[med-svn] [Git][med-team/unifrac-tools][master] 2 commits: Adapt baseline patch even further to enable building on non-x86.

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch master at Debian Med / unifrac-tools


Commits:
5ab28fa7 by Michael R. Crusoe at 2023-08-17T14:49:44+02:00
Adapt baseline patch even further to enable building on non-x86.

- - - - -
a9525b85 by Michael R. Crusoe at 2023-08-17T14:54:08+02:00
routine-update: Ready to upload to unstable

- - - - -


4 changed files:

- debian/changelog
- debian/patches/baseline.patch
- debian/patches/enable-debug-flag.patch
- debian/patches/enable_linking_to_shared_hdf5_lib.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+unifrac-tools (1.3.2-4) unstable; urgency=medium
+
+  * Team upload.
+  * Adapt baseline patch even further to enable building on non-x86.
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Thu, 17 Aug 2023 14:54:08 +0200
+
 unifrac-tools (1.3.2-3) unstable; urgency=medium
 
   [ Adrian Bunk ]


=====================================
debian/patches/baseline.patch
=====================================
@@ -5,9 +5,9 @@ Forwarded: not-needed
 Last-Update: 2023-07-26
 ---
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- unifrac-tools-1.3.2.orig/src/Makefile
-+++ unifrac-tools-1.3.2/src/Makefile
-@@ -44,7 +44,7 @@ ifeq ($(PLATFORM),Darwin)
+--- unifrac-tools.orig/src/Makefile
++++ unifrac-tools/src/Makefile
+@@ -44,7 +44,7 @@
  else
  	AVX2 := $(shell grep "^flags" /proc/cpuinfo | head -n 1 | grep -c avx2)
  	LDDFLAGS = -shared
@@ -16,7 +16,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
  endif
  
  EXEFLAGS =
-@@ -77,39 +77,6 @@ ifndef NOGPU
+@@ -77,39 +77,6 @@
  	endif
  endif
  
@@ -56,3 +56,32 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
  ifeq (,$(findstring pgi,$(COMPILER)))
      ifneq ($(PERFORMING_CONDA_BUILD),True)
  	# basically, not gcc
+--- unifrac-tools.orig/combined/libssu.c
++++ unifrac-tools/combined/libssu.c
+@@ -24,6 +24,8 @@
+ 
+ /* Pick the right libssu implementation */
+ static const char *ssu_get_lib_name() {
++   const char *ssu = "libssu_nv.so";
++#if defined (__i386__) || defined (__x86_64__)
+    __builtin_cpu_init ();
+    bool has_avx  = __builtin_cpu_supports ("avx");
+    bool has_avx2 = __builtin_cpu_supports ("avx2");
+@@ -35,7 +37,6 @@
+       has_avx2 = false;
+    }
+ 
+-   const char *ssu = "libssu_nv.so";
+    if (has_avx) {
+       if ((env_max_cpu!=NULL) && (strcmp(env_max_cpu,"avx")==0)) {
+          has_avx2 = false;
+@@ -52,6 +53,9 @@
+       }
+       ssu="libssu_cpu_basic.so";
+    }
++#else
++   ssu="libssu_cpu_basic.so";
++#endif
+ 
+    const char* env_cpu_info = getenv("UNIFRAC_CPU_INFO");
+    if ((env_cpu_info!=NULL) && (env_cpu_info[0]=='Y')) {


=====================================
debian/patches/enable-debug-flag.patch
=====================================
@@ -1,9 +1,9 @@
 Description: Add debug flag to cppflags
 Author: Nilesh Patra <nilesh at debian.org>
 Last-Update: 2023-01-05
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -118,7 +118,7 @@ ifeq (,$(findstring pgi,$(COMPILER)))
+--- unifrac-tools.orig/src/Makefile
++++ unifrac-tools/src/Makefile
+@@ -85,7 +85,7 @@
  endif
  
  


=====================================
debian/patches/enable_linking_to_shared_hdf5_lib.patch
=====================================
@@ -3,9 +3,9 @@ Date: Wed, 27 Jul 2022 07:44:28 -0400
 Origin: https://lists.debian.org/debian-med/2022/07/msg00078.html
 Description: Enable linking ro shared hdf5 library
 
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -55,7 +55,7 @@ else
+--- unifrac-tools.orig/src/Makefile
++++ unifrac-tools/src/Makefile
+@@ -55,7 +55,7 @@
  	MPFLAG = -fopenmp
  endif
  
@@ -14,7 +14,7 @@ Description: Enable linking ro shared hdf5 library
  CPPFLAGS += $(MPFLAG)
  
  UNIFRAC_FILES = unifrac_internal.o unifrac_cmp_cpu.o
-@@ -142,8 +142,8 @@ $(FPD): faithpd.cpp tree.o biom.o biom_i
+@@ -109,8 +109,8 @@
  	$(CXX) $(CPPFLAGS) $(EXEFLAGS) faithpd.cpp -o $(FPD) tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 $(BLASLIB) -lpthread
  
  lib$(SSU).so: tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac.o cmd.o skbio_alt.o api.o $(UNIFRAC_FILES)



View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/compare/699abd4cc76869bd6c0d4467aea94306a8a4266b...a9525b858ee784c610a30557f80964a80f7aae36

-- 
View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/compare/699abd4cc76869bd6c0d4467aea94306a8a4266b...a9525b858ee784c610a30557f80964a80f7aae36
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