Étienne Mollier pushed to branch master at Debian Med / python-pysam
Commits: 95a63e2a by Étienne Mollier at 2024-05-29T13:21:22+02:00 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 - - - - - a0548822 by Étienne Mollier at 2024-05-29T13:23:33+02:00 ready to upload to unstable. - - - - - 3 changed files: - debian/changelog - + debian/patches/htslib-1.20.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,13 @@ +python-pysam (0.22.1+ds-2) unstable; urgency=medium + + * 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 to John Marshall + + -- Étienne Mollier <[email protected]> Wed, 29 May 2024 13:23:03 +0200 + python-pysam (0.22.1+ds-1) unstable; urgency=medium * New upstream version 0.22.1+ds ===================================== debian/patches/htslib-1.20.patch ===================================== @@ -0,0 +1,19 @@ +Description: 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 <[email protected]> +Last-Update: 2024-05-29 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- python-pysam.orig/tests/pysam_data/MM-chebi.sam ++++ python-pysam/tests/pysam_data/MM-chebi.sam +@@ -1,2 +1,2 @@ + @CO Separate m, h and N modifications +-* 0 * 0 0 * * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA * Mm:Z:C+m,2,2,1,4,1;C+76792,6,7;N+n,15; Ml:B:C,102,128,153,179,204,161,187,212,169 ++* 0 * 0 0 * * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA * Mm:Z:C+m,2,2,1,4,1;C+76792,6,7;N+n,15; Ml:B:C,102,128,153,179,204,161,187,212 ===================================== debian/patches/series ===================================== @@ -1,3 +1,4 @@ skip_test_remote.patch clean_less skip-test-on-32-bit.patch +htslib-1.20.patch View it on GitLab: https://salsa.debian.org/med-team/python-pysam/-/compare/97456260302d085ea6f5ae54f2b679dc41a657e7...a0548822fe326d405407d653cdf9ff19a362a28f -- This project does not include diff previews in email notifications. View it on GitLab: https://salsa.debian.org/med-team/python-pysam/-/compare/97456260302d085ea6f5ae54f2b679dc41a657e7...a0548822fe326d405407d653cdf9ff19a362a28f You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
