[med-svn] [Git][med-team/libwfa2][master] 2 commits: --no-parallel is also needed with cmake

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / libwfa2


Commits:
5525c954 by Andreas Tille at 2023-01-26T12:51:47+01:00
--no-parallel is also needed with cmake

- - - - -
67615fd9 by Andreas Tille at 2023-01-26T17:01:35+01:00
Build shared lib and use d-shlibs

- - - - -


5 changed files:

- debian/control
- − debian/libwfa2-dev.install
- + debian/patches/series
- + debian/patches/shared_and_static.patch
- debian/rules


Changes:

=====================================
debian/control
=====================================
@@ -4,6 +4,7 @@ Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
+               d-shlibs,
                cmake
 Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/libwfa2
@@ -11,8 +12,9 @@ Vcs-Git: https://salsa.debian.org/med-team/libwfa2.git
 Homepage: https://github.com/smarco/WFA2-lib
 Rules-Requires-Root: no
 
-Package: libwfa2-dev
+Package: libwfa2-0
 Architecture: any
+Section: libs
 Depends: ${shlibs:Depends},
          ${misc:Depends}
 Description: exact gap-affine algorithm
@@ -30,3 +32,25 @@ Description: exact gap-affine algorithm
  based algorithm (like Smith-Waterman or Needleman Wunsch). In contrast,
  the right panel shows the cells computed by the WFA algorithm to obtain
  the same result (i.e., the optimal alignment).
+
+Package: libwfa2-dev
+Architecture: any
+Section: libdevel
+Depends: libwfa2-0 (= ${binary:Version}),
+         ${shlibs:Depends},
+         ${misc:Depends}
+Description: exact gap-affine algorithm
+ The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm
+ that takes advantage of homologous regions between the sequences to
+ accelerate the alignment process. Unlike to traditional dynamic
+ programming algorithms that run in quadratic time, the WFA runs in time
+ O(ns+s^2), proportional to the sequence length n and the alignment score
+ s, using O(s^2) memory (or O(s) using the ultralow/BiWFA mode).
+ Moreover, the WFA algorithm exhibits simple computational patterns that
+ the modern compilers can automatically vectorize for different
+ architectures without adapting the code. To intuitively illustrate why
+ the WFA algorithm is so interesting, look at the following figure. The
+ left panel shows the cells computed by a classical dynamic programming
+ based algorithm (like Smith-Waterman or Needleman Wunsch). In contrast,
+ the right panel shows the cells computed by the WFA algorithm to obtain
+ the same result (i.e., the optimal alignment).


=====================================
debian/libwfa2-dev.install deleted
=====================================
@@ -1,3 +0,0 @@
-#lib/*.a			usr/lib/${DEB_HOST_MULTIARCH}/
-#wavefront/*.h*		usr/include/wavefront
-#bindings/cpp/*.hpp	usr/include/bindings/cpp


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


=====================================
debian/patches/shared_and_static.patch
=====================================
@@ -0,0 +1,26 @@
+--- 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/rules
=====================================
@@ -9,4 +9,13 @@ include /usr/share/dpkg/default.mk
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 %:
-	dh $@
+	dh $@ --buildsystem=cmake
+
+override_dh_install:
+	dh_install
+	d-shlibmove --commit \
+		    --multiarch \
+		    --devunversioned \
+		    --exclude-la \
+		    --movedev debian/tmp/usr/include usr \
+		    debian/tmp/usr/lib/*/*.so



View it on GitLab: https://salsa.debian.org/med-team/libwfa2/-/compare/d75e37fbdb32d4d49b12fc291eb5e3c265223ed1...67615fd921256c9294199e06e934718464f529f3

-- 
View it on GitLab: https://salsa.debian.org/med-team/libwfa2/-/compare/d75e37fbdb32d4d49b12fc291eb5e3c265223ed1...67615fd921256c9294199e06e934718464f529f3
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