kallisto: Clean up build options and patches

[Jason W. Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Mon Jul 24 09:03:02 2023 -0500
Changeset:	a59c0f439f4e94a732f68d57d2bd68f6ebd7494a

Modified Files:
	kallisto/Makefile
	kallisto/distinfo
	kallisto/patches/patch-CMakeLists.txt
	kallisto/patches/patch-ext_bifrost_CMakeLists.txt
	kallisto/patches/patch-src_Bootstrap.h
	kallisto/patches/patch-src_CMakeLists.txt
	kallisto/patches/patch-src_kseq.h
Added Files:
	kallisto/patches/patch-ext_bifrost_src_libpopcnt.h

Log Message:
kallisto: Clean up build options and patches

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=a59c0f439f4e94a732f68d57d2bd68f6ebd7494a

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

diffstat:
 kallisto/Makefile                                  |  2 +-
 kallisto/distinfo                                  | 11 ++++---
 kallisto/patches/patch-CMakeLists.txt              |  6 +++-
 kallisto/patches/patch-ext_bifrost_CMakeLists.txt  | 37 ++++++++++++++++++++--
 kallisto/patches/patch-ext_bifrost_src_libpopcnt.h | 22 +++++++++++++
 kallisto/patches/patch-src_Bootstrap.h             |  4 +++
 kallisto/patches/patch-src_CMakeLists.txt          |  4 +++
 kallisto/patches/patch-src_kseq.h                  |  4 +++
 8 files changed, 81 insertions(+), 9 deletions(-)

diffs:
diff --git a/kallisto/Makefile b/kallisto/Makefile
index a509dafb0e..cefd851d5d 100644
--- a/kallisto/Makefile
+++ b/kallisto/Makefile
@@ -19,7 +19,7 @@ SUBST_STAGE.test=	pre-configure
 SUBST_FILES.test=	kallisto-test
 SUBST_SED.test=		-e 's|/usr/local/share/kallisto|${DATADIR}|g'
 
-CMAKE_ARGS+=		-DUSE_HDF5:BOOL=ON
+CMAKE_ARGS+=		-DUSE_HDF5:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
 INSTALLATION_DIRS+=	${DATADIR}
 
 DATADIR=		${PREFIX}/share/kallisto
diff --git a/kallisto/distinfo b/kallisto/distinfo
index 346c872404..11894388f8 100644
--- a/kallisto/distinfo
+++ b/kallisto/distinfo
@@ -3,9 +3,10 @@ $NetBSD$
 BLAKE2s (kallisto-0.50.0.tar.gz) = aac5851f8f3c92f655ad7d248d30faa6d74c3d0c81d23607050d38417ca886f3
 SHA512 (kallisto-0.50.0.tar.gz) = be43f4070102a5a8ed259460044b02e243ad80ce79e8dc66bc5b8062feeaa792837b1df9c0bc6c2e9f3dc4bb807f77ff3eae6d25e30f5049dfef8514f1a07457
 Size (kallisto-0.50.0.tar.gz) = 5939018 bytes
-SHA1 (patch-CMakeLists.txt) = afb94f2cce3006fbaee452373445f5c82904fe75
-SHA1 (patch-ext_bifrost_CMakeLists.txt) = b102318a748809a42f4ad5cff361af06874bcf36
+SHA1 (patch-CMakeLists.txt) = 2672475d3fd0f3b837cafc9faa62cdc094f6fd4b
+SHA1 (patch-ext_bifrost_CMakeLists.txt) = ff5cebb2f38c4fa90bd651690ef58e588396c2ac
+SHA1 (patch-ext_bifrost_src_libpopcnt.h) = 3f31a47f40f341b1f6f72552b06990a81946e425
 SHA1 (patch-ext_bifrost_src_strict__fstream.hpp) = a4eab7784c3502fcc79ba0c87d31ac7275e5043c
-SHA1 (patch-src_Bootstrap.h) = 02aa0f3d928cd49ba23bf9bb08831e445c54a589
-SHA1 (patch-src_CMakeLists.txt) = 7c41c43b1659c2d58f189d3bfe57ea8826c015e5
-SHA1 (patch-src_kseq.h) = 4b6617f46b43fd7cdcd410295338804768d34bc2
+SHA1 (patch-src_Bootstrap.h) = 29a07a6fbaedf4387b70afb3b2caeb1a9b17f8e8
+SHA1 (patch-src_CMakeLists.txt) = 33d0e3cf985d2e400315788d3ee1c74987a6ebee
+SHA1 (patch-src_kseq.h) = 034e65bdcf5d3851b4e3d65afd06843bdff0d8a9
diff --git a/kallisto/patches/patch-CMakeLists.txt b/kallisto/patches/patch-CMakeLists.txt
index 7c6d4c95b5..c17bcf1f7c 100644
--- a/kallisto/patches/patch-CMakeLists.txt
+++ b/kallisto/patches/patch-CMakeLists.txt
@@ -1,4 +1,8 @@
---- CMakeLists.txt.orig	2023-06-27 10:45:00 UTC
+$NetBSD$
+
+# Unbundle htslib and zlib, use gmake
+
+--- CMakeLists.txt.orig	2023-06-27 10:45:00.000000000 +0000
 +++ CMakeLists.txt
 @@ -56,42 +56,16 @@ ENDIF(LINK MATCHES static)
  
diff --git a/kallisto/patches/patch-ext_bifrost_CMakeLists.txt b/kallisto/patches/patch-ext_bifrost_CMakeLists.txt
index c4c22a5e06..202be008b4 100644
--- a/kallisto/patches/patch-ext_bifrost_CMakeLists.txt
+++ b/kallisto/patches/patch-ext_bifrost_CMakeLists.txt
@@ -1,6 +1,30 @@
---- ext/bifrost/CMakeLists.txt.orig	2023-07-14 14:27:24 UTC
+$NetBSD$
+
+# Portability
+
+--- ext/bifrost/CMakeLists.txt.orig	2023-06-27 10:45:00.000000000 +0000
 +++ ext/bifrost/CMakeLists.txt
-@@ -30,8 +30,6 @@ if(COMPILATION_ARCH MATCHES "OFF")
+@@ -7,18 +7,12 @@ 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 "${MAX_KMER_SIZE}" CACHE STRING "MAX_GMER_SIZE")
+-# Enable architecture optimizations
+-SET(COMPILATION_ARCH "native" CACHE STRING "COMPILATION_ARCH")
+-# Enable AVX2 instructions
+-SET(ENABLE_AVX2 "ON" CACHE STRING "ENABLE_AVX2")
++SET(CMAKE_VERBOSE_MAKEFILE "ON")
+ 
+ # Set some default compile flags
+ set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c11")
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+ 
+-set_property(SOURCE BlockedBloomFilter.cpp APPEND_STRING PROPERTY COMPILE_FLAGS " -funroll-loops")
+-
+-
+ #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}")
@@ -9,3 +33,12 @@
  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)
+ 
diff --git a/kallisto/patches/patch-ext_bifrost_src_libpopcnt.h b/kallisto/patches/patch-ext_bifrost_src_libpopcnt.h
new file mode 100644
index 0000000000..8483c5d8d6
--- /dev/null
+++ b/kallisto/patches/patch-ext_bifrost_src_libpopcnt.h
@@ -0,0 +1,22 @@
+$NetBSD$
+
+# Use native popcnt
+
+--- ext/bifrost/src/libpopcnt.h.orig	2023-07-24 12:34:08.037669065 +0000
++++ ext/bifrost/src/libpopcnt.h
+@@ -32,6 +32,8 @@
+ #ifndef LIBPOPCNT_H
+ #define LIBPOPCNT_H
+ 
++#ifndef __NetBSD__
++
+ #include <stdint.h>
+ 
+ #ifndef __has_builtin
+@@ -584,4 +586,6 @@ static inline uint64_t popcnt(const void
+ 
+ #endif
+ 
++#endif /* NetBSD */
++
+ #endif /* LIBPOPCNT_H */
diff --git a/kallisto/patches/patch-src_Bootstrap.h b/kallisto/patches/patch-src_Bootstrap.h
index 6fc3bd4528..6c84babc65 100644
--- a/kallisto/patches/patch-src_Bootstrap.h
+++ b/kallisto/patches/patch-src_Bootstrap.h
@@ -1,3 +1,7 @@
+$NetBSD$
+
+# Portability
+
 --- src/Bootstrap.h.orig	2020-04-01 16:56:42 UTC
 +++ src/Bootstrap.h
 @@ -1,6 +1,7 @@
diff --git a/kallisto/patches/patch-src_CMakeLists.txt b/kallisto/patches/patch-src_CMakeLists.txt
index c7927b9e14..b4d679dafc 100644
--- a/kallisto/patches/patch-src_CMakeLists.txt
+++ b/kallisto/patches/patch-src_CMakeLists.txt
@@ -1,3 +1,7 @@
+$NetBSD$
+
+# Unbundle htslib
+
 --- src/CMakeLists.txt.orig	2023-07-06 14:07:38 UTC
 +++ src/CMakeLists.txt
 @@ -3,10 +3,6 @@ file(GLOB headers *.h *.hpp)
diff --git a/kallisto/patches/patch-src_kseq.h b/kallisto/patches/patch-src_kseq.h
index f7712a023f..4c29c78ebc 100644
--- a/kallisto/patches/patch-src_kseq.h
+++ b/kallisto/patches/patch-src_kseq.h
@@ -1,3 +1,7 @@
+$NetBSD$
+
+# Portability
+
 --- src/kseq.h.orig	2019-11-04 16:28:52 UTC
 +++ src/kseq.h
 @@ -32,6 +32,9 @@