kallisto: Update to 0.51.0

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: kallisto: Update to 0.51.0
From: Jason W. Bacon <bacon%NetBSD.org@localhost>
Date: Tue, 23 Jul 2024 12:27:38 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Tue Jul 23 07:27:25 2024 -0500
Changeset:	854f03980fe472092828f44f61939acfa8f87a85

Modified Files:
	kallisto/Makefile
	kallisto/distinfo
	kallisto/patches/patch-CMakeLists.txt
	kallisto/patches/patch-ext_bifrost_CMakeLists.txt
	kallisto/patches/patch-src_CMakeLists.txt

Log Message:
kallisto: Update to 0.51.0

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=854f03980fe472092828f44f61939acfa8f87a85

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 kallisto/Makefile                                 |  5 +--
 kallisto/distinfo                                 | 12 +++----
 kallisto/patches/patch-CMakeLists.txt             | 26 +++++++++++---
 kallisto/patches/patch-ext_bifrost_CMakeLists.txt | 43 ++++++++++++-----------
 kallisto/patches/patch-src_CMakeLists.txt         | 18 +++++-----
 5 files changed, 63 insertions(+), 41 deletions(-)

diffs:
diff --git a/kallisto/Makefile b/kallisto/Makefile
index 0f9a549fd0..9aa4cbb3b7 100644
--- a/kallisto/Makefile
+++ b/kallisto/Makefile
@@ -1,9 +1,9 @@
 # $NetBSD: Makefile,v 1.1 2018/12/21 19:00:56 bacon Exp $
 
-DISTNAME=	kallisto-0.50.1
+DISTNAME=	kallisto-0.51.0
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=pachterlab/}
-GITHUB_TAG=	v${PKGVERSION_NOREV}
+GITHUB_TAG=	V${PKGVERSION_NOREV}
 
 OWNER=		bacon%NetBSD.org@localhost
 HOMEPAGE=	https://pachterlab.github.io/kallisto/
@@ -19,6 +19,7 @@ SUBST_STAGE.test=	pre-configure
 SUBST_FILES.test=	kallisto-test
 SUBST_SED.test=		-e 's|/usr/local/share/kallisto|${DATADIR}|g'
 
+WRKSRC=			${WRKDIR}/${DISTNAME}
 CMAKE_ARGS+=		-DUSE_HDF5:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
 # Build fails on 8-core Mac M1
 MAKE_JOBS_SAFE=		no
diff --git a/kallisto/distinfo b/kallisto/distinfo
index 953f9584e0..93efce703b 100644
--- a/kallisto/distinfo
+++ b/kallisto/distinfo
@@ -1,15 +1,15 @@
 $NetBSD$
 
-BLAKE2s (kallisto-0.50.1.tar.gz) = 2fcdb884dd3f8c381b16648862551c1632780b5f942c4c1296b7581a48092054
-SHA512 (kallisto-0.50.1.tar.gz) = 767319f1b96d29c10dba9a66410764978eb8dcf36186d247821458e977a76adab7c871675e10e56d7e85ac312cd0c75c7651008f612db998699a95e0c63cb8e9
-Size (kallisto-0.50.1.tar.gz) = 5947303 bytes
-SHA1 (patch-CMakeLists.txt) = 2672475d3fd0f3b837cafc9faa62cdc094f6fd4b
-SHA1 (patch-ext_bifrost_CMakeLists.txt) = ff5cebb2f38c4fa90bd651690ef58e588396c2ac
+BLAKE2s (kallisto-0.51.0.tar.gz) = 759bef4d378b5ca762196ec7c74f80030d5109175a31806112b59e23c92fa747
+SHA512 (kallisto-0.51.0.tar.gz) = 3616d3030e0bc989d3d43786500dddf1bb8243bb51473695b11ace6eb57b15b6c692b0bdc5463a9075573a267fee8b8dea48165d6af8029f603b19ad56aef661
+Size (kallisto-0.51.0.tar.gz) = 5952096 bytes
+SHA1 (patch-CMakeLists.txt) = 76746ef3999fca26d7cfe597172303ce7b023708
+SHA1 (patch-ext_bifrost_CMakeLists.txt) = 7b28282604691dc985c135f7048cc48fec1ae826
 SHA1 (patch-ext_bifrost_src_BitContainer.cpp) = 88a3b8b0d53bc4e96ec02f38f3f6e6bbd1e80dd7
 SHA1 (patch-ext_bifrost_src_ColorSet.cpp) = 55bb84a31ca97d21e6eefd44e2d3d6391f1e9304
 SHA1 (patch-ext_bifrost_src_libpopcnt.h) = 3f31a47f40f341b1f6f72552b06990a81946e425
 SHA1 (patch-ext_bifrost_src_strict__fstream.hpp) = a4eab7784c3502fcc79ba0c87d31ac7275e5043c
 SHA1 (patch-src_Bootstrap.h) = 29a07a6fbaedf4387b70afb3b2caeb1a9b17f8e8
-SHA1 (patch-src_CMakeLists.txt) = 33d0e3cf985d2e400315788d3ee1c74987a6ebee
+SHA1 (patch-src_CMakeLists.txt) = 8a66bdca6a15948d60a16016b4b62f79d03deef3
 SHA1 (patch-src_kseq.h) = 034e65bdcf5d3851b4e3d65afd06843bdff0d8a9
 SHA1 (patch-src_main.cpp) = 65c9af813f558cebd6086a95b56a499aab02e566
diff --git a/kallisto/patches/patch-CMakeLists.txt b/kallisto/patches/patch-CMakeLists.txt
index c17bcf1f7c..ecefca6064 100644
--- a/kallisto/patches/patch-CMakeLists.txt
+++ b/kallisto/patches/patch-CMakeLists.txt
@@ -1,10 +1,28 @@
 $NetBSD$
 
-# Unbundle htslib and zlib, use gmake
+# Use external htslib
 
---- CMakeLists.txt.orig	2023-06-27 10:45:00.000000000 +0000
+--- CMakeLists.txt.orig	2024-07-20 19:07:27.000000000 +0000
 +++ CMakeLists.txt
-@@ -56,42 +56,16 @@ ENDIF(LINK MATCHES static)
+@@ -23,16 +23,12 @@ add_compile_definitions("MAX_KMER_SIZE=$
+ 
+ 
+ option(USE_HDF5 "Compile with HDF5 support" OFF) #OFF by default
+-option(USE_BAM "Compile with HTSLIB support" OFF) # OFF by default
++option(USE_BAM "Compile with HTSLIB support" ON)
+ 
+ if(USE_HDF5)
+     add_compile_definitions("USE_HDF5=ON")
+ endif(USE_HDF5)
+ 
+-if(NOT USE_BAM)
+-    add_compile_definitions("NO_HTSLIB=ON")
+-endif()
+-
+ set(EXT_PROJECTS_DIR ${PROJECT_SOURCE_DIR}/ext)
+ set(CMAKE_CXX_FLAGS_PROFILE "-g")
+ 
+@@ -73,42 +69,16 @@ ENDIF(LINK MATCHES static)
  
  
  include(ExternalProject)
@@ -24,7 +42,7 @@ $NetBSD$
      PREFIX ${PROJECT_SOURCE_DIR}/ext/bifrost
      SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/bifrost
      BUILD_IN_SOURCE 1
-     CONFIGURE_COMMAND mkdir -p build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_CXX_FLAGS=${PROJECT_BIFROST_CMAKE_CXX_FLAGS}
+     CONFIGURE_COMMAND mkdir -p build && cd build && cmake .. -DMAX_KMER_SIZE=${MAX_KMER_SIZE} -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_CXX_FLAGS=${PROJECT_BIFROST_CMAKE_CXX_FLAGS} ${DO_ENABLE_AVX2} ${DO_ENABLE_COMPILATION_ARCH}
 -    BUILD_COMMAND cd build && make
 +    BUILD_COMMAND cd build && gmake
      INSTALL_COMMAND ""
diff --git a/kallisto/patches/patch-ext_bifrost_CMakeLists.txt b/kallisto/patches/patch-ext_bifrost_CMakeLists.txt
index 202be008b4..06cee77105 100644
--- a/kallisto/patches/patch-ext_bifrost_CMakeLists.txt
+++ b/kallisto/patches/patch-ext_bifrost_CMakeLists.txt
@@ -1,12 +1,12 @@
 $NetBSD$
 
-# Portability
+# Respect pkgsrc build flags
 
---- ext/bifrost/CMakeLists.txt.orig	2023-06-27 10:45:00.000000000 +0000
+--- ext/bifrost/CMakeLists.txt.orig	2024-07-23 11:56:13.172038229 +0000
 +++ ext/bifrost/CMakeLists.txt
-@@ -7,18 +7,12 @@ find_package(Threads REQUIRED)
+@@ -6,18 +6,12 @@ find_package(Threads REQUIRED)
+ 
  # To enable a larger default k-mer size, replace MAX_KMER_SIZE with a larger multiple of 32: actual maximum k-mer size will be MAX_KMER_SIZE-1.
- SET(MAX_KMER_SIZE "32" CACHE STRING "MAX_KMER_SIZE")
  SET(MAX_GMER_SIZE "${MAX_KMER_SIZE}" CACHE STRING "MAX_GMER_SIZE")
 -# Enable architecture optimizations
 -SET(COMPILATION_ARCH "native" CACHE STRING "COMPILATION_ARCH")
@@ -24,21 +24,24 @@ $NetBSD$
  #check if we are on arm64 and apple, if so, disable AVX2
  if(APPLE AND CMAKE_SYSTEM_PROCESSOR MATCHES "arm")
  	message("Disabling AVX2 instructions on arm64")
-@@ -30,8 +24,6 @@ if(COMPILATION_ARCH MATCHES "OFF")
- 	message("Disabling native architecture compilation (including AVX2)")
- else(COMPILATION_ARCH MATCHES "OFF")
- 	message("Compilation architecture: ${COMPILATION_ARCH}")
+@@ -25,20 +19,6 @@ if(APPLE AND CMAKE_SYSTEM_PROCESSOR MATC
+ 	set(COMPILATION_ARCH "OFF")
+ endif(APPLE AND CMAKE_SYSTEM_PROCESSOR MATCHES "arm")
+ 
+-if(COMPILATION_ARCH MATCHES "OFF")
+-	message("Disabling native architecture compilation (including AVX2)")
+-else(COMPILATION_ARCH MATCHES "OFF")
+-	message("Compilation architecture: ${COMPILATION_ARCH}")
 -	set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -march=${COMPILATION_ARCH}")
 -	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=${COMPILATION_ARCH}")
- endif(COMPILATION_ARCH MATCHES "OFF")
- 
- if(ENABLE_AVX2 MATCHES "OFF")
-@@ -56,7 +48,7 @@ else(CMAKE_BUILD_TYPE MATCHES Debug)
- 		set(CMAKE_EXE_LINKER_FLAGS "-pg")
- 	else(CMAKE_BUILD_TYPE MATCHES Profile)
- 		message("Build type: Release")
--		add_compile_options(-O3)
-+		add_compile_options(-O2)
- 	endif(CMAKE_BUILD_TYPE MATCHES Profile) 
- endif(CMAKE_BUILD_TYPE MATCHES Debug)
- 
+-endif(COMPILATION_ARCH MATCHES "OFF")
+-
+-if(ENABLE_AVX2 MATCHES "OFF")
+-	message("Disabling AVX2 instructions")
+-	set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -mno-avx2")
+-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mno-avx2")
+-endif(ENABLE_AVX2 MATCHES "OFF")
+-
+ # Manages build types
+ if(NOT CMAKE_BUILD_TYPE)
+   set(CMAKE_BUILD_TYPE "Release")
diff --git a/kallisto/patches/patch-src_CMakeLists.txt b/kallisto/patches/patch-src_CMakeLists.txt
index b4d679dafc..75516d793c 100644
--- a/kallisto/patches/patch-src_CMakeLists.txt
+++ b/kallisto/patches/patch-src_CMakeLists.txt
@@ -1,8 +1,8 @@
 $NetBSD$
 
-# Unbundle htslib
+# Use external htslib
 
---- src/CMakeLists.txt.orig	2023-07-06 14:07:38 UTC
+--- src/CMakeLists.txt.orig	2024-07-23 11:52:01.089699466 +0000
 +++ src/CMakeLists.txt
 @@ -3,10 +3,6 @@ file(GLOB headers *.h *.hpp)
  
@@ -12,15 +12,15 @@ $NetBSD$
 -include_directories(../ext/htslib)
 -endif(USE_BAM)
 -
- add_compile_options(-Wno-subobject-linkage) # Suppress bifrost warning
- 
- add_library(kallisto_core ${sources} ${headers})
-@@ -17,7 +13,7 @@ add_executable(kallisto main.cpp)
+ if(NOT MAX_KMER_SIZE)
+ set(MAX_KMER_SIZE "32")
+ endif()
+@@ -21,7 +17,7 @@ add_executable(kallisto main.cpp)
  find_package( Threads REQUIRED )
  ExternalProject_Get_Property(bifrost install_dir)
  if (USE_BAM)
--target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a ${install_dir}/build/src/libbifrost.a)
-+target_link_libraries(kallisto kallisto_core pthread hts ${install_dir}/build/src/libbifrost.a)
+-target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a ${install_dir}/build/src/libbifrost.a  -DMAX_KMER_SIZE=${MAX_KMER_SIZE})
++target_link_libraries(kallisto kallisto_core pthread hts ${install_dir}/build/src/libbifrost.a  -DMAX_KMER_SIZE=${MAX_KMER_SIZE})
  else()
- target_link_libraries(kallisto kallisto_core pthread ${install_dir}/build/src/libbifrost.a)
+ target_link_libraries(kallisto kallisto_core pthread ${install_dir}/build/src/libbifrost.a -DMAX_KMER_SIZE=${MAX_KMER_SIZE})
  endif(USE_BAM)
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