Étienne Mollier pushed to branch master at Debian Med / obitools
Commits: fb6053e4 by Étienne Mollier at 2024-04-20T10:39:12+02:00 qsort.patch: new: replace heapsort by qsort. Closes: #1066369 - - - - - dfb043ab by Étienne Mollier at 2024-04-20T10:40:53+02:00 d/control: declare compliance to standards version 4.7.0. - - - - - fd4fb6a9 by Étienne Mollier at 2024-04-20T10:44:10+02:00 ready to upload to unstable. - - - - - 4 changed files: - debian/changelog - debian/control - + debian/patches/qsort.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +obitools (1.2.13+dfsg-8) unstable; urgency=medium + + * Team upload. + * qsort.patch: new: replace heapsort by qsort. (Closes: #1066369) + * d/control: declare compliance to standards version 4.7.0. + + -- Étienne Mollier <[email protected]> Sat, 20 Apr 2024 10:41:15 +0200 + obitools (1.2.13+dfsg-7) unstable; urgency=medium * Drop cython3 dependency from binary package ===================================== debian/control ===================================== @@ -12,7 +12,7 @@ Build-Depends: debhelper-compat (= 13), ipython3, python3-wheel, python3-virtualenv -Standards-Version: 4.6.2 +Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/obitools Vcs-Git: https://salsa.debian.org/med-team/obitools.git Homepage: https://pypi.python.org/pypi/OBITools ===================================== debian/patches/qsort.patch ===================================== @@ -0,0 +1,34 @@ +Description: Replace heapsort call by qsort. + heapsort is a Berkeley function not available by default in Debian libc. + This patch implements a change to call qsort instead of heapsort in obitools + where needed. + . + Note that this possibly trades a performance pattern provided by heapsort for + the one of qsort: probably increased stack memory consumption according to the + manual. This also makes the sorting result more reproducible when two entries + sort equal. +Author: Étienne Mollier <[email protected]> +Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1066369 +Forwarded: no +Last-Update: 2024-04-20 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- obitools.orig/src/obitools/word/_readindex.pyx ++++ obitools/src/obitools/word/_readindex.pyx +@@ -56,7 +56,6 @@ + ctypedef void* pconstvoid "const void*" + + cdef extern from "stdlib.h": +- void heapsort(void *base, size_t nel, size_t width, int (*compar)(pconstvoid, pconstvoid)) + void qsort(void *base, size_t nel, size_t width, int (*compar)(pconstvoid, pconstvoid)) + void* bsearch(pconstvoid key, pconstvoid base, size_t nel, size_t width, int (*compar) (pconstvoid, pconstvoid)) + +@@ -505,7 +504,7 @@ + + cmpwordlengthLock.acquire() + self._globalwordlength[0]=lword +- heapsort(self._wordlist,i,sizeof(pobinuc),cmpwords) ++ qsort(self._wordlist,i,sizeof(pobinuc),cmpwords) + cmpwordlengthLock.release() + + self._lindex=6 if lword >=6 else lword ===================================== debian/patches/series ===================================== @@ -4,3 +4,4 @@ fix_path_interpreter port_python3.patch deocde-bytes-to-str.patch no_cython_in_binary_package.patch +qsort.patch View it on GitLab: https://salsa.debian.org/med-team/obitools/-/compare/695747eb6703d11dc62ff0a66bd26baa6abd0e1d...fd4fb6a94c0e9e62a89be1f41fc68c7be7c93d1e -- View it on GitLab: https://salsa.debian.org/med-team/obitools/-/compare/695747eb6703d11dc62ff0a66bd26baa6abd0e1d...fd4fb6a94c0e9e62a89be1f41fc68c7be7c93d1e You're receiving this email because of your account on salsa.debian.org.
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