debian/changelog

 obitools (1.2.11+dfsg-1) unstable; urgency=low
 
-  [ Olivier Sallou ]
   * Initial release (Closes: #783833)
 
- -- Andreas Tille <tille@debian.org>  Wed, 13 Dec 2017 20:10:00 +0100
+ -- Andreas Tille <tille@debian.org>  Mon, 12 Feb 2018 00:31:32 +0100

debian/control

 Source: obitools
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
-Uploaders: Olivier Sallou <osallou@debian.org>
+Uploaders: Olivier Sallou <osallou@debian.org>,
+           Andreas Tille <tille@debian.org>
 Section: python
 Priority: optional
 Build-Depends: debhelper (>= 10),
@@ -10,7 +11,7 @@ Build-Depends: debhelper (>= 10),
                cython,
                ipython,
                python-wheel
-Standards-Version: 4.1.2
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/obitools.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/obitools.git
 Homepage: https://pypi.python.org/pypi/OBITools

debian/copyright

@@ -4,6 +4,8 @@ Source: http://metabarcoding.org//obitools
 Files-Excluded:
     distutils.ext/obidistutils/serenity/pip
     build
+    */*.egg-info
+    */_readindex.ext.1.c
 
 Files: *
 Copyright: 2014 Eric Coissac <eric@coissac.eu>
@@ -43,23 +45,6 @@ License: BSD-4-clause
  OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
  OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-Files: src/obitools/word/_readindex.ext.1.c
-Copyright: 1999 Apple Computer, Inc.
-License: APPLE_LICENSE
- The contents of this file constitute Original Code as defined in and
- are subject to the Apple Public Source License Version 1.1 (the
- "License").  You may not use this file except in compliance with the
- License.  Please obtain a copy of the License at
- http://www.apple.com/publicsource and read it before using this file.
- .
- This Original Code and all software distributed under the License are
- distributed on an "AS IS" basis, WITHOUT WARRANTY OF ANY KIND, EITHER
- EXPRESS OR IMPLIED, AND APPLE HEREBY DISCLAIMS ALL SUCH WARRANTIES,
- INCLUDING WITHOUT LIMITATION, ANY WARRANTIES OF MERCHANTABILITY,
- FITNESS FOR A PARTICULAR PURPOSE OR NON-INFRINGEMENT.  Please see the
- License for the specific language governing rights and limitations
- under the License.
-
 License: CeCILL-2.1
  CeCILL FREE SOFTWARE LICENSE AGREEMENT
  .

src/OBITools.egg-info/PKG-INFO

-Metadata-Version: 1.1
-Name: OBITools
-Version: 1.2.11
-Summary: Scripts and library for sequence analysis
-Home-page: http://metabarcoding.org/obitools
-Author: Eric Coissac
-Author-email: eric@coissac.eu
-License: CeCILL-V2
-Description: UNKNOWN
-Platform: UNKNOWN
-Classifier: Development Status :: 5 - Production/Stable
-Classifier: Environment :: Console
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: Other/Proprietary License
-Classifier: Operating System :: Unix
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 2
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Classifier: Topic :: Utilities

src/OBITools.egg-info/dependency_links.txt

-

src/OBITools.egg-info/not-zip-safe

-

src/OBITools.egg-info/requires.txt

-Cython>=0.24
-Sphinx>=1.2.0
-wheel>=0.24.0
-virtualenv>=1.11.0
-ipython<6.0

src/OBITools.egg-info/top_level.txt

-obitools

src/obitools/word/_readindex.ext.1.c

-/*
- * Copyright (c) 1999 Apple Computer, Inc. All rights reserved.
- *
- * @APPLE_LICENSE_HEADER_START@
- * 
- * The contents of this file constitute Original Code as defined in and
- * are subject to the Apple Public Source License Version 1.1 (the
- * "License").  You may not use this file except in compliance with the
- * License.  Please obtain a copy of the License at
- * http://www.apple.com/publicsource and read it before using this file.
- * 
- * This Original Code and all software distributed under the License are
- * distributed on an "AS IS" basis, WITHOUT WARRANTY OF ANY KIND, EITHER
- * EXPRESS OR IMPLIED, AND APPLE HEREBY DISCLAIMS ALL SUCH WARRANTIES,
- * INCLUDING WITHOUT LIMITATION, ANY WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE OR NON-INFRINGEMENT.  Please see the
- * License for the specific language governing rights and limitations
- * under the License.
- * 
- * @APPLE_LICENSE_HEADER_END@
- */
-/*
- * Copyright (c) 1991, 1993
- *	The Regents of the University of California.  All rights reserved.
- *
- * This code is derived from software contributed to Berkeley by
- * Ronnie Kon at Mindcraft Inc., Kevin Lew and Elmer Yglesias.
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- * 1. Redistributions of source code must retain the above copyright
- *    notice, this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright
- *    notice, this list of conditions and the following disclaimer in the
- *    documentation and/or other materials provided with the distribution.
- * 3. All advertising materials mentioning features or use of this software
- *    must display the following acknowledgement:
- *	This product includes software developed by the University of
- *	California, Berkeley and its contributors.
- * 4. Neither the name of the University nor the names of its contributors
- *    may be used to endorse or promote products derived from this software
- *    without specific prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND
- * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED.  IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE
- * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
- * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
- * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
- * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
- * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
- * SUCH DAMAGE.
- */
-
-
-#include <sys/types.h>
-#include <errno.h>
-#include <stdlib.h>
-#include <stddef.h>
-
-/*
- * Swap two areas of size number of bytes.  Although qsort(3) permits random
- * blocks of memory to be sorted, sorting pointers is almost certainly the
- * common case (and, were it not, could easily be made so).  Regardless, it
- * isn't worth optimizing; the SWAP's get sped up by the cache, and pointer
- * arithmetic gets lost in the time required for comparison function calls.
- */
-#define	SWAP(a, b, count, size, tmp) { \
-	count = size; \
-	do { \
-		tmp = *a; \
-		*a++ = *b; \
-		*b++ = tmp; \
-	} while (--count); \
-}
-
-/* Copy one block of size size to another. */
-#define COPY(a, b, count, size, tmp1, tmp2) { \
-	count = size; \
-	tmp1 = a; \
-	tmp2 = b; \
-	do { \
-		*tmp1++ = *tmp2++; \
-	} while (--count); \
-}
-
-/*
- * Build the list into a heap, where a heap is defined such that for
- * the records K1 ... KN, Kj/2 >= Kj for 1 <= j/2 <= j <= N.
- *
- * There two cases.  If j == nmemb, select largest of Ki and Kj.  If
- * j < nmemb, select largest of Ki, Kj and Kj+1.
- */
-#define CREATE(initval, nmemb, par_i, child_i, par, child, size, count, tmp) { \
-	for (par_i = initval; (child_i = par_i * 2) <= nmemb; \
-	    par_i = child_i) { \
-		child = base + child_i * size; \
-		if (child_i < nmemb && compar(child, child + size) < 0) { \
-			child += size; \
-			++child_i; \
-		} \
-		par = base + par_i * size; \
-		if (compar(child, par) <= 0) \
-			break; \
-		SWAP(par, child, count, size, tmp); \
-	} \
-}
-
-/*
- * Select the top of the heap and 'heapify'.  Since by far the most expensive
- * action is the call to the compar function, a considerable optimization
- * in the average case can be achieved due to the fact that k, the displaced
- * elememt, is ususally quite small, so it would be preferable to first
- * heapify, always maintaining the invariant that the larger child is copied
- * over its parent's record.
- *
- * Then, starting from the *bottom* of the heap, finding k's correct place,
- * again maintianing the invariant.  As a result of the invariant no element
- * is 'lost' when k is assigned its correct place in the heap.
- *
- * The time savings from this optimization are on the order of 15-20% for the
- * average case. See Knuth, Vol. 3, page 158, problem 18.
- *
- * XXX Don't break the #define SELECT line, below.  Reiser cpp gets upset.
- */
-#define SELECT(par_i, child_i, nmemb, par, child, size, k, count, tmp1, tmp2) { \
-	for (par_i = 1; (child_i = par_i * 2) <= nmemb; par_i = child_i) { \
-		child = base + child_i * size; \
-		if (child_i < nmemb && compar(child, child + size) < 0) { \
-			child += size; \
-			++child_i; \
-		} \
-		par = base + par_i * size; \
-		COPY(par, child, count, size, tmp1, tmp2); \
-	} \
-	for (;;) { \
-		child_i = par_i; \
-		par_i = child_i / 2; \
-		child = base + child_i * size; \
-		par = base + par_i * size; \
-		if (child_i == 1 || compar(k, par) < 0) { \
-			COPY(child, k, count, size, tmp1, tmp2); \
-			break; \
-		} \
-		COPY(child, par, count, size, tmp1, tmp2); \
-	} \
-}
-
-/*
- * Heapsort -- Knuth, Vol. 3, page 145.  Runs in O (N lg N), both average
- * and worst.  While heapsort is faster than the worst case of quicksort,
- * the BSD quicksort does median selection so that the chance of finding
- * a data set that will trigger the worst case is nonexistent.  Heapsort's
- * only advantage over quicksort is that it requires little additional memory.
- */
-int
-heapsort(vbase, nmemb, size, compar)
-	void *vbase;
-	size_t nmemb, size;
-	int (*compar) __P((const void *, const void *));
-{
-	register int cnt, i, j, l;
-	register char tmp, *tmp1, *tmp2;
-	char *base, *k, *p, *t;
-
-	if (nmemb <= 1)
-		return (0);
-
-	if (!size) {
-		errno = EINVAL;
-		return (-1);
-	}
-
-	if ((k = malloc(size)) == NULL)
-		return (-1);
-
-	/*
-	 * Items are numbered from 1 to nmemb, so offset from size bytes
-	 * below the starting address.
-	 */
-	base = (char *)vbase - size;
-
-	for (l = nmemb / 2 + 1; --l;)
-		CREATE(l, nmemb, i, j, t, p, size, cnt, tmp);
-
-	/*
-	 * For each element of the heap, save the largest element into its
-	 * final slot, save the displaced element (k), then recreate the
-	 * heap.
-	 */
-	while (nmemb > 1) {
-		COPY(k, base + nmemb * size, cnt, size, tmp1, tmp2);
-		COPY(base + nmemb * size, base + size, cnt, size, tmp1, tmp2);
-		--nmemb;
-		SELECT(i, j, nmemb, t, p, size, k, cnt, tmp1, tmp2);
-	}
-	free(k);
-	return (0);
-}