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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Uploaders: Charles Plessy <[email protected]>, - Andreas Tille <[email protected]> + Andreas Tille <[email protected]>, + Étienne Mollier <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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