[med-svn] [Git][med-team/diamond-aligner][master] 3 commits: Add two patches to build on all supported architectures
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Aug 14 10:50:51 BST 2026
Andreas Tille pushed to branch master at Debian Med / diamond-aligner
Commits:
eb1c0f5a by Andreas Tille at 2026-08-14T11:39:00+02:00
Add two patches to build on all supported architectures
- - - - -
452e562d by Andreas Tille at 2026-08-14T11:46:09+02:00
Upload to unstable
- - - - -
6fe0cfa0 by Andreas Tille at 2026-08-14T11:50:41+02:00
Cleanup d/copyright from unneeded stanzas
- - - - -
5 changed files:
- debian/changelog
- debian/copyright
- + debian/patches/compatibility.patch
- + debian/patches/remove-duplicated-traits.patch
- + debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,8 +1,15 @@
-diamond-aligner (2.2.5-2) UNRELEASED; urgency=medium
+diamond-aligner (2.2.5-3) UNRELEASED; urgency=medium
+
+ * Cleanup d/copyright from unneeded stanzas
+
+ -- Andreas Tille <tille at debian.org> Fri, 14 Aug 2026 11:50:06 +0200
+
+diamond-aligner (2.2.5-2) unstable; urgency=medium
* Drop src/lib/Eigen from d/copyright since upstream stopped shipping this
+ * Add two patches to build on all supported architectures
- -- Andreas Tille <tille at debian.org> Thu, 13 Aug 2026 16:36:26 +0200
+ -- Andreas Tille <tille at debian.org> Fri, 14 Aug 2026 11:39:08 +0200
diamond-aligner (2.2.5-1) unstable; urgency=medium
=====================================
debian/copyright
=====================================
@@ -18,14 +18,6 @@ Files: src/lib/mio/*
Copyright: 2017 https://github.com/mandreyel
License: Expat
-Files: src/lib/WFA2-lib.diamond/*
-Copyright: 2017 by Santiago Marco-Sola
-License: Expat
-
-Files: src/lib/WFA2-lib.diamond/tools/align_benchmark/edit/edit_bpm.*
-Copyright: 2017 by Santiago Marco-Sola
-License: GPL-3+
-
Files: src/lib/murmurhash/MurmurHash3.*
Copyright: Austin Appleby
License: public-domain
@@ -47,13 +39,6 @@ Files: debian/*
Copyright: 2016 Andreas Tille <tille at debian.org>
License: BSD-3-clause
-########################################################################
-
-License: MPL-2.0
- This Source Code Form is subject to the terms of the Mozilla Public
- License, v. 2.0. On Debian systems a full copy of the MPL-2.0 is
- available at /usr/share/common-licenses/MPL-2.0
-
License: BSD-2-clause
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
@@ -130,40 +115,6 @@ License: GPL-3+
On Debian systems, a full copy of the GPL v3.0 is available at the
following location: /usr/share/common-licenses/GPL-3
-License: MIT~Boehm
- THIS MATERIAL IS PROVIDED AS IS, WITH ABSOLUTELY NO WARRANTY
- EXPRESSED OR IMPLIED. ANY USE IS AT YOUR OWN RISK.
- .
- Permission is hereby granted to use or copy this program for any
- purpose, provided the above notices are retained on all copies.
- Permission to modify the code and to distribute modified code is
- granted, provided the above notices are retained, and a notice that
- the code was modified is included with the above copyright notice.
-
-License: LGPL-2.1+
- This library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Lesser General Public
- License as published by the Free Software Foundation; either
- version 2.1 of the License, or (at your option) any later version.
- .
- This library is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- Lesser General Public License for more details.
- .
- On Debian systems, a full copy of the LGPL-2.1 is available in the
- file /usr/share/common-licenses/LGPL-2.1.
- .
- Permission is hereby granted to use or copy this program under the
- terms of the GNU LGPL, provided that the Copyright, this License,
- and the Availability of the original version is retained on all copies.
- User documentation of any code that uses this code or any modified
- version of this code must cite the Copyright, this License, the
- Availability note, and "Used by permission." Permission to modify
- the code and to distribute modified code is granted, provided the
- Copyright, this License, and the Availability note are retained,
- and a notice that the code was modified is included.
-
License: CC-BY-3.0
CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE
LEGAL SERVICES. DISTRIBUTION OF THIS LICENSE DOES NOT CREATE AN
=====================================
debian/patches/compatibility.patch
=====================================
@@ -0,0 +1,24 @@
+Description: Probe -mtune=generic instead of hardcoding it
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2026-08-14
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -211,10 +211,16 @@ else()
+ include(CheckCXXCompilerFlag)
+
+ set(ARCH_GENERIC_CXX_FLAGS
+- -mtune=generic
+ -fno-stack-protector
+ )
+
++ check_cxx_compiler_flag("-mtune=generic"
++ HAVE_CXX_FLAG_MTUNE_GENERIC)
++
++ if(HAVE_CXX_FLAG_MTUNE_GENERIC)
++ list(APPEND ARCH_GENERIC_CXX_FLAGS -mtune=generic)
++ endif()
++
+ check_cxx_compiler_flag("-fcf-protection=none"
+ HAVE_CXX_FLAG_FCF_PROTECTION_NONE)
+
=====================================
debian/patches/remove-duplicated-traits.patch
=====================================
@@ -0,0 +1,19 @@
+Description: Remove duplicated Traits<float> specialization in generic SIMD fallback
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2026-08-14
+
+--- a/src/util/simd/vector_generic.h
++++ b/src/util/simd/vector_generic.h
+@@ -84,12 +84,6 @@ struct Traits<float> {
+ using Register = float;
+ };
+
+-template<>
+-struct Traits<float> {
+- static constexpr size_t LANES = 1;
+- using Register = float;
+-};
+-
+ static inline float zero(float) {
+ return 0.0f;
+ }
=====================================
debian/patches/series
=====================================
@@ -0,0 +1,2 @@
+compatibility.patch
+remove-duplicated-traits.patch
View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/-/compare/82c8b501b113a4a5c965d3d05d8f206c996cb443...6fe0cfa0a516c547ab9ab89f1f908d727d686bdc
--
View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/-/compare/82c8b501b113a4a5c965d3d05d8f206c996cb443...6fe0cfa0a516c547ab9ab89f1f908d727d686bdc
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