[med-svn] [Git][med-team/spoa][master] 9 commits: New upstream version 4.1.5
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Wed Oct 8 21:25:34 BST 2025
Étienne Mollier pushed to branch master at Debian Med / spoa
Commits:
2c26298f by Étienne Mollier at 2025-10-08T22:02:07+02:00
New upstream version 4.1.5
- - - - -
489da143 by Étienne Mollier at 2025-10-08T22:02:08+02:00
Update upstream source from tag 'upstream/4.1.5'
Update to upstream version '4.1.5'
with Debian dir 38fce683ad79becc550d76df137d37a358df97cb
- - - - -
a1122ab2 by Étienne Mollier at 2025-10-08T22:06:48+02:00
d/*symbols*: mark few leaked symbols as optional.
Closes: #1097922
- - - - -
3fb9f2fc by Étienne Mollier at 2025-10-08T22:23:05+02:00
d/control: declare compliance to standards version 4.7.2.
- - - - -
e92bd9a6 by Étienne Mollier at 2025-10-08T22:23:23+02:00
d/control: drop redundant Rules-Requires-Root: no.
- - - - -
e5b8580d by Étienne Mollier at 2025-10-08T22:23:44+02:00
d/watch: convert to v5 Github template.
- - - - -
a0297e07 by Étienne Mollier at 2025-10-08T22:24:02+02:00
d/patches/*: normalize Last-Update timestamp.
- - - - -
02388c58 by Étienne Mollier at 2025-10-08T22:24:22+02:00
d/*symbols*: add a couple of optional leaked symbols.
- - - - -
adf87afe by Étienne Mollier at 2025-10-08T22:25:05+02:00
d/changelog: ready for upload to unstable.
- - - - -
11 changed files:
- .github/workflows/spoa.yml
- .gitignore
- CMakeLists.txt
- debian/changelog
- debian/control
- debian/libspoa7.0.0.symbols.amd64
- debian/patches/shared_and_static.patch
- debian/patches/use_debian_packaged_libs.patch
- debian/watch
- meson.build
- src/simd_alignment_engine_implementation.hpp
Changes:
=====================================
.github/workflows/spoa.yml
=====================================
@@ -14,12 +14,10 @@ jobs:
strategy:
matrix:
compiler:
- - g++-7
- g++
- - clang++-6.0
- clang++
- runs-on: ubuntu-20.04
+ runs-on: ubuntu-latest
steps:
- uses: actions/checkout at v3
=====================================
.gitignore
=====================================
@@ -1,5 +1,5 @@
-# Compiled Object files
-build/
-
+.cache/
+.vscode/
+build*
/subprojects/*
!/subprojects/*.wrap
=====================================
CMakeLists.txt
=====================================
@@ -1,6 +1,6 @@
cmake_minimum_required(VERSION 3.12)
-project(spoa VERSION 4.1.4
+project(spoa VERSION 4.1.5
LANGUAGES CXX
DESCRIPTION "Spoa is a c++ library (and tool) for SIMD vectorized partial order alignment.")
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+spoa (4.1.5-1) unstable; urgency=medium
+
+ * New upstream version 4.1.5
+ * d/*symbols*: mark few leaked symbols as optional. (Closes: #1097922)
+ * d/control: declare compliance to standards version 4.7.2.
+ * d/control: drop redundant Rules-Requires-Root: no.
+ * d/watch: convert to v5 Github template.
+ * d/patches/*: normalize Last-Update timestamp.
+ * d/*symbols*: add a couple of optional leaked symbols.
+
+ -- Étienne Mollier <emollier at debian.org> Wed, 08 Oct 2025 22:24:58 +0200
+
spoa (4.1.4-2) unstable; urgency=medium
* d/libspoa7.0.0.symbols.amd64: mark some compiler symbols as optional.
=====================================
debian/control
=====================================
@@ -13,11 +13,10 @@ Build-Depends: debhelper-compat (= 13),
zlib1g-dev,
libsimde-dev,
libcpu-features-dev [any-amd64 any-i386]
-Standards-Version: 4.7.0
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/spoa
Vcs-Git: https://salsa.debian.org/med-team/spoa.git
Homepage: https://github.com/rvaser/spoa
-Rules-Requires-Root: no
Package: spoa
Architecture: any
=====================================
debian/libspoa7.0.0.symbols.amd64
=====================================
@@ -135,10 +135,12 @@ libspoa.so.7.0.0 libspoa7.0.0 #MINVER#
_ZNK4spoa5Graph8SubgraphEjjPSt6vectorIPKNS0_4NodeESaIS4_EE at Base 4.0.5
_ZNKSt5ctypeIcE8do_widenEc at Base 1.1.5
(optional)_ZNSt10_HashtableISt10type_indexSt4pairIKS0_St13unordered_mapIS0_St6vectorIPKN6cereal6detail17PolymorphicCasterESaIS9_EESt4hashIS0_ESt8equal_toIS0_ESaIS1_IS2_SB_EEEESaISJ_ENSt8__detail10_Select1stESF_SD_NSL_18_Mod_range_hashingENSL_20_Default_ranged_hashENSL_20_Prime_rehash_policyENSL_17_Hashtable_traitsILb0ELb0ELb1EEEE5clearEv at Base 4.0.5
+ (optional)_ZNSt10_HashtableIjjSaIjENSt8__detail9_IdentityESt8equal_toIjESt4hashIjENS1_18_Mod_range_hashingENS1_20_Default_ranged_hashENS1_20_Prime_rehash_policyENS1_17_Hashtable_traitsILb0ELb1ELb1EEEE15_M_emplace_uniqIJRKjEEESt4pairINS1_14_Node_iteratorIjLb1ELb0EEEbEDpOT_ at Base 4.1.5
(optional)_ZNSt10_HashtableIjjSaIjENSt8__detail9_IdentityESt8equal_toIjESt4hashIjENS1_18_Mod_range_hashingENS1_20_Default_ranged_hashENS1_20_Prime_rehash_policyENS1_17_Hashtable_traitsILb0ELb1ELb1EEEE21_M_insert_unique_nodeEmmPNS1_10_Hash_nodeIjLb0EEEm at Base 4.1.4
_ZNSt13_Bvector_baseISaIbEE13_M_deallocateEv at Base 1.1.3
- _ZNSt5dequeIPKN4spoa5Graph4NodeESaIS4_EE16_M_push_back_auxIJRKS4_EEEvDpOT_ at Base 4.0.5
- _ZNSt5dequeIPN4spoa5Graph4NodeESaIS3_EE16_M_push_back_auxIJRKS3_EEEvDpOT_ at Base 4.0.5
+ (optional)_ZNSt5dequeIPKN4spoa5Graph4NodeESaIS4_EE16_M_push_back_auxIJRKS4_EEEvDpOT_ at Base 4.0.5
+ (optional)_ZNSt5dequeIPKN4spoa5Graph4NodeESaIS4_EE17_M_reallocate_mapEmb at Base 4.1.5
+ (optional)_ZNSt5dequeIPN4spoa5Graph4NodeESaIS3_EE16_M_push_back_auxIJRKS3_EEEvDpOT_ at Base 4.0.5
_ZNSt5dequeIPN4spoa5Graph4NodeESaIS3_EE17_M_reallocate_mapEmb at Base 4.0.5
_ZNSt6vectorIN4spoa7StorageESaIS1_EE17_M_default_appendEm at Base 4.1.4
(optional)_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_appendIJRS5_EEEvDpOT_ at Base 4.1.4
=====================================
debian/patches/shared_and_static.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 08 Jun 2018 13:20:51 +0200
+Last-Update: 2018-06-08
Description: Build shared and static lib
--- spoa.orig/CMakeLists.txt
=====================================
debian/patches/use_debian_packaged_libs.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 08 Jun 2018 13:20:51 +0200
+Last-Update: 2018-06-08
Description: Use Debian packaged libraries
Forwarded: not-needed
--- spoa.orig/CMakeLists.txt
=====================================
debian/watch
=====================================
@@ -1,4 +1,7 @@
-version=4
+Version: 5
-opts="repacksuffix=+ds,dversionmangle=auto,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
- https://github.com/rvaser/spoa/tags .*/v?@ANY_VERSION@@ARCHIVE_EXT@
+Template: Github
+Owner: rvaser
+Project: spoa
+Dversionmangle: auto
+Repacksuffix: +ds
=====================================
meson.build
=====================================
@@ -1,7 +1,7 @@
project(
'spoa',
['cpp'],
- version : '4.1.4',
+ version : '4.1.5',
default_options : [
'buildtype=release',
'warning_level=3',
=====================================
src/simd_alignment_engine_implementation.hpp
=====================================
@@ -1961,10 +1961,10 @@ Alignment SimdAlignmentEngine<A>::Convex(
j_div = j / T::kNumVar;
j_mod = j % T::kNumVar;
if ((j == -1) ||
- (j_mod != T::kNumVar - 1 && E[j_mod] + e_ != E[j_mod + 1]) ||
- (j_mod == T::kNumVar - 1 && E_left[j_mod] + e_ != E[0]) ||
- (j_mod != T::kNumVar - 1 && Q[j_mod] + c_ != Q[j_mod + 1]) ||
- (j_mod == T::kNumVar - 1 && Q_left[j_mod] + c_ != Q[0])) {
+ (((j_mod != T::kNumVar - 1 && E[j_mod] + e_ != E[j_mod + 1]) ||
+ (j_mod == T::kNumVar - 1 && E_left[j_mod] + e_ != E[0])) &&
+ ((j_mod != T::kNumVar - 1 && Q[j_mod] + c_ != Q[j_mod + 1]) ||
+ (j_mod == T::kNumVar - 1 && Q_left[j_mod] + c_ != Q[0])))) {
break;
}
}
View it on GitLab: https://salsa.debian.org/med-team/spoa/-/compare/0605386869970233a81f5c88a68ca1c691fe72c9...adf87afe9af84ba6a51337cd62f09cbeee72f700
--
View it on GitLab: https://salsa.debian.org/med-team/spoa/-/compare/0605386869970233a81f5c88a68ca1c691fe72c9...adf87afe9af84ba6a51337cd62f09cbeee72f700
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