[med-svn] [Git][med-team/unifrac-tools][master] 5 commits: python3.patch: fix remaining python calls

Gilles Filippini (@pini) gitlab at salsa.debian.org
Wed Jul 1 18:16:09 BST 2026 


Gilles Filippini pushed to branch master at Debian Med / unifrac-tools


Commits:
34f81756 by Gilles Filippini at 2026-07-01T18:57:17+02:00
python3.patch: fix remaining python calls

- - - - -
221fcd39 by Gilles Filippini at 2026-07-01T18:59:43+02:00
soname.patch: fix typo

(or maybe a misunderstanding about how globs work)

- - - - -
66dea109 by Gilles Filippini at 2026-07-01T19:01:14+02:00
baseline.patch: tentative fix after messed-up refresh

- - - - -
97dc8831 by Gilles Filippini at 2026-07-01T19:02:32+02:00
hdf5: fix messed-up patch

- - - - -
5d6710ab by Gilles Filippini at 2026-07-01T19:03:41+02:00
d/rules: prevent deletion of debian/tmp after build

- - - - -


5 changed files:

- debian/patches/baseline.patch
- debian/patches/enable_linking_to_shared_hdf5_lib.patch
- debian/patches/python3.patch
- debian/patches/soname.patch
- debian/rules


Changes:

=====================================
debian/patches/baseline.patch
=====================================
@@ -5,8 +5,10 @@ Forwarded: not-needed
 Last-Update: 2023-07-26
 ---
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- a/src/Makefile
-+++ b/src/Makefile
+Index: unifrac-tools-1.6.1/src/Makefile
+===================================================================
+--- unifrac-tools-1.6.1.orig/src/Makefile
++++ unifrac-tools-1.6.1/src/Makefile
 @@ -123,46 +123,6 @@ ifndef NOGPU
     endif
  endif
@@ -54,15 +56,16 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
  ifeq (,$(findstring pgi,$(COMPILER)))
      ifeq ($(PERFORMING_CONDA_BUILD),False)
  	# basically, not gcc
---- a/combined/libssu.c
-+++ b/combined/libssu.c
-@@ -48,6 +48,9 @@ static const char *ssu_get_lib_name() {
-       has_v4 = false;
-     }
-    }
-+#else
-+   ssu="libssu_cpu_basic.so";
-+#endif
- 
-    const char *ssu = "unknown"; // just to have a default
-    if (has_v4) {
+Index: unifrac-tools-1.6.1/combined/libssu.c
+===================================================================
+--- unifrac-tools-1.6.1.orig/combined/libssu.c
++++ unifrac-tools-1.6.1/combined/libssu.c
+@@ -24,7 +24,7 @@
+ /* Must be before the include of ssu_ld */
+ #ifndef BASIC_ONLY
+ static const char *ssu_get_lib_name() {
+-#if defined(__x86_64__)
++#if defined (__i386__) || defined(__x86_64__)
+    __builtin_cpu_init ();
+    bool has_v2  = __builtin_cpu_supports ("x86-64-v2");
+    bool has_v3  = __builtin_cpu_supports ("x86-64-v3");


=====================================
debian/patches/enable_linking_to_shared_hdf5_lib.patch
=====================================
@@ -6,22 +6,16 @@ Description: Enable linking to shared hdf5 library
 Forwarded: not-needed
 FIXME: Aaron, please review the changes
 
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -2,6 +2,7 @@
- 
- PLATFORM := $(shell uname -s)
- COMPILER := $(shell (h5c++ -v 2>&1) | tr A-Z a-z )
-+CPPFLAGS += -shlib
- 
- ifeq ($(BUILD_VARIANT),)
- 	SSU = ssu
-@@ -172,7 +173,7 @@ $(FPD): faithpd.cpp api.hpp $(PREFIX)/li
+Index: unifrac-tools-1.6.1/src/Makefile
+===================================================================
+--- unifrac-tools-1.6.1.orig/src/Makefile
++++ unifrac-tools-1.6.1/src/Makefile
+@@ -172,7 +172,7 @@ $(FPD): faithpd.cpp api.hpp $(PREFIX)/li
  
  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)
  #	h5c++ $(LDDFLAGS) -o lib$(SSU).so tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 $(SKBBLIB) -L$(PREFIX)/lib -noshlib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5
 -	h5c++ $(LDDFLAGS) -o lib$(SSU).so.0 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 -shlib -Wl,-soname,lib$(SSU).so.0 $(SKBBLIB) -L$(PREFIX)/lib -noshlib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5
-+	h5c++ $(LDDFLAGS) -o lib$(SSU).so.0 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 -Wl,-soname,lib$(SSU).so.0 $(SKBBLIB) -L$(PREFIX)/lib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5
++	h5c++ -shlib $(LDDFLAGS) -o lib$(SSU).so.0 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 -Wl,-soname,lib$(SSU).so.0 $(SKBBLIB) -L$(PREFIX)/lib
  	ln -sf lib$(SSU).so.0 lib$(SSU).so
  	# FIXME: Should build static lib as well
  	# $(CXX) $(LDDFLAGS) -o libssu.a tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -lhdf5_cpp -llz4 $(BLASLIB) -L$(PREFIX)/lib


=====================================
debian/patches/python3.patch
=====================================
@@ -3,8 +3,28 @@ Last-Update: 2022-10-10
 Description: Call Python3
 Forwarded: not-needed
 
---- a/ci/crawford_test.sh
-+++ b/ci/crawford_test.sh
+Index: unifrac-tools-1.6.1/ci/crawford_test.sh
+===================================================================
+--- unifrac-tools-1.6.1.orig/ci/crawford_test.sh
++++ unifrac-tools-1.6.1/ci/crawford_test.sh
+@@ -17,7 +17,7 @@ cat test.ssu.exp |awk '{printf("%s %.4f
+ 
+ exp=$($MD5 test.dm.f4 | awk '{ print $1 }')
+ obs=$($MD5 test.ssu.exp.f4 | awk '{ print $1 }')
+-python -c "assert '${obs}' == '${exp}'"
++python3 -c "assert '${obs}' == '${exp}'"
+ 
+ ssu -i crawford.biom -t crawford.tre -o test.vaw.dm -m unweighted_fp64 --vaw
+ 
+@@ -27,7 +27,7 @@ cat test.ssu_vaw.exp |awk '{printf("%s %
+ 
+ exp=$($MD5 test.dm.f4 | awk '{ print $1 }')
+ obs=$($MD5 test.ssu.exp.f4 | awk '{ print $1 }')
+-python -c "assert '${obs}' == '${exp}'"
++python3 -c "assert '${obs}' == '${exp}'"
+ 
+ ssu -i crawford.biom -t crawford.tre -o test.dm.start0.stop3 -m unweighted_fp64 --mode partial --start 0 --stop 3
+ ssu -i crawford.biom -t crawford.tre -o test.dm.start3.stop5 -m unweighted_fp64 --mode partial --start 3 --stop 5
 @@ -35,12 +35,12 @@ ssu -i crawford.biom -t crawford.tre -o
  
  exp=$($MD5 test.dm | awk '{ print $1 }')


=====================================
debian/patches/soname.patch
=====================================
@@ -3,8 +3,10 @@ Last-Update: 2022-07-26
 Description: Create SONAME for libssu
 Forwarded: not-needed
 
---- a/src/Makefile
-+++ b/src/Makefile
+Index: unifrac-tools-1.6.1/src/Makefile
+===================================================================
+--- unifrac-tools-1.6.1.orig/src/Makefile
++++ unifrac-tools-1.6.1/src/Makefile
 @@ -211,7 +211,11 @@ $(FPD): faithpd.cpp api.hpp $(PREFIX)/li
  	h5c++ $(CPPFLAGS) $(EXEFLAGS) faithpd.cpp -o $@ -l$(SSU)
  
@@ -23,7 +25,7 @@ Forwarded: not-needed
  
  install_lib: lib$(SSU).so
 -	for f in lib$(SSU).so ; do rm -f "${PREFIX}/lib/$${f}"; cp "$${f}" ${PREFIX}/lib/; done
-+	for f in lib$(SSU).so ; do rm -f "${PREFIX}/lib/$${f}"; cp -a "$${f}*" ${PREFIX}/lib/; done
++	for f in lib$(SSU).so ; do rm -f "${PREFIX}/lib/$${f}"; cp -a "$${f}"* ${PREFIX}/lib/; done
  
  
  install_lib_acc: $(UNIFRAC_ACC_SHLIBS)


=====================================
debian/rules
=====================================
@@ -18,14 +18,15 @@ override_dh_auto_build:
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	export PATH=${PATH}:$(CURDIR)/debian/tmp/usr/bin ; \
+	export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:$(CURDIR)/debian/tmp/usr/lib ; \
 	cd ci ; \
 	./crawford_test.sh
 endif
 
-override_dh_auto_install:
-	mkdir -p $(CURDIR)/debian/tmp/usr/bin
-	mkdir -p $(CURDIR)/debian/tmp/usr/lib
-	dh_auto_install -- PREFIX=$(CURDIR)/debian/tmp/usr
+override_dh_prep:;
+	dh_prep -Xtmp
+
+override_dh_auto_install:;
 
 override_dh_install:
 	chrpath -d debian/tmp/usr/bin/ssu



View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/compare/6295f42c390df38d1598576dc91ef4c4b12c5c5b...5d6710abf179d34f592728c857921ad572f1c570

-- 
View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/compare/6295f42c390df38d1598576dc91ef4c4b12c5c5b...5d6710abf179d34f592728c857921ad572f1c570
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