[med-svn] [Git][med-team/spoa][master] 5 commits: routine-update: New upstream version
Michael R. Crusoe
gitlab at salsa.debian.org
Fri Jan 8 12:29:49 GMT 2021
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
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20210108/0da2b7dd/attachment-0001.html>
More information about the debian-med-commit
mailing list