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  • med-team/obitools
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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 <emollier@debian.org> Sat, 20 Apr 2024 10:41:15 +0200
obitools (1.2.13+dfsg-7) unstable; urgency=medium
* Drop cython3 dependency from binary package
......
......@@ -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
......
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 <emollier@debian.org>
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
......@@ -4,3 +4,4 @@ fix_path_interpreter
port_python3.patch
deocde-bytes-to-str.patch
no_cython_in_binary_package.patch
qsort.patch