:26 BST 2022
Étienne Mollier pushed to branch master at Debian Med / python-pysam
Commits:
5f4a833d by Étienne Mollier at 2022-10-02T11:24:57+02:00
test-truncated-bam.patch: added; fix test truncated BAM failure.
Thanks: John Marshall
- - - - -
600880b3 by Étienne Mollier at 2022-10-02T11:31:33+02:00
d/*.lintian-overrides: refresh mismatches.
- - - - -
8d48df2d by Étienne Mollier at 2022-10-02T11:40:08+02:00
d/control: add myself to uploaders.
- - - - -
83ab688f by Étienne Mollier at 2022-10-02T11:41:00+02:00
d/*.lintian-overrides: remove unused overrides.
- - - - -
27dffc0a by Étienne Mollier at 2022-10-02T11:42:18+02:00
ready to upload to unstable.
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/test-truncated-bam.patch
- debian/python-pysam-tests.lintian-overrides
- debian/python3-pysam.lintian-overrides
Changes:
=====================================
debian/changelog
=====================================
@@ -1,10 +1,18 @@
-python-pysam (0.19.1+ds-1) UNRELEASED; urgency=medium
+python-pysam (0.19.1+ds-1) unstable; urgency=medium
+ [ Andreas Tille ]
* New upstream version
* Standards-Version: 4.6.1 (routine-update)
* Remove unused license definitions for LGPL-2.1+, BSD-3-clause.
- -- Andreas Tille <tille at debian.org> Fri, 30 Sep 2022 12:00:06 +0200
+ [ Étienne Mollier ]
+ * test-truncated-bam.patch: added; fix test truncated BAM failure.
+ Thanks to John Marshall
+ * d/*.lintian-overrides: refresh mismatches.
+ * d/control: add myself to uploaders.
+ * d/*.lintian-overrides: remove unused overrides.
+
+ -- Étienne Mollier <emollier at debian.org> Sun, 02 Oct 2022 11:41:36 +0200
python-pysam (0.18.0+ds-1~exp2) experimental; urgency=medium
=====================================
debian/control
=====================================
@@ -1,7 +1,8 @@
Source: python-pysam
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy at debian.org>,
- Andreas Tille <tille at debian.org>
+ Andreas Tille <tille at debian.org>,
+ Étienne Mollier <emollier at debian.org>
Section: python
Testsuite: autopkgtest-pkg-python
Priority: optional
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
skip_test_remote.patch
clean_less
skip-test-on-32-bit.patch
+test-truncated-bam.patch
=====================================
debian/patches/test-truncated-bam.patch
=====================================
@@ -0,0 +1,28 @@
+Description: Truncate ex2.bam irrespective of its size
+ 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.
+Author: John Marshall
+Bug: https://github.com/pysam-developers/pysam/issues/1128
+Applied-Upstream: 56b1624c21b02762fdcea3aa5f657a4152ca178e
+Reviewed-by: Étienne Mollier <emollier at debian.org>
+Last-Update: 2022-10-02
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-pysam.orig/tests/pysam_data/Makefile
++++ python-pysam/tests/pysam_data/Makefile
+@@ -70,7 +70,7 @@
+ samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz
+
+ ex2_truncated.bam: ex2.bam
+- head -c 124000 ex2.bam > ex2_truncated.bam
++ dd if=ex2.bam of=ex2_truncated.bam bs=$$((`wc -c < ex2.bam`-512)) count=1
+
+ # Append a corrupt read with block_size < sizeof(bam_core_t fields)
+ ex2_corrupt.bam: ex2.bam
=====================================
debian/python-pysam-tests.lintian-overrides
=====================================
@@ -1,5 +1,3 @@
# These files are intentionally empty to be used for testing
-zero-byte-file-in-doc-directory usr/share/doc/python-pysam/tests/cbcf_data/example_empty.vcf
-zero-byte-file-in-doc-directory usr/share/doc/python-pysam/tests/tabix_data/empty.bed.gz
-# The duplicate is used for testing and needs to be there
-compressed-duplicate usr/share/doc/python-pysam/tests/tabix_data/example.bed.gz
+zero-byte-file-in-doc-directory [usr/share/doc/python-pysam/tests/cbcf_data/example_empty.vcf]
+zero-byte-file-in-doc-directory [usr/share/doc/python-pysam/tests/tabix_data/empty.bed.gz]
=====================================
debian/python3-pysam.lintian-overrides
=====================================
@@ -1,4 +1,4 @@
# These are apparently false-positives
# Inspection of the build logs shows that these are indeed compiled with
# -D_FORTIFY_SOURCE=2
-hardening-no-fortify-functions usr/lib/python3/dist-packages/pysam/lib*.so
+hardening-no-fortify-functions [usr/lib/python3/dist-packages/pysam/lib*.so]
View it on GitLab: https://salsa.debian.org/med-team/python-pysam/-/compare/f28c92849632edf1bf39eeb528abdcc99c385ee4...27dffc0abf8f3e34bd463d6ddc75644717168f0e
--
View it on GitLab: https://salsa.debian.org/med-team/python-pysam/-/compare/f28c92849632edf1bf39eeb528abdcc99c385ee4...27dffc0abf8f3e34bd463d6ddc75644717168f0e
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