[med-svn] [Git][med-team/spoa][master] 5 commits: routine-update: New upstream version

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / spoa


Commits:
42295a4c by Michael R. Crusoe at 2021-01-08T13:24:44+01:00
routine-update: New upstream version

- - - - -
b3265c2c by Michael R. Crusoe at 2021-01-08T13:24:45+01:00
New upstream version 4.0.6+ds
- - - - -
bff1cb22 by Michael R. Crusoe at 2021-01-08T13:24:46+01:00
Update upstream source from tag 'upstream/4.0.6+ds'

Update to upstream version '4.0.6+ds'
with Debian dir 95df5aa35ce71617eebb1ab64a841488656f2591
- - - - -
162d6d51 by Michael R. Crusoe at 2021-01-08T13:25:27+01:00
debian/patches/shared_lib_creation.patch: incorporated upstream, deleted.

- - - - -
31075e8e by Michael R. Crusoe at 2021-01-08T13:25:47+01:00
routine-update: Ready to upload to unstable

- - - - -


6 changed files:

- .travis.yml
- CMakeLists.txt
- README.md
- debian/changelog
- debian/patches/series
- − debian/patches/shared_lib_creation.patch


Changes:

=====================================
.travis.yml
=====================================
@@ -34,7 +34,7 @@ matrix:
 
 before_install:
   - eval "${SET_COMPILER}"
-  - git clone https://github.com/google/googletest && cd googletest && mkdir build && cd build
+  - git clone https://github.com/google/googletest && cd googletest && mkdir build && cd build && git checkout 703bd9c
   - cmake -DCMAKE_CXX_FLAGS="-std=c++11" .. && make && sudo make install
   - cd ../../
 


=====================================
CMakeLists.txt
=====================================
@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.9)
 
-project(spoa VERSION 4.0.5
+project(spoa VERSION 4.0.6
              LANGUAGES CXX
              DESCRIPTION "Spoa is a c++ library (and tool) for SIMD vectorized partial order alignment.")
 
@@ -61,7 +61,7 @@ target_include_directories(${PROJECT_NAME} PUBLIC
 target_link_libraries(${PROJECT_NAME}
   cereal)
 if (BUILD_SHARED_LIBS)
-  set_property(TARGET ${PROJECT_NAME} PROPERTY SOVERSION = "7.0.0")
+  set_property(TARGET ${PROJECT_NAME} PROPERTY SOVERSION "7.0.0")
 endif ()
 
 if (spoa_generate_dispatch)


=====================================
README.md
=====================================
@@ -1,7 +1,7 @@
 # Spoa
 
 [![Latest GitHub release](https://img.shields.io/github/release/rvaser/spoa.svg)](https://github.com/rvaser/spoa/releases/latest)
-[![Build status for gcc/clang](https://travis-ci.org/rvaser/spoa.svg?branch=master)](https://travis-ci.org/rvaser/spoa)
+[![Build status for gcc/clang](https://travis-ci.com/rvaser/spoa.svg?branch=master)](https://travis-ci.com/rvaser/spoa)
 [![Published in Genome Research](https://img.shields.io/badge/published%20in-Genome%20Research-blue.svg)](https://doi.org/10.1101/gr.214270.116)
 
 Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which is used to generate consensus sequences (as described in 10.1093/bioinformatics/btg109). It supports three alignment modes: local (Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment (overlap), and three gap modes: linear, affine and convex (piecewise affine). It also supports Intel SSE4.1+ and AVX2 vectorization (marginally faster due to high latency shifts), [SIMDe](https://github.com/simd-everywhere/simde) and dispatching.


=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+spoa (4.0.6+ds-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * debian/patches/shared_lib_creation.patch: incorporated upstream,
+    deleted.
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Fri, 08 Jan 2021 13:25:47 +0100
+
 spoa (4.0.5+ds-1) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/patches/series
=====================================
@@ -1,4 +1,3 @@
-shared_lib_creation.patch
 fix-ftbfs-gcc-10.patch
 use_debian_packaged_libs.patch
 shared_and_static.patch


=====================================
debian/patches/shared_lib_creation.patch deleted
=====================================
@@ -1,18 +0,0 @@
-From 6f421bfdaeb1f2178d6768ef97c88500a2b5110e Mon Sep 17 00:00:00 2001
-From: rvaser <robert.vaser at gmail.com>
-Date: Mon, 4 Jan 2021 10:47:07 +0800
-Subject: Fix shared lib creation
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index d61e74d..ddd0440 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -61,7 +61,7 @@ target_include_directories(${PROJECT_NAME} PUBLIC
- target_link_libraries(${PROJECT_NAME}
-   cereal)
- if (BUILD_SHARED_LIBS)
--  set_property(TARGET ${PROJECT_NAME} PROPERTY SOVERSION = "7.0.0")
-+  set_property(TARGET ${PROJECT_NAME} PROPERTY SOVERSION "7.0.0")
- endif ()
- 
- if (spoa_generate_dispatch)



View it on GitLab: https://salsa.debian.org/med-team/spoa/-/compare/bed75419522098b096e91b684bb090fa59c44af4...31075e8e0ce71b1cef7b54acaa2f2ff0c78db840

-- 
View it on GitLab: https://salsa.debian.org/med-team/spoa/-/compare/bed75419522098b096e91b684bb090fa59c44af4...31075e8e0ce71b1cef7b54acaa2f2ff0c78db840
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