[med-svn] [Git][med-team/unifrac-tools][master] 3 commits: Enable linking ro shared hdf5 library

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / unifrac-tools


Commits:
797d2ec7 by Andreas Tille at 2022-07-27T14:24:11+02:00
Enable linking ro shared hdf5 library

- - - - -
513c1192 by Andreas Tille at 2022-07-27T15:46:16+02:00
Fix build time test and install

- - - - -
3d6c64fd by Andreas Tille at 2022-07-27T16:29:20+02:00
Fix installation

- - - - -


10 changed files:

- debian/control
- debian/libssu-dev.install
- − debian/libssu-tools.install
- debian/libssu0.install
- + debian/patches/enable_linking_to_shared_hdf5_lib.patch
- + debian/patches/python3.patch
- debian/patches/series
- debian/rules
- + debian/unifrac-tools.install
- debian/libssu-tools.manpages → debian/unifrac-tools.manpages


Changes:

=====================================
debian/control
=====================================
@@ -11,7 +11,8 @@ Build-Depends: debhelper-compat (= 13),
                liblz4-dev,
                libblas-dev,
                liblapacke-dev,
-               chrpath
+               chrpath,
+               python3 <!nocheck>
 Standards-Version: 4.6.1
 Vcs-Browser: https://salsa.debian.org/med-team/unifrac-tools
 Vcs-Git: https://salsa.debian.org/med-team/unifrac-tools.git


=====================================
debian/libssu-dev.install
=====================================
@@ -1,3 +1,3 @@
 #! /usr/bin/dh-exec
-sucpp/*.hpp	usr/include/sucpp
-sucpp/*.so	usr/lib/${DEB_HOST_MULTIARCH}/
+/usr/include/unifrac
+#sucpp/*.so	usr/lib/${DEB_HOST_MULTIARCH}/


=====================================
debian/libssu-tools.install deleted
=====================================
@@ -1,2 +0,0 @@
-sucpp/ssu      usr/bin
-sucpp/faithpd  usr/bin


=====================================
debian/libssu0.install
=====================================
@@ -1,2 +1,2 @@
 #! /usr/bin/dh-exec
-sucpp/*.so.*	usr/lib/${DEB_HOST_MULTIARCH}/
+usr/lib/*.so	usr/lib/${DEB_HOST_MULTIARCH}/


=====================================
debian/patches/enable_linking_to_shared_hdf5_lib.patch
=====================================
@@ -0,0 +1,16 @@
+From: ucko at debian.org (Aaron M. Ucko)
+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
+@@ -44,7 +44,7 @@ else
+ 	MPFLAG = -fopenmp
+ endif
+ 
+-LDDFLAGS += $(MPFLAG)
++LDDFLAGS += $(MPFLAG) -shlib
+ CPPFLAGS += $(MPFLAG)
+ 
+ UNIFRAC_FILES = unifrac_internal.o unifrac_cmp_cpu.o


=====================================
debian/patches/python3.patch
=====================================
@@ -0,0 +1,17 @@
+--- a/ci/crawford_test.sh
++++ b/ci/crawford_test.sh
+@@ -17,12 +17,12 @@ ssu -i crawford.biom -t crawford.tre -o
+ 
+ exp=$($MD5 test.dm | awk '{ print $1 }')
+ obs=$($MD5 test.dm.partial | awk '{ print $1 }')
+-python -c "assert '${obs}' == '${exp}'"
++python3 -c "assert '${obs}' == '${exp}'"
+ 
+ faithpd -i crawford.biom -t crawford.tre -o test.faith.obs
+ tail -n +2 test.faith.obs > test.faith.header-removed.obs
+ exp1=$($MD5 test.faith.exp | awk '{ print $1 }')
+ obs1=$($MD5 test.faith.header-removed.obs | awk '{ print $1 }')
+-python -c "assert '${obs1}' == '${exp1}'"
++python3 -c "assert '${obs1}' == '${exp1}'"
+ 
+ echo "All tests succeeded"


=====================================
debian/patches/series
=====================================
@@ -1 +1,3 @@
 remove_non-free_headers.patch
+enable_linking_to_shared_hdf5_lib.patch
+python3.patch


=====================================
debian/rules
=====================================
@@ -9,15 +9,27 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 %:
 	dh $@
 
+override_dh_auto_build:
+	mkdir -p $(CURDIR)/debian/tmp/usr/bin
+	mkdir -p $(CURDIR)/debian/tmp/usr/lib
+	dh_auto_build -- PREFIX=$(CURDIR)/debian/tmp/usr
+
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-	LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:$(CURDIR)/sucpp ci/crawford_test.sh
+	export PATH=${PATH}:`pwd`/debian/tmp/usr/bin ; \
+	cd ci ; \
+	./crawford_test.sh
 endif
 
-execute_after_dh_install:
-	chrpath -d debian/libssu-tools/usr/bin/ssu
-	chrpath -d debian/libssu-tools/usr/bin/faithpd
-	chrpath -d debian/libssu0/usr/lib/$(DEB_HOST_MULTIARCH)/libssu.so.0
+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
+
+#execute_after_dh_install:
+#	chrpath -d debian/libssu-tools/usr/bin/ssu
+#	chrpath -d debian/libssu-tools/usr/bin/faithpd
+#	chrpath -d debian/libssu0/usr/lib/$(DEB_HOST_MULTIARCH)/libssu.so.0
 
 override_dh_auto_clean:
 	dh_auto_clean


=====================================
debian/unifrac-tools.install
=====================================
@@ -0,0 +1 @@
+usr/bin


=====================================
debian/libssu-tools.manpages → debian/unifrac-tools.manpages
=====================================



View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/compare/538b778ae146ea76a3e6f38306dad3ef61164125...3d6c64fd5fe03df9cfce34a5c39a60b4c323bee1

-- 
View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/compare/538b778ae146ea76a3e6f38306dad3ef61164125...3d6c64fd5fe03df9cfce34a5c39a60b4c323bee1
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