[med-svn] [Git][med-team/seqwish][master] 2 commits: Build-Depends: libiitii-dev

Andreas Tille gitlab at salsa.debian.org
Tue Jun 9 22:22:39 BST 2020 


Andreas Tille pushed to branch master at Debian Med / seqwish


Commits:
58354c56 by Andreas Tille at 2020-06-09T23:05:23+02:00
Build-Depends: libiitii-dev

- - - - -
4ba6ba4a by Andreas Tille at 2020-06-09T23:22:12+02:00
Use Debian packaged iitii, add more todo links

- - - - -


4 changed files:

- CMakeLists.txt
- debian/changelog
- debian/control
- debian/patches/use_debian_packaged_libs.patch


Changes:

=====================================
CMakeLists.txt
=====================================
@@ -25,6 +25,7 @@ include_directories("${PROJECT_SOURCE_DIR}")
 # Add external projects
 include(${CMAKE_ROOT}/Modules/ExternalProject.cmake)
 
+if(!DEBIAN_BUILD)
 # sdsl-lite (full build using its cmake config)
 ExternalProject_Add(sdsl-lite
   SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/sdsl-lite"
@@ -36,6 +37,11 @@ set(sdsl-lite_INCLUDE "${INSTALL_DIR}/src/sdsl-lite-build/include")
 set(sdsl-lite-divsufsort_INCLUDE "${INSTALL_DIR}/src/sdsl-lite-build/external/libdivsufsort/include")
 set(sdsl-lite_LIB "${INSTALL_DIR}/src/sdsl-lite-build/lib")
 set(sdsl-lite-divsufsort_LIB "${INSTALL_DIR}/src/sdsl-lite-build/external/libdivsufsort/lib")
+else()
+message("Use Debian packaged sdsl-lite")
+message("=================================")
+# FIXME: Not yet tested
+# add_custom_target(libsdsl)
 
 # taywee's C++ args library, header only
 ExternalProject_Add(tayweeargs
@@ -52,6 +58,7 @@ ExternalProject_Add(gzipreader
   INSTALL_COMMAND "")
 ExternalProject_Get_property(gzipreader SOURCE_DIR)
 set(gzipreader_INCLUDE "${SOURCE_DIR}")
+endif()
 
 # mmmulti (memory mapped multimap, multiset, and interval tree)
 ExternalProject_Add(mmmulti
@@ -63,6 +70,7 @@ ExternalProject_Add(mmmulti
 ExternalProject_Get_property(mmmulti SOURCE_DIR)
 set(mmmulti_INCLUDE "${SOURCE_DIR}/src")
 
+if(!DEBIAN_BUILD)
 # iitii, like cgranges but with interpolation and memory mapping
 ExternalProject_Add(iitii
   SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/iitii"
@@ -72,6 +80,7 @@ ExternalProject_Add(iitii
   CONFIGURE_COMMAND "")
 ExternalProject_Get_property(iitii SOURCE_DIR)
 set(iitii_INCLUDE "${SOURCE_DIR}/src")
+endif()
 
 ExternalProject_Add(mmap_allocator
   SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/mmap_allocator"
@@ -81,6 +90,7 @@ ExternalProject_Get_property(mmap_allocator INSTALL_DIR)
 set(mmap_allocator_INCLUDE "${INSTALL_DIR}/include/mmap_allocator")
 set(mmap_allocator_LIB "${INSTALL_DIR}/lib")
 
+if(!DEBIAN_BUILD)
 # In-place Parallel Super Scalar Samplesort (IPS⁴o), header only
 ExternalProject_Add(ips4o
   SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/ips4o"
@@ -109,6 +119,7 @@ ExternalProject_Add(atomicbitvector
   CONFIGURE_COMMAND "")
 ExternalProject_Get_property(atomicbitvector SOURCE_DIR)
 set(atomicbitvector_INCLUDE "${SOURCE_DIR}/include")
+endif()
 
 # atomic queue library
 ExternalProject_Add(atomicqueue


=====================================
debian/changelog
=====================================
@@ -3,7 +3,8 @@ seqwish (0.6-1) UNRELEASED; urgency=medium
   * Initial release (Closes: #<bug>)
   TODO:
    * https://github.com/ekg/mmmulti
-   
-   ... and more
+   * https://github.com/max0x7ba/atomic_queue.git
+   * https://github.com/skarupke/flat_hash_map
+   * https://github.com/ekg/paryfor.git
 
  -- Andreas Tille <tille at debian.org>  Sun, 24 May 2020 16:17:07 +0200


=====================================
debian/control
=====================================
@@ -9,6 +9,7 @@ Build-Depends: debhelper-compat (= 12),
                libargs-dev,
                libatomicbitvector-dev,
                libbbhash-dev,
+               libiitii-dev,
                libips4o-dev,
                libgzstream-dev
 Standards-Version: 4.5.0


=====================================
debian/patches/use_debian_packaged_libs.patch
=====================================
@@ -8,7 +8,7 @@
  # sdsl-lite (full build using its cmake config)
  ExternalProject_Add(sdsl-lite
    SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/sdsl-lite"
-@@ -36,7 +37,14 @@ set(sdsl-lite_INCLUDE "${INSTALL_DIR}/sr
+@@ -36,6 +37,11 @@ set(sdsl-lite_INCLUDE "${INSTALL_DIR}/sr
  set(sdsl-lite-divsufsort_INCLUDE "${INSTALL_DIR}/src/sdsl-lite-build/external/libdivsufsort/include")
  set(sdsl-lite_LIB "${INSTALL_DIR}/src/sdsl-lite-build/lib")
  set(sdsl-lite-divsufsort_LIB "${INSTALL_DIR}/src/sdsl-lite-build/external/libdivsufsort/lib")
@@ -17,33 +17,46 @@
 +message("=================================")
 +# FIXME: Not yet tested
 +# add_custom_target(libsdsl)
-+endif()
  
-+if(!DEBIAN_BUILD)
  # taywee's C++ args library, header only
  ExternalProject_Add(tayweeargs
-   SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/args"
-@@ -52,6 +60,7 @@ ExternalProject_Add(gzipreader
+@@ -52,6 +58,7 @@ ExternalProject_Add(gzipreader
    INSTALL_COMMAND "")
  ExternalProject_Get_property(gzipreader SOURCE_DIR)
  set(gzipreader_INCLUDE "${SOURCE_DIR}")
-+endif
++endif()
  
  # mmmulti (memory mapped multimap, multiset, and interval tree)
  ExternalProject_Add(mmmulti
-@@ -90,6 +99,7 @@ ExternalProject_Add(ips4o
- ExternalProject_Get_property(ips4o SOURCE_DIR)
- set(ips4o_INCLUDE "${SOURCE_DIR}")
+@@ -63,6 +70,7 @@ ExternalProject_Add(mmmulti
+ ExternalProject_Get_property(mmmulti SOURCE_DIR)
+ set(mmmulti_INCLUDE "${SOURCE_DIR}/src")
  
 +if(!DEBIAN_BUILD)
- # BBHash perfect hasher
- ExternalProject_Add(bbhash
-   SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/BBHash"
+ # iitii, like cgranges but with interpolation and memory mapping
+ ExternalProject_Add(iitii
+   SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/iitii"
+@@ -72,6 +80,7 @@ ExternalProject_Add(iitii
+   CONFIGURE_COMMAND "")
+ ExternalProject_Get_property(iitii SOURCE_DIR)
+ set(iitii_INCLUDE "${SOURCE_DIR}/src")
++endif()
+ 
+ ExternalProject_Add(mmap_allocator
+   SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/mmap_allocator"
+@@ -81,6 +90,7 @@ ExternalProject_Get_property(mmap_alloca
+ set(mmap_allocator_INCLUDE "${INSTALL_DIR}/include/mmap_allocator")
+ set(mmap_allocator_LIB "${INSTALL_DIR}/lib")
+ 
++if(!DEBIAN_BUILD)
+ # In-place Parallel Super Scalar Samplesort (IPS⁴o), header only
+ ExternalProject_Add(ips4o
+   SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/ips4o"
 @@ -109,6 +119,7 @@ ExternalProject_Add(atomicbitvector
    CONFIGURE_COMMAND "")
  ExternalProject_Get_property(atomicbitvector SOURCE_DIR)
  set(atomicbitvector_INCLUDE "${SOURCE_DIR}/include")
-+endif
++endif()
  
  # atomic queue library
  ExternalProject_Add(atomicqueue



View it on GitLab: https://salsa.debian.org/med-team/seqwish/-/compare/d22cd37f6eb2e5980516aabd2b05ea3bbb969523...4ba6ba4a7654157a724c2178a31ba95ef8045de7

-- 
View it on GitLab: https://salsa.debian.org/med-team/seqwish/-/compare/d22cd37f6eb2e5980516aabd2b05ea3bbb969523...4ba6ba4a7654157a724c2178a31ba95ef8045de7
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