[med-svn] [Git][med-team/hyphy][master] 6 commits: rm_arch_specific_flags.patch: update to include NEON variants.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / hyphy


Commits:
46e0fe05 by Étienne Mollier at 2025-03-05T12:38:24+01:00
rm_arch_specific_flags.patch: update to include NEON variants.

This is needed to fix illegal instruction errors seen in autopkgtest.

- - - - -
d61b3a59 by Étienne Mollier at 2025-03-05T12:39:37+01:00
d/rules: leave a note to build NEON SIMDe variants.

- - - - -
a4241868 by Étienne Mollier at 2025-03-05T12:41:15+01:00
New upstream version 2.5.69+dfsg
- - - - -
78fe4f34 by Étienne Mollier at 2025-03-05T12:41:22+01:00
Update upstream source from tag 'upstream/2.5.69+dfsg'

Update to upstream version '2.5.69+dfsg'
with Debian dir effcc6cc20bba7d7a1b1f6430709075a5e402621
- - - - -
73680020 by Étienne Mollier at 2025-03-05T12:42:51+01:00
d/control: declare compliance to standards version 4.7.2.

- - - - -
ecf9f78c by Étienne Mollier at 2025-03-05T12:43:52+01:00
d/changelog: ready for upload to unstable.

- - - - -


4 changed files:

- debian/changelog
- debian/control
- debian/patches/rm_arch_specific_flags.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+hyphy (2.5.69+dfsg-1) unstable; urgency=medium
+
+  * New upstream version 2.5.69+dfsg (no changes).
+  * rm_arch_specific_flags.patch: update to include NEON variants.
+    This is needed to fix illegal instruction errors seen in autopkgtest.
+  * d/rules: leave a note to build NEON SIMDe variants.
+  * d/control: declare compliance to standards version 4.7.2.
+
+ -- Étienne Mollier <emollier at debian.org>  Wed, 05 Mar 2025 12:43:12 +0100
+
 hyphy (2.5.68+dfsg-1) unstable; urgency=medium
 
   * New upstream version 2.5.68+dfsg


=====================================
debian/control
=====================================
@@ -15,7 +15,7 @@ Build-Depends: debhelper-compat (= 13),
                libpython3-all-dev,
                python3-all-dev:any,
                chrpath
-Standards-Version: 4.7.0
+Standards-Version: 4.7.2
 Vcs-Browser: https://salsa.debian.org/med-team/hyphy
 Vcs-Git: https://salsa.debian.org/med-team/hyphy.git
 Homepage: https://hyphy.org/


=====================================
debian/patches/rm_arch_specific_flags.patch
=====================================
@@ -29,6 +29,15 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
              add_definitions (-D_SLKP_USE_AVX_INTRINSICS)
              PCL_CHECK_FOR_FMA3()
              if (${HAVE_FMA3})
+@@ -238,7 +238,7 @@
+ 		PCL_CHECK_FOR_NEON()
+ 		if(${HAVE_NEON_EXTENSIONS})
+ 			add_definitions (-D_SLKP_USE_ARM_NEON)
+-			set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mcpu=native -mtune=native ")
++			set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ")
+ 		endif(${HAVE_NEON_EXTENSIONS})
+ 	endif(NOT NONEON)
+ 
 @@ -251,7 +251,7 @@
      if(NOAVX)
          if(NOSSE4)
@@ -47,3 +56,12 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
              add_definitions (-D_SLKP_USE_AVX_INTRINSICS)
              PCL_CHECK_FOR_FMA3()
              if (${HAVE_FMA3})
+@@ -286,7 +286,7 @@
+ 		PCL_CHECK_FOR_NEON()
+ 		if(${HAVE_NEON_EXTENSIONS})
+ 			add_definitions (-D_SLKP_USE_ARM_NEON)
+-			set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mcpu=native -mtune=native ")
++			set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ")
+ 
+ 		endif(${HAVE_NEON_EXTENSIONS})
+ 	endif(NOT NONEON)


=====================================
debian/rules
=====================================
@@ -17,6 +17,8 @@ ISOFILES += $(DTMP)/usr/share/hyphy/TemplateBatchFiles/TemplateModels/models.lst
 %:
 	dh $@ --buildsystem=cmake
 
+# FIXME: build NEON SIMDe variants for Aarch64.
+
 override_dh_auto_clean:
 ifeq (amd64,$(DEB_HOST_ARCH))
 	dh_auto_clean --builddirectory obj-avx



View it on GitLab: https://salsa.debian.org/med-team/hyphy/-/compare/cab2836da06a67c36d4d8e44d103577abde69da1...ecf9f78c402ad8378e6c1b81a2e18bc3bd42af41

-- 
View it on GitLab: https://salsa.debian.org/med-team/hyphy/-/compare/cab2836da06a67c36d4d8e44d103577abde69da1...ecf9f78c402ad8378e6c1b81a2e18bc3bd42af41
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