[med-svn] [Git][med-team/minimap2][master] Add SIMDe bits to python-sse4-arch.patch ; adjust SIMDe patch

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch master at Debian Med / minimap2


Commits:
0bc2dbcf by Michael R. Crusoe at 2021-11-07T19:24:38+01:00
Add SIMDe bits to python-sse4-arch.patch ; adjust SIMDe patch

- - - - -


4 changed files:

- debian/changelog
- debian/patches/python-sse4-arch.patch
- debian/patches/simde
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+minimap2 (2.22+dfsg-3) unstable; urgency=medium
+
+  * Team upload
+  * Add SIMDe bits to python-sse4-arch.patch ; adjust SIMDe patch.
+    Closes: #998015
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Sun, 07 Nov 2021 19:23:30 +0100
+
 minimap2 (2.22+dfsg-2) unstable; urgency=medium
 
   * Team upload


=====================================
debian/patches/python-sse4-arch.patch
=====================================
@@ -5,12 +5,28 @@ Description: Only pass -msse4.1 to the compiler on amd64
 
 --- minimap2.orig/setup.py
 +++ minimap2/setup.py
-@@ -16,8 +16,6 @@
- if platform.machine() in ["aarch64", "arm64"]:
- 	include_dirs.append("sse2neon/")
- 	extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-D__SSE2__'])
+@@ -5,6 +5,7 @@
+ 	from distutils.extension import Extension
+ 
+ import sys, platform
++import subprocess
+ 
+ sys.path.append('python')
+ 
+@@ -13,11 +14,11 @@
+ extra_objects = ['libminimap2.a']
+ include_dirs = ["."]
+ 
+-if platform.machine() in ["aarch64", "arm64"]:
+-	include_dirs.append("sse2neon/")
+-	extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-D__SSE2__'])
 -else:
 -	extra_compile_args.append('-msse4.1') # WARNING: ancient x86_64 CPUs don't have SSE4
++arch = subprocess.run(["dpkg-architecture", "-qDEB_HOST_ARCH"], capture_output=True, text=True).stdout.strip()
++if arch in ["aarch64", "arm64"]:
++	extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-DUSE_SIMDE', '-D__SSE2__', '-DSIMDE_ENABLE_NATIVE_ALIASES', '-fopenmp-simd', '-O3', '-DSIMDE_ENABLE_OPENMP'])
++elif arch != "amd64":
++	extra_compile_args.extend(['-DKSW_SSE2_ONLY', '-DUSE_SIMDE', '-DSIMDE_ENABLE_NATIVE_ALIASES', '-fopenmp-simd', '-O3', '-DSIMDE_ENABLE_OPENMP'])
  
  def readme():
  	with open('python/README.rst') as f:


=====================================
debian/patches/simde
=====================================
@@ -1,13 +1,12 @@
 --- minimap2.orig/Makefile.simde
 +++ minimap2/Makefile.simde
-@@ -1,8 +1,9 @@
+@@ -1,8 +1,8 @@
 -CFLAGS=		-g -Wall -O2 -Wc++-compat #-Wextra
 -CPPFLAGS=	-DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES
 -INCLUDES=	-Ilib/simde
 -OBJS=		kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o lchain.o align.o hit.o map.o format.o pe.o seed.o esterr.o splitidx.o \
 -			ksw2_extz2_simde.o ksw2_extd2_simde.o ksw2_exts2_simde.o ksw2_ll_simde.o
-+CFLAGS+=		-g -Wall -O2 -Wc++-compat #-Wextra
-+CPPFLAGS+=	-DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES
++CFLAGS+=		-g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES
 +INCLUDES=
 +OBJS=		kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o \
 +			lchain.o align.o hit.o seed.o map.o format.o pe.o esterr.o splitidx.o \
@@ -15,7 +14,7 @@
  PROG=		minimap2
  PROG_EXTRA=	sdust minimap2-lite
  LIBS=		-lm -lz -lpthread
-@@ -37,28 +38,27 @@
+@@ -37,28 +37,27 @@
  extra:all $(PROG_EXTRA)
  
  minimap2:main.o libminimap2.a
@@ -56,14 +55,13 @@
  
  # other non-file targets
  
-@@ -80,10 +80,6 @@
+@@ -80,9 +79,6 @@
  index.o: kthread.h bseq.h minimap.h mmpriv.h kseq.h kvec.h kalloc.h khash.h
  index.o: ksort.h
  kalloc.o: kalloc.h
 -ksw2_extd2_sse.o: ksw2.h kalloc.h
 -ksw2_exts2_sse.o: ksw2.h kalloc.h
 -ksw2_extz2_sse.o: ksw2.h kalloc.h
--ksw2_ll_sse.o: ksw2.h kalloc.h
+ ksw2_ll_sse.o: ksw2.h kalloc.h
  kthread.o: kthread.h
  main.o: bseq.h minimap.h mmpriv.h kseq.h ketopt.h
- map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h kseq.h


=====================================
debian/rules
=====================================
@@ -15,7 +15,7 @@ override_dh_auto_clean:
 	rm -f tex/minimap2.aux tex/minimap2.bbl tex/minimap2.blg tex/minimap2.log tex/minimap2.out tex/minimap2.pdf
 	rm -f libminimap2.a
 
-ifeq (,$(filter $(DEB_HOST_ARCH_CPU),amd64))
+ifeq (,$(filter $(DEB_HOST_ARCH_CPU),amd64 i386))
 build_vars = -f Makefile.simde
 export DEB_CFLAGS_MAINT_APPEND += -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP
 endif



View it on GitLab: https://salsa.debian.org/med-team/minimap2/-/commit/0bc2dbcf576c2554da3acbf1fa4ccfc1a60ddb44

-- 
View it on GitLab: https://salsa.debian.org/med-team/minimap2/-/commit/0bc2dbcf576c2554da3acbf1fa4ccfc1a60ddb44
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