[med-svn] [Git][med-team/mash][master] 8 commits: Remove code copy of MurmurHash and use libmurmurhash-dev instead
Andreas Tille
gitlab at salsa.debian.org
Tue Feb 5 15:56:17 GMT 2019
Andreas Tille pushed to branch master at Debian Med / mash
Commits:
d0bb204e by Andreas Tille at 2019-02-05T14:59:17Z
Remove code copy of MurmurHash and use libmurmurhash-dev instead
- - - - -
b25647e4 by Andreas Tille at 2019-02-05T15:29:12Z
use debian packaged libmurmurhash
- - - - -
8b1fc519 by Andreas Tille at 2019-02-05T15:30:00Z
Fix exclusion pattern
- - - - -
4308967e by Andreas Tille at 2019-02-05T15:32:29Z
New upstream version 2.1+dfsg
- - - - -
ff922e93 by Andreas Tille at 2019-02-05T15:33:09Z
Update upstream source from tag 'upstream/2.1+dfsg'
Update to upstream version '2.1+dfsg'
with Debian dir 05de30ce17d2202c8dd7989481349fe144ff539b
- - - - -
aadf9780 by Andreas Tille at 2019-02-05T15:34:11Z
Spelling
- - - - -
2071a2e1 by Andreas Tille at 2019-02-05T15:53:55Z
Package builds now with libmurmurhash-dev
- - - - -
a26e7942 by Andreas Tille at 2019-02-05T15:55:52Z
Close bugs
- - - - -
8 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/series
- + debian/patches/use_debian_packaged_libmurmurhash.patch
- debian/watch
- − src/mash/MurmurHash3.cpp
- − src/mash/MurmurHash3.h
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+mash (2.1+dfsg-1) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Remove code copy of MurmurHash and use libmurmurhash-dev instead
+ Closes: #919778, #918566
+
+ -- Andreas Tille <tille at debian.org> Tue, 05 Feb 2019 15:58:23 +0100
+
mash (2.1-2) unstable; urgency=medium
* Adjust CXXFLAGS due to new dependency requirements.
=====================================
debian/control
=====================================
@@ -10,7 +10,8 @@ Build-Depends: debhelper (>= 11),
zlib1g-dev,
python3-sphinx,
libjs-mathjax,
- asciidoctor
+ asciidoctor,
+ libmurmurhash-dev
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/mash
Vcs-Git: https://salsa.debian.org/med-team/mash.git
=====================================
debian/copyright
=====================================
@@ -2,6 +2,7 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: Mash
Upstream-Contact: Adam Phillippy <adam.phillippy at nih.gov>
Source: https://github.com/marbl/Mash
+Files-Excluded: */MurmurHash3*
Files: *
Copyright: © 2015 Battelle National Biodefense Institute (BNBI)
@@ -72,12 +73,6 @@ License: MIT
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
-Files: src/mash/MurmurHash3.*
-Copyright: Austin Appleby
-License: public-domain
- The original C++ code was placed in the public domain by its author,
- Austin Appleby.
-
Files: src/mash/bloom_filter.hpp
Copyright: (c) 2000 Arash Partow
License: CPL
=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ drop_memcpy_wrapper.patch
link_dynamically_against_capnp.patch
parallel.patch
capnp0_7.patch
+use_debian_packaged_libmurmurhash.patch
=====================================
debian/patches/use_debian_packaged_libmurmurhash.patch
=====================================
@@ -0,0 +1,45 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 05 Feb 2019 15:58:23 +0100
+Description: use debian packaged libmurmurhash
+
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -24,7 +24,6 @@ SOURCES=\
+ src/mash/HashPriorityQueue.cpp \
+ src/mash/HashSet.cpp \
+ src/mash/MinHashHeap.cpp \
+- src/mash/MurmurHash3.cpp \
+ src/mash/mash.cpp \
+ src/mash/Sketch.cpp \
+ src/mash/sketchParameterSetup.cpp \
+@@ -34,7 +33,7 @@ OBJECTS=$(SOURCES:.cpp=.o) src/mash/capn
+ all : mash libmash.a
+
+ mash : $(OBJECTS)
+- $(CXX) $(CXXFLAGS) $(CPPFLAGS) -o mash $(OBJECTS) -lkj -lcapnp @mathlib@ -lstdc++ -lz -lm -lpthread $(LDFLAGS)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -o mash $(OBJECTS) -lkj -lcapnp @mathlib@ -lstdc++ -lz -lm -lpthread -lmurmurhash $(LDFLAGS)
+
+ libmash.a : $(OBJECTS)
+ ar -cr libmash.a $(OBJECTS)
+--- a/src/mash/Sketch.cpp
++++ b/src/mash/Sketch.cpp
+@@ -12,7 +12,7 @@
+ #include <fcntl.h>
+ #include <map>
+ #include "kseq.h"
+-#include "MurmurHash3.h"
++#include <murmurhash.h>
+ #include <assert.h>
+ #include <queue>
+ #include <deque>
+--- a/src/mash/hash.cpp
++++ b/src/mash/hash.cpp
+@@ -5,7 +5,7 @@
+ // See the LICENSE.txt file included with this software for license information.
+
+ #include "hash.h"
+-#include "MurmurHash3.h"
++#include <murmurhash.h>
+
+ hash_u getHash(const char * seq, int length, uint32_t seed, bool use64)
+ {
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
-version=3
+version=4
-opts="compress=xz" \
-https://github.com/marbl/Mash/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+opts="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \
+ https://github.com/marbl/Mash/releases .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@
=====================================
src/mash/MurmurHash3.cpp deleted
=====================================
@@ -1,335 +0,0 @@
-//-----------------------------------------------------------------------------
-// MurmurHash3 was written by Austin Appleby, and is placed in the public
-// domain. The author hereby disclaims copyright to this source code.
-
-// Note - The x86 and x64 versions do _not_ produce the same results, as the
-// algorithms are optimized for their respective platforms. You can still
-// compile and run any of them on any platform, but your performance with the
-// non-native version will be less than optimal.
-
-#include "MurmurHash3.h"
-
-//-----------------------------------------------------------------------------
-// Platform-specific functions and macros
-
-// Microsoft Visual Studio
-
-#if defined(_MSC_VER)
-
-#define FORCE_INLINE __forceinline
-
-#include <stdlib.h>
-
-#define ROTL32(x,y) _rotl(x,y)
-#define ROTL64(x,y) _rotl64(x,y)
-
-#define BIG_CONSTANT(x) (x)
-
-// Other compilers
-
-#else // defined(_MSC_VER)
-
-#define FORCE_INLINE inline __attribute__((always_inline))
-
-inline uint32_t rotl32 ( uint32_t x, int8_t r )
-{
- return (x << r) | (x >> (32 - r));
-}
-
-inline uint64_t rotl64 ( uint64_t x, int8_t r )
-{
- return (x << r) | (x >> (64 - r));
-}
-
-#define ROTL32(x,y) rotl32(x,y)
-#define ROTL64(x,y) rotl64(x,y)
-
-#define BIG_CONSTANT(x) (x##LLU)
-
-#endif // !defined(_MSC_VER)
-
-//-----------------------------------------------------------------------------
-// Block read - if your platform needs to do endian-swapping or can only
-// handle aligned reads, do the conversion here
-
-FORCE_INLINE uint32_t getblock32 ( const uint32_t * p, int i )
-{
- return p[i];
-}
-
-FORCE_INLINE uint64_t getblock64 ( const uint64_t * p, int i )
-{
- return p[i];
-}
-
-//-----------------------------------------------------------------------------
-// Finalization mix - force all bits of a hash block to avalanche
-
-FORCE_INLINE uint32_t fmix32 ( uint32_t h )
-{
- h ^= h >> 16;
- h *= 0x85ebca6b;
- h ^= h >> 13;
- h *= 0xc2b2ae35;
- h ^= h >> 16;
-
- return h;
-}
-
-//----------
-
-FORCE_INLINE uint64_t fmix64 ( uint64_t k )
-{
- k ^= k >> 33;
- k *= BIG_CONSTANT(0xff51afd7ed558ccd);
- k ^= k >> 33;
- k *= BIG_CONSTANT(0xc4ceb9fe1a85ec53);
- k ^= k >> 33;
-
- return k;
-}
-
-//-----------------------------------------------------------------------------
-
-void MurmurHash3_x86_32 ( const void * key, int len,
- uint32_t seed, void * out )
-{
- const uint8_t * data = (const uint8_t*)key;
- const int nblocks = len / 4;
-
- uint32_t h1 = seed;
-
- const uint32_t c1 = 0xcc9e2d51;
- const uint32_t c2 = 0x1b873593;
-
- //----------
- // body
-
- const uint32_t * blocks = (const uint32_t *)(data + nblocks*4);
-
- for(int i = -nblocks; i; i++)
- {
- uint32_t k1 = getblock32(blocks,i);
-
- k1 *= c1;
- k1 = ROTL32(k1,15);
- k1 *= c2;
-
- h1 ^= k1;
- h1 = ROTL32(h1,13);
- h1 = h1*5+0xe6546b64;
- }
-
- //----------
- // tail
-
- const uint8_t * tail = (const uint8_t*)(data + nblocks*4);
-
- uint32_t k1 = 0;
-
- switch(len & 3)
- {
- case 3: k1 ^= tail[2] << 16;
- case 2: k1 ^= tail[1] << 8;
- case 1: k1 ^= tail[0];
- k1 *= c1; k1 = ROTL32(k1,15); k1 *= c2; h1 ^= k1;
- };
-
- //----------
- // finalization
-
- h1 ^= len;
-
- h1 = fmix32(h1);
-
- *(uint32_t*)out = h1;
-}
-
-//-----------------------------------------------------------------------------
-
-void MurmurHash3_x86_128 ( const void * key, const int len,
- uint32_t seed, void * out )
-{
- const uint8_t * data = (const uint8_t*)key;
- const int nblocks = len / 16;
-
- uint32_t h1 = seed;
- uint32_t h2 = seed;
- uint32_t h3 = seed;
- uint32_t h4 = seed;
-
- const uint32_t c1 = 0x239b961b;
- const uint32_t c2 = 0xab0e9789;
- const uint32_t c3 = 0x38b34ae5;
- const uint32_t c4 = 0xa1e38b93;
-
- //----------
- // body
-
- const uint32_t * blocks = (const uint32_t *)(data + nblocks*16);
-
- for(int i = -nblocks; i; i++)
- {
- uint32_t k1 = getblock32(blocks,i*4+0);
- uint32_t k2 = getblock32(blocks,i*4+1);
- uint32_t k3 = getblock32(blocks,i*4+2);
- uint32_t k4 = getblock32(blocks,i*4+3);
-
- k1 *= c1; k1 = ROTL32(k1,15); k1 *= c2; h1 ^= k1;
-
- h1 = ROTL32(h1,19); h1 += h2; h1 = h1*5+0x561ccd1b;
-
- k2 *= c2; k2 = ROTL32(k2,16); k2 *= c3; h2 ^= k2;
-
- h2 = ROTL32(h2,17); h2 += h3; h2 = h2*5+0x0bcaa747;
-
- k3 *= c3; k3 = ROTL32(k3,17); k3 *= c4; h3 ^= k3;
-
- h3 = ROTL32(h3,15); h3 += h4; h3 = h3*5+0x96cd1c35;
-
- k4 *= c4; k4 = ROTL32(k4,18); k4 *= c1; h4 ^= k4;
-
- h4 = ROTL32(h4,13); h4 += h1; h4 = h4*5+0x32ac3b17;
- }
-
- //----------
- // tail
-
- const uint8_t * tail = (const uint8_t*)(data + nblocks*16);
-
- uint32_t k1 = 0;
- uint32_t k2 = 0;
- uint32_t k3 = 0;
- uint32_t k4 = 0;
-
- switch(len & 15)
- {
- case 15: k4 ^= tail[14] << 16;
- case 14: k4 ^= tail[13] << 8;
- case 13: k4 ^= tail[12] << 0;
- k4 *= c4; k4 = ROTL32(k4,18); k4 *= c1; h4 ^= k4;
-
- case 12: k3 ^= tail[11] << 24;
- case 11: k3 ^= tail[10] << 16;
- case 10: k3 ^= tail[ 9] << 8;
- case 9: k3 ^= tail[ 8] << 0;
- k3 *= c3; k3 = ROTL32(k3,17); k3 *= c4; h3 ^= k3;
-
- case 8: k2 ^= tail[ 7] << 24;
- case 7: k2 ^= tail[ 6] << 16;
- case 6: k2 ^= tail[ 5] << 8;
- case 5: k2 ^= tail[ 4] << 0;
- k2 *= c2; k2 = ROTL32(k2,16); k2 *= c3; h2 ^= k2;
-
- case 4: k1 ^= tail[ 3] << 24;
- case 3: k1 ^= tail[ 2] << 16;
- case 2: k1 ^= tail[ 1] << 8;
- case 1: k1 ^= tail[ 0] << 0;
- k1 *= c1; k1 = ROTL32(k1,15); k1 *= c2; h1 ^= k1;
- };
-
- //----------
- // finalization
-
- h1 ^= len; h2 ^= len; h3 ^= len; h4 ^= len;
-
- h1 += h2; h1 += h3; h1 += h4;
- h2 += h1; h3 += h1; h4 += h1;
-
- h1 = fmix32(h1);
- h2 = fmix32(h2);
- h3 = fmix32(h3);
- h4 = fmix32(h4);
-
- h1 += h2; h1 += h3; h1 += h4;
- h2 += h1; h3 += h1; h4 += h1;
-
- ((uint32_t*)out)[0] = h1;
- ((uint32_t*)out)[1] = h2;
- ((uint32_t*)out)[2] = h3;
- ((uint32_t*)out)[3] = h4;
-}
-
-//-----------------------------------------------------------------------------
-
-void MurmurHash3_x64_128 ( const void * key, const int len,
- const uint32_t seed, void * out )
-{
- const uint8_t * data = (const uint8_t*)key;
- const int nblocks = len / 16;
-
- uint64_t h1 = seed;
- uint64_t h2 = seed;
-
- const uint64_t c1 = BIG_CONSTANT(0x87c37b91114253d5);
- const uint64_t c2 = BIG_CONSTANT(0x4cf5ad432745937f);
-
- //----------
- // body
-
- const uint64_t * blocks = (const uint64_t *)(data);
-
- for(int i = 0; i < nblocks; i++)
- {
- uint64_t k1 = getblock64(blocks,i*2+0);
- uint64_t k2 = getblock64(blocks,i*2+1);
-
- k1 *= c1; k1 = ROTL64(k1,31); k1 *= c2; h1 ^= k1;
-
- h1 = ROTL64(h1,27); h1 += h2; h1 = h1*5+0x52dce729;
-
- k2 *= c2; k2 = ROTL64(k2,33); k2 *= c1; h2 ^= k2;
-
- h2 = ROTL64(h2,31); h2 += h1; h2 = h2*5+0x38495ab5;
- }
-
- //----------
- // tail
-
- const uint8_t * tail = (const uint8_t*)(data + nblocks*16);
-
- uint64_t k1 = 0;
- uint64_t k2 = 0;
-
- switch(len & 15)
- {
- case 15: k2 ^= ((uint64_t)tail[14]) << 48;
- case 14: k2 ^= ((uint64_t)tail[13]) << 40;
- case 13: k2 ^= ((uint64_t)tail[12]) << 32;
- case 12: k2 ^= ((uint64_t)tail[11]) << 24;
- case 11: k2 ^= ((uint64_t)tail[10]) << 16;
- case 10: k2 ^= ((uint64_t)tail[ 9]) << 8;
- case 9: k2 ^= ((uint64_t)tail[ 8]) << 0;
- k2 *= c2; k2 = ROTL64(k2,33); k2 *= c1; h2 ^= k2;
-
- case 8: k1 ^= ((uint64_t)tail[ 7]) << 56;
- case 7: k1 ^= ((uint64_t)tail[ 6]) << 48;
- case 6: k1 ^= ((uint64_t)tail[ 5]) << 40;
- case 5: k1 ^= ((uint64_t)tail[ 4]) << 32;
- case 4: k1 ^= ((uint64_t)tail[ 3]) << 24;
- case 3: k1 ^= ((uint64_t)tail[ 2]) << 16;
- case 2: k1 ^= ((uint64_t)tail[ 1]) << 8;
- case 1: k1 ^= ((uint64_t)tail[ 0]) << 0;
- k1 *= c1; k1 = ROTL64(k1,31); k1 *= c2; h1 ^= k1;
- };
-
- //----------
- // finalization
-
- h1 ^= len; h2 ^= len;
-
- h1 += h2;
- h2 += h1;
-
- h1 = fmix64(h1);
- h2 = fmix64(h2);
-
- h1 += h2;
- h2 += h1;
-
- ((uint64_t*)out)[0] = h1;
- ((uint64_t*)out)[1] = h2;
-}
-
-//-----------------------------------------------------------------------------
-
=====================================
src/mash/MurmurHash3.h deleted
=====================================
@@ -1,37 +0,0 @@
-//-----------------------------------------------------------------------------
-// MurmurHash3 was written by Austin Appleby, and is placed in the public
-// domain. The author hereby disclaims copyright to this source code.
-
-#ifndef _MURMURHASH3_H_
-#define _MURMURHASH3_H_
-
-//-----------------------------------------------------------------------------
-// Platform-specific functions and macros
-
-// Microsoft Visual Studio
-
-#if defined(_MSC_VER) && (_MSC_VER < 1600)
-
-typedef unsigned char uint8_t;
-typedef unsigned int uint32_t;
-typedef unsigned __int64 uint64_t;
-
-// Other compilers
-
-#else // defined(_MSC_VER)
-
-#include <stdint.h>
-
-#endif // !defined(_MSC_VER)
-
-//-----------------------------------------------------------------------------
-
-void MurmurHash3_x86_32 ( const void * key, int len, uint32_t seed, void * out );
-
-void MurmurHash3_x86_128 ( const void * key, int len, uint32_t seed, void * out );
-
-void MurmurHash3_x64_128 ( const void * key, int len, uint32_t seed, void * out );
-
-//-----------------------------------------------------------------------------
-
-#endif // _MURMURHASH3_H_
View it on GitLab: https://salsa.debian.org/med-team/mash/compare/076de3b2231b779b412ddaa1d8e160203a08f5c5...a26e7942ea08229ae68aa7b3786c1f4b9d99c561
--
View it on GitLab: https://salsa.debian.org/med-team/mash/compare/076de3b2231b779b412ddaa1d8e160203a08f5c5...a26e7942ea08229ae68aa7b3786c1f4b9d99c561
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