[med-svn] [Git][med-team/scikit-bio-binaries][master] 4 commits: Rely on checks of d-shlibs

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / scikit-bio-binaries


Commits:
9078b7e7 by Andreas Tille at 2026-06-19T12:56:15+02:00
Rely on checks of d-shlibs

- - - - -
15a5e9c3 by Andreas Tille at 2026-06-19T12:59:44+02:00
We do not build for i386

- - - - -
c099bb01 by Andreas Tille at 2026-06-19T14:34:05+02:00
Fix package name in autopkgtest

- - - - -
2a346c60 by Andreas Tille at 2026-06-19T14:38:14+02:00
Use Debian build options

- - - - -


8 changed files:

- debian/control
- − debian/libskbb-dev.install
- − debian/libskbb1.install
- + debian/patches/hardening.patch
- debian/patches/series
- debian/rules
- debian/salsa-ci.yml
- debian/tests/run-unit-test


Changes:

=====================================
debian/control
=====================================
@@ -3,6 +3,7 @@ Section: science
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille at debian.org>
 Build-Depends: debhelper-compat (= 13),
+               d-shlibs,
                architecture-is-64-bit,
                architecture-is-little-endian,
                python3,


=====================================
debian/libskbb-dev.install deleted
=====================================
@@ -1,3 +0,0 @@
-src/extern/*.h	usr/include/scikit-bio-binaries
-src/*.so	usr/lib/${DEB_HOST_GNU_TYPE}
-src/libskbb.a	usr/lib/${DEB_HOST_GNU_TYPE}


=====================================
debian/libskbb1.install deleted
=====================================
@@ -1 +0,0 @@
-src/*.so.*	usr/lib/${DEB_HOST_GNU_TYPE}


=====================================
debian/patches/hardening.patch
=====================================
@@ -0,0 +1,25 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2026-06-19
+Description: Use Debian build options
+Forwarded: not-needed
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -51,7 +51,7 @@ ifeq ($(ARCH),x86_64)
+   endif
+ endif
+ 
+-CXXFLAGS += -O3 -ffast-math -fopenmp -Wall -std=c++17 -pedantic -I. $(OPT) -fPIC
++CXXFLAGS += $(CPPFLAGS) -O3 -ffast-math -fopenmp -Wall -std=c++17 -pedantic -I. $(OPT) -fPIC
+ 
+ ifneq ($(SKBB_ENABLE_ACC_NV),)
+   ifneq ($(NV_CUDA),)
+@@ -353,7 +353,7 @@ libskbb_acc_amd.so: skbb_accapi_dyn_acc_
+ else
+ #OpenMP Target version
+ libskbb_acc_amd.so: skbb_accapi_dyn_acc_amd.o permanova_dyn_acc_amd.o
+-	$(AMD_CXX) $(AMD_LDFLAGS) $(SO_LDDFLAGS) -o $@ skbb_accapi_dyn_acc_amd.o permanova_dyn_acc_amd.o
++	$(AMD_CXX) $(AMD_LDFLAGS) $(SO_LDDFLAGS) $(LDFLAGS) -o $@ skbb_accapi_dyn_acc_amd.o permanova_dyn_acc_amd.o
+ endif
+ 
+ endif


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 openblas.patch
 no_install.patch
 shared-lib.patch
+hardening.patch


=====================================
debian/rules
=====================================
@@ -5,3 +5,12 @@
 
 override_dh_auto_install:
 	echo "Rather use dh_install"
+
+override_dh_install:
+	dh_install
+	d-shlibmove --commit \
+                    --multiarch \
+                    --devunversioned \
+                    --override s/liblapacke3-dev/liblapacke-dev/ \
+		    --movedev "src/extern/*.h" usr/include/scikit-bio-binaries \
+		    src/libskbb.so


=====================================
debian/salsa-ci.yml
=====================================
@@ -1,3 +1,7 @@
 ---
 include:
   - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/recipes/debian.yml
+
+variables:
+# We do not build for i386
+  SALSA_CI_DISABLE_BUILD_PACKAGE_I386: 1


=====================================
debian/tests/run-unit-test
=====================================
@@ -1,7 +1,7 @@
 #!/bin/bash
 set -e
 
-pkg=libscikit-bio-dev
+pkg=libskbb-dev
 
 export LC_ALL=C.UTF-8
 if [ "${AUTOPKGTEST_TMP}" = "" ] ; then



View it on GitLab: https://salsa.debian.org/med-team/scikit-bio-binaries/-/compare/ce76c12602df8753b1a8dce089882eddf3cad6c3...2a346c60adf6ae7daf2bfeb55526042ec87c0e80

-- 
View it on GitLab: https://salsa.debian.org/med-team/scikit-bio-binaries/-/compare/ce76c12602df8753b1a8dce089882eddf3cad6c3...2a346c60adf6ae7daf2bfeb55526042ec87c0e80
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