Accepting request 1086716 from science

OBS-URL: https://build.opensuse.org/request/show/1086716
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/htscodecs?expand=0&rev=3

fix_ix86_build.patch

@@ -1,99 +0,0 @@
-From 843d4f63b1c64905881b4648916a4d027baa1a1c Mon Sep 17 00:00:00 2001
-From: James Bonfield <jkb@sanger.ac.uk>
-Date: Wed, 17 Aug 2022 15:27:04 +0100
-Subject: [PATCH] Improvements for intel -m32 builds.
-
-On this platform _mm256_extract_epi64 isn't defined, but the rest of
-AVX2 is.  It needs to fail auto-detection.
-
-Also we get unaligned accesses in the SSE4 code with tbuf due to
-differing data alignment caused by 32-bit pointers instead of 64-bit.
-This exposes an underlying problem of using aligned SIMD writes on
-tbuf without explicitly asking for alignment. (The new code is also
-sometimes a little faster.)
-
-See also samtools/htslib#1500
----
- configure.ac                          | 3 ++-
- htscodecs/rANS_static32x16pr_avx2.c   | 2 +-
- htscodecs/rANS_static32x16pr_avx512.c | 2 +-
- htscodecs/rANS_static32x16pr_sse4.c   | 2 +-
- m4/ax_check_compile_flag.m4           | 6 +++++-
- 5 files changed, 10 insertions(+), 5 deletions(-)
-
-diff --git a/configure.ac b/configure.ac
-index 4c8ad54..eb2f44e 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -165,7 +165,8 @@ AX_CHECK_COMPILE_FLAG([-mavx2], [
- 	]],[[
- 	  __m256i a = _mm256_set_epi32(1, 2, 3, 4, 5, 6, 7, 8);
- 	  __m256i b = _mm256_add_epi32(a, a);
--	  return *((char *) &b);
-+	  long long c = _mm256_extract_epi64(b, 0);
-+	  return (int) c;
- 	]])
- ])
- AM_CONDITIONAL([RANS_32x16_AVX2],[test "x$MAVX2" != "x"])
-diff --git a/htscodecs/rANS_static32x16pr_avx2.c b/htscodecs/rANS_static32x16pr_avx2.c
-index 2dd14f1..c36f23c 100644
---- a/htscodecs/rANS_static32x16pr_avx2.c
-+++ b/htscodecs/rANS_static32x16pr_avx2.c
-@@ -1123,7 +1123,7 @@ unsigned char *rans_uncompress_O1_32x16_avx2(unsigned char *in,
-     union {
-         unsigned char tbuf[32][32];
-         uint64_t tbuf64[32][4];
--    } u;
-+    } u  __attribute__((aligned(32)));
-     unsigned int tidx = 0;
- 
-     if (0) {
-diff --git a/htscodecs/rANS_static32x16pr_avx512.c b/htscodecs/rANS_static32x16pr_avx512.c
-index 0d1456f..e9cce46 100644
---- a/htscodecs/rANS_static32x16pr_avx512.c
-+++ b/htscodecs/rANS_static32x16pr_avx512.c
-@@ -735,7 +735,7 @@ unsigned char *rans_uncompress_O1_32x16_avx512(unsigned char *in,
-     union {
-         unsigned char tbuf[32][32];
-         uint64_t tbuf64[32][4];
--    } u;
-+    } u __attribute__((aligned(32)));
- #else
-     uint32_t tbuf[32][32];
- #endif
-diff --git a/htscodecs/rANS_static32x16pr_sse4.c b/htscodecs/rANS_static32x16pr_sse4.c
-index fe0345f..88bcbe0 100644
---- a/htscodecs/rANS_static32x16pr_sse4.c
-+++ b/htscodecs/rANS_static32x16pr_sse4.c
-@@ -1423,7 +1423,7 @@ unsigned char *rans_uncompress_O1_32x16_sse4(unsigned char *in,
-         uint16_t *sp = (uint16_t *)ptr;
-         const uint32_t mask = ((1u << TF_SHIFT_O1_FAST)-1);
-         __m128i maskv  = _mm_set1_epi32(mask); // set mask in all lanes
--        uint8_t tbuf[32][32];
-+        uint8_t tbuf[32][32] __attribute__((aligned(32)));
-         int tidx = 0;
-         LOAD128(Rv, R);
-         LOAD128(Lv, l);
-diff --git a/m4/ax_check_compile_flag.m4 b/m4/ax_check_compile_flag.m4
-index bd753b3..c2bd2c6 100644
---- a/m4/ax_check_compile_flag.m4
-+++ b/m4/ax_check_compile_flag.m4
-@@ -36,13 +36,17 @@
- 
- #serial 6
- 
-+# LOCAL modification; change AC_COMPILE_IFELSE to AC_LINK_IFELSE so
-+# _mm256_extract_epi64 tests on a x86_64 running under -m32 still
-+# fails. (Otherwise it compiles, but fails to link.)
-+
- AC_DEFUN([AX_CHECK_COMPILE_FLAG],
- [AC_PREREQ(2.64)dnl for _AC_LANG_PREFIX and AS_VAR_IF
- AS_VAR_PUSHDEF([CACHEVAR],[ax_cv_check_[]_AC_LANG_ABBREV[]flags_$4_$1])dnl
- AC_CACHE_CHECK([whether _AC_LANG compiler accepts $1], CACHEVAR, [
-   ax_check_save_flags=$[]_AC_LANG_PREFIX[]FLAGS
-   _AC_LANG_PREFIX[]FLAGS="$[]_AC_LANG_PREFIX[]FLAGS $4 $1"
--  AC_COMPILE_IFELSE([m4_default([$5],[AC_LANG_PROGRAM()])],
-+  AC_LINK_IFELSE([m4_default([$5],[AC_LANG_PROGRAM()])],
-     [AS_VAR_SET(CACHEVAR,[yes])],
-     [AS_VAR_SET(CACHEVAR,[no])])
-   _AC_LANG_PREFIX[]FLAGS=$ax_check_save_flags])

htscodecs-1.3.0.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:696c0affbfa7e59276e0dfc71dcba2f04b0a6db12998f30f1baf2fc21e9113f4
-size 3368716

htscodecs-1.5.0.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:34def7341d01a374583d61c9012a80f6b40af078b11bfcaacba1a2412e34dab3
+size 3498542

htscodecs.changes

@@ -1,3 +1,23 @@
+-------------------------------------------------------------------
+Thu May  4 14:47:16 UTC 2023 - Andrea Manzini <andrea.manzini@suse.com>
+
+- Update to 1.5.0:
+  * Significant speed ups to the fqzcomp codec via code restructuring
+    and use of memory prefetch instructions. Encode is 30-40% faster
+    and decode 5-8% faster.
+  * Remove unused ax_with_libdeflate.m4 file from build system
+
+- removed patch fix_ix86_build.patch already merged in upstream
+
+- Update to 1.4.0:
+  * This is almost entirely minor bug fixing with a few small updates.
+  * Optimise compression / speed of the name tokeniser
+  * Improvements for Intel -m32 builds, including better AVX2 validation
+  * Detect Neon capability at runtime via operating system APIs.
+  * Update hts_pack to operate in line with CRAMcodecs spec, where the number of symbols > 16.
+  * Fixed too-stringent buffer overflow checking in O1 rans decoder.
+
+
 -------------------------------------------------------------------
 Thu Sep  8 21:52:47 UTC 2022 - Stefan Brüns <stefan.bruens@rwth-aachen.de>
 

htscodecs.spec

@@ -1,7 +1,7 @@
 #
 # spec file for package htscodecs
 #
-# Copyright (c) 2022 SUSE LLC
+# Copyright (c) 2023 SUSE LLC
 #
 # All modifications and additions to the file contributed by third parties
 # remain the property of their copyright owners, unless otherwise agreed
@@ -18,7 +18,7 @@
 
 %define   sonum 2
 Name:           htscodecs
-Version:        1.3.0
+Version:        1.5.0
 Release:        0
 Summary:        C library for custom compression for CRAM and other formats
 License:        MIT
@@ -26,8 +26,6 @@ Group:          Productivity/Scientific/Other
 URL:            https://github.com/samtools/htscodecs
 Source0:        https://github.com/samtools/htscodecs/releases/download/v%{version}/htscodecs-%{version}.tar.gz
 Source100:      baselibs.conf
-# PATCH-FIX-UPSTREAM
-Patch0:         https://github.com/samtools/htscodecs/commit/843d4f63b1c64905881b4648916a4d027baa1a1c.patch#/fix_ix86_build.patch
 BuildRequires:  autoconf
 BuildRequires:  gcc-c++
 BuildRequires:  pkgconfig
@@ -64,8 +62,6 @@ Header files and libraries of the samtools project for compiling against %{name}
 %autosetup -p1
 
 %build
-# Rebuild configure script after Patch0
-autoconf
 %configure --disable-static
 %make_build