[med-svn] [Git][med-team/libwfa2][master] 6 commits: New upstream version 2.3.2

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / libwfa2


Commits:
34b70b7e by Andreas Tille at 2023-02-04T09:12:16+01:00
New upstream version 2.3.2
- - - - -
7c3b640c by Andreas Tille at 2023-02-04T09:12:16+01:00
routine-update: New upstream version

- - - - -
785cff29 by Andreas Tille at 2023-02-04T09:12:32+01:00
Update upstream source from tag 'upstream/2.3.2'

Update to upstream version '2.3.2'
with Debian dir 04124c3970a4032e8466ad35e6a0e1a070233249
- - - - -
538a38aa by Andreas Tille at 2023-02-04T09:12:48+01:00
Set upstream metadata fields: Repository.

Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html

- - - - -
4553b3a4 by Andreas Tille at 2023-02-04T09:13:36+01:00
Upstream has applied patch

- - - - -
436d506c by Andreas Tille at 2023-02-04T09:15:00+01:00
Upload to unstable

- - - - -


5 changed files:

- CMakeLists.txt
- debian/changelog
- − debian/patches/series
- − debian/patches/shared_and_static.patch
- debian/upstream/metadata


Changes:

=====================================
CMakeLists.txt
=====================================
@@ -1,3 +1,10 @@
+# For Debian currently with
+#
+#   cd build
+#   cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo ..
+#   make
+#   make test
+#   make install
 # See below option statements and the README for build information
 
 cmake_minimum_required(VERSION 3.16)
@@ -83,8 +90,16 @@ include_directories(.)
 
 file(GLOB INCLUDES
   wavefront/*.h*
+  )
+file(GLOB UTILS_INCLUDES
   utils/*.h*
   )
+file(GLOB ALIGNMENT_INCLUDES
+  alignment/*.h*
+  )
+file(GLOB SYSTEM_INCLUDES
+  system/*.h*
+  )
 
 set(wfa2lib_SOURCE
   wavefront/wavefront_align.c
@@ -111,12 +126,30 @@ set(wfa2lib_SOURCE
   wavefront/wavefront_plot.c
   wavefront/wavefront_slab.c
   wavefront/wavefront_unialign.c
+  system/mm_stack.c
+  system/mm_allocator.c
+  system/profiler_counter.c
+  system/profiler_timer.c
+  utils/bitmap.c
+  utils/dna_text.c
+  utils/sequence_buffer.c
+  utils/vector.c
+  utils/commons.c
+  utils/heatmap.c
+  utils/string_padded.c
+  alignment/affine2p_penalties.c
+  alignment/affine_penalties.c
+  alignment/cigar.c
+  alignment/score_matrix.c
 )
 
-
-add_library(wfa
+add_library(wfa2_static
     ${wfa2lib_SOURCE}
     )
+add_library(wfa2 SHARED ${wfa2lib_SOURCE})
+set_target_properties(wfa2_static PROPERTIES OUTPUT_NAME wfa2)
+set_target_properties(wfa2 PROPERTIES SOVERSION 0)
+
 
 # ---- Get version
 
@@ -148,6 +181,10 @@ add_wfa_test()
 
 # ---- Install
 
-install(TARGETS wfa ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} )
+install(TARGETS wfa2_static ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} )
+install(TARGETS wfa2 ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} )
 
-install(FILES ${INCLUDES} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/wfa2lib)
+install(FILES ${INCLUDES} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/wfa2lib/wavefront)
+install(FILES ${UTILS_INCLUDES} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/wfa2lib/utils)
+install(FILES ${ALIGNMENT_INCLUDES} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/wfa2lib/alignment)
+install(FILES ${SYSTEM_INCLUDES} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/wfa2lib/system)


=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+libwfa2 (2.3.2-1) unstable; urgency=medium
+
+  * New upstream version
+
+ -- Andreas Tille <tille at debian.org>  Sat, 04 Feb 2023 09:14:13 +0100
+
 libwfa2 (2.3.1-2) unstable; urgency=medium
 
   * Source-only upload


=====================================
debian/patches/series deleted
=====================================
@@ -1 +0,0 @@
-shared_and_static.patch


=====================================
debian/patches/shared_and_static.patch deleted
=====================================
@@ -1,30 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 26 Jan 2023 18:01:17 +0100
-Description: Create shared and static lib
-
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -114,9 +114,13 @@ set(wfa2lib_SOURCE
- )
- 
- 
--add_library(wfa
-+add_library(wfa2_static
-     ${wfa2lib_SOURCE}
-     )
-+add_library(wfa2 SHARED ${wfa2lib_SOURCE})
-+set_target_properties(wfa2_static PROPERTIES OUTPUT_NAME wfa2)
-+set_target_properties(wfa2 PROPERTIES SOVERSION 0)
-+
- 
- # ---- Get version
- 
-@@ -148,6 +152,7 @@ add_wfa_test()
- 
- # ---- Install
- 
--install(TARGETS wfa ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} )
-+install(TARGETS wfa2_static ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} )
-+install(TARGETS wfa2 ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} )
- 
- install(FILES ${INCLUDES} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/wfa2lib)


=====================================
debian/upstream/metadata
=====================================
@@ -1,4 +1,5 @@
 ---
 Bug-Database: https://github.com/smarco/WFA2-lib/issues
 Bug-Submit: https://github.com/smarco/WFA2-lib/issues/new
+Repository: https://github.com/smarco/WFA2-lib.git
 Repository-Browse: https://github.com/smarco/WFA2-lib



View it on GitLab: https://salsa.debian.org/med-team/libwfa2/-/compare/8486a48ea48db4f2f7b23a3f27a9cae44e8b9209...436d506caf3b9532f0156825fe15167c2e42236c

-- 
View it on GitLab: https://salsa.debian.org/med-team/libwfa2/-/compare/8486a48ea48db4f2f7b23a3f27a9cae44e8b9209...436d506caf3b9532f0156825fe15167c2e42236c
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