[med-svn] [Git][med-team/python-pysam][master] 5 commits: test-truncated-bam.patch: added; fix test truncated BAM failure.

[Étienne Mollier (@emollier)]

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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