Cleanup in root folderpjotrp-w-claude

5 files changed, 0 insertions, 224 deletions

diff --git a/.guix-shell b/.guix-shell
deleted file mode 100644
index dc03df2..0000000
--- a/.guix-shell
+++ /dev/null
@@ -1 +0,0 @@
-~/opt/guix/bin/guix environment -C guix --ad-hoc guile
diff --git a/VERSION b/VERSION
deleted file mode 100644
index 55f4bc9..0000000
--- a/VERSION
+++ /dev/null
@@ -1 +0,0 @@
-fada73a28020a2996c708d8c0a992d38a2cdd05d
diff --git a/seqwish-paryfor-riscv.diff b/seqwish-paryfor-riscv.diff
deleted file mode 100644
index cecf806..0000000
--- a/seqwish-paryfor-riscv.diff
+++ /dev/null
@@ -1,20 +0,0 @@
-diff --git a/deps/paryfor/paryfor.hpp b/deps/paryfor/paryfor.hpp
-index b8ced09..0536580 100644
---- a/deps/paryfor/paryfor.hpp
-+++ b/deps/paryfor/paryfor.hpp
-@@ -51,6 +51,15 @@ static inline void spin_loop_pause() noexcept {
- }
- } // namespace atomic_queue
- } // namespace paryfor
-+#elif defined(__riscv) && (__riscv_xlen == 64)
-+namespace paryfor {
-+namespace atomic_queue {
-+constexpr int CACHE_LINE_SIZE = 64;
-+static inline void spin_loop_pause() noexcept {
-+    asm volatile ("nop" ::: "memory");
-+}
-+}
-+}
- #else
- #error "Unknown CPU architecture."
- #endif
diff --git a/seqwish-shared-library.diff b/seqwish-shared-library.diff
deleted file mode 100644
index be982de..0000000
--- a/seqwish-shared-library.diff
+++ /dev/null
@@ -1,195 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 09eafb5..a39f90f 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -7,6 +7,8 @@ project(seqwish)
- # We build using c++14
- set(CMAKE_CXX_STANDARD 14)
- 
-+include(GNUInstallDirs)
-+
- set(THREADS_PREFER_PTHREAD_FLAG ON)
- find_package(Threads REQUIRED)
- 
-@@ -26,6 +28,8 @@ if(NOT DEFINED EXTRA_FLAGS)
-           "Extra compilation flags for C and CXX." FORCE)
- endif()
- 
-+set(SEQWISH_LINK_SHARED_LIBRARY OFF CACHE BOOL "Do not link against the libseqwish shared library")
-+
- if (${CMAKE_BUILD_TYPE} MATCHES Release)
-   set(EXTRA_FLAGS "-Ofast ${EXTRA_FLAGS}")
-   set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG") # reset CXX_FLAGS to replace -O3 with -Ofast
-@@ -82,7 +86,7 @@ include(${CMAKE_ROOT}/Modules/ExternalProject.cmake)
- # sdsl-lite (full build using its cmake config)
- ExternalProject_Add(sdsl-lite
-   SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/sdsl-lite"
--  CMAKE_ARGS "${CMAKE_ARGS};-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>"
-+  CMAKE_ARGS "${CMAKE_ARGS};-DCMAKE_CXX_FLAGS=-fPIC;-DCMAKE_C_FLAGS=-fPIC;-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>"
-   UPDATE_COMMAND ""
-   INSTALL_COMMAND "")
- ExternalProject_Get_property(sdsl-lite INSTALL_DIR)
-@@ -203,27 +207,125 @@ set(mio_INCLUDE "${SOURCE_DIR}/include")
- #set(CMAKE_BUILD_TYPE Debug)
- set(CMAKE_BUILD_TYPE Release)
- 
-+# set up our target libraries and specify its dependencies and includes
-+add_library( libseqwish_static
-+  ${CMAKE_SOURCE_DIR}/src/utils.cpp
-+  ${CMAKE_SOURCE_DIR}/src/tempfile.cpp
-+  ${CMAKE_SOURCE_DIR}/src/main.cpp
-+  ${CMAKE_SOURCE_DIR}/src/seqindex.cpp
-+  ${CMAKE_SOURCE_DIR}/src/paf.cpp
-+  ${CMAKE_SOURCE_DIR}/src/sxs.cpp
-+  ${CMAKE_SOURCE_DIR}/src/cigar.cpp
-+  ${CMAKE_SOURCE_DIR}/src/alignments.cpp
-+  ${CMAKE_SOURCE_DIR}/src/pos.cpp
-+  ${CMAKE_SOURCE_DIR}/src/match.cpp
-+  ${CMAKE_SOURCE_DIR}/src/transclosure.cpp
-+  ${CMAKE_SOURCE_DIR}/src/links.cpp
-+  ${CMAKE_SOURCE_DIR}/src/compact.cpp
-+  ${CMAKE_SOURCE_DIR}/src/dna.cpp
-+  ${CMAKE_SOURCE_DIR}/src/gfa.cpp
-+  ${CMAKE_SOURCE_DIR}/src/vgp.cpp
-+  ${CMAKE_SOURCE_DIR}/src/exists.cpp
-+  ${CMAKE_SOURCE_DIR}/src/time.cpp
-+  ${CMAKE_SOURCE_DIR}/src/mmap.cpp
-+  )
-+add_dependencies(libseqwish_static tayweeargs)
-+add_dependencies(libseqwish_static sdsl-lite)
-+add_dependencies(libseqwish_static gzipreader)
-+add_dependencies(libseqwish_static mmmulti)
-+add_dependencies(libseqwish_static iitii)
-+add_dependencies(libseqwish_static ips4o)
-+add_dependencies(libseqwish_static bbhash)
-+add_dependencies(libseqwish_static atomicbitvector)
-+add_dependencies(libseqwish_static atomicqueue)
-+add_dependencies(libseqwish_static ska)
-+add_dependencies(libseqwish_static paryfor)
-+add_dependencies(libseqwish_static mio)
-+target_include_directories(libseqwish_static PUBLIC
-+  "${sdsl-lite_INCLUDE}"
-+  "${sdsl-lite-divsufsort_INCLUDE}"
-+  "${tayweeargs_INCLUDE}"
-+  "${gzipreader_INCLUDE}"
-+  "${ips4o_INCLUDE}"
-+  "${mmmulti_INCLUDE}"
-+  "${iitii_INCLUDE}"
-+  "${bbhash_INCLUDE}"
-+  "${atomicbitvector_INCLUDE}"
-+  "${atomicqueue_INCLUDE}"
-+  "${ska_INCLUDE}"
-+  "${paryfor_INCLUDE}"
-+  "${mio_INCLUDE}")
-+target_link_libraries(libseqwish_static
-+  "${sdsl-lite_LIB}/libsdsl.a"
-+  "${sdsl-lite-divsufsort_LIB}/libdivsufsort.a"
-+  "${sdsl-lite-divsufsort_LIB}/libdivsufsort64.a"
-+  "-latomic"
-+  Threads::Threads
-+  jemalloc
-+  z)
-+set_target_properties(libseqwish_static PROPERTIES OUTPUT_NAME "seqwish")
-+
-+add_library( libseqwish SHARED
-+  ${CMAKE_SOURCE_DIR}/src/utils.cpp
-+  ${CMAKE_SOURCE_DIR}/src/tempfile.cpp
-+  ${CMAKE_SOURCE_DIR}/src/main.cpp
-+  ${CMAKE_SOURCE_DIR}/src/seqindex.cpp
-+  ${CMAKE_SOURCE_DIR}/src/paf.cpp
-+  ${CMAKE_SOURCE_DIR}/src/sxs.cpp
-+  ${CMAKE_SOURCE_DIR}/src/cigar.cpp
-+  ${CMAKE_SOURCE_DIR}/src/alignments.cpp
-+  ${CMAKE_SOURCE_DIR}/src/pos.cpp
-+  ${CMAKE_SOURCE_DIR}/src/match.cpp
-+  ${CMAKE_SOURCE_DIR}/src/transclosure.cpp
-+  ${CMAKE_SOURCE_DIR}/src/links.cpp
-+  ${CMAKE_SOURCE_DIR}/src/compact.cpp
-+  ${CMAKE_SOURCE_DIR}/src/dna.cpp
-+  ${CMAKE_SOURCE_DIR}/src/gfa.cpp
-+  ${CMAKE_SOURCE_DIR}/src/vgp.cpp
-+  ${CMAKE_SOURCE_DIR}/src/exists.cpp
-+  ${CMAKE_SOURCE_DIR}/src/time.cpp
-+  ${CMAKE_SOURCE_DIR}/src/mmap.cpp
-+  ${CMAKE_SOURCE_DIR}/src/version.cpp
-+  )
-+add_dependencies(libseqwish tayweeargs)
-+add_dependencies(libseqwish sdsl-lite)
-+add_dependencies(libseqwish gzipreader)
-+add_dependencies(libseqwish mmmulti)
-+add_dependencies(libseqwish iitii)
-+add_dependencies(libseqwish ips4o)
-+add_dependencies(libseqwish bbhash)
-+add_dependencies(libseqwish atomicbitvector)
-+add_dependencies(libseqwish atomicqueue)
-+add_dependencies(libseqwish ska)
-+add_dependencies(libseqwish paryfor)
-+add_dependencies(libseqwish mio)
-+target_include_directories(libseqwish PUBLIC
-+  "${sdsl-lite_INCLUDE}"
-+  "${sdsl-lite-divsufsort_INCLUDE}"
-+  "${tayweeargs_INCLUDE}"
-+  "${gzipreader_INCLUDE}"
-+  "${ips4o_INCLUDE}"
-+  "${mmmulti_INCLUDE}"
-+  "${iitii_INCLUDE}"
-+  "${bbhash_INCLUDE}"
-+  "${atomicbitvector_INCLUDE}"
-+  "${atomicqueue_INCLUDE}"
-+  "${ska_INCLUDE}"
-+  "${paryfor_INCLUDE}"
-+  "${mio_INCLUDE}")
-+target_link_libraries(libseqwish
-+  "${sdsl-lite_LIB}/libsdsl.a"
-+  "${sdsl-lite-divsufsort_LIB}/libdivsufsort.a"
-+  "${sdsl-lite-divsufsort_LIB}/libdivsufsort64.a"
-+  "-latomic"
-+  Threads::Threads
-+  jemalloc
-+  z)
-+set_target_properties(libseqwish PROPERTIES OUTPUT_NAME "seqwish")
-+
- # set up our target executable and specify its dependencies and includes
- add_executable(seqwish
--  ${CMAKE_SOURCE_DIR}/src/utils.cpp
--  ${CMAKE_SOURCE_DIR}/src/tempfile.cpp
-   ${CMAKE_SOURCE_DIR}/src/main.cpp
--  ${CMAKE_SOURCE_DIR}/src/seqindex.cpp
--  ${CMAKE_SOURCE_DIR}/src/paf.cpp
--  ${CMAKE_SOURCE_DIR}/src/sxs.cpp
--  ${CMAKE_SOURCE_DIR}/src/cigar.cpp
--  ${CMAKE_SOURCE_DIR}/src/alignments.cpp
--  ${CMAKE_SOURCE_DIR}/src/pos.cpp
--  ${CMAKE_SOURCE_DIR}/src/match.cpp
--  ${CMAKE_SOURCE_DIR}/src/transclosure.cpp
--  ${CMAKE_SOURCE_DIR}/src/links.cpp
--  ${CMAKE_SOURCE_DIR}/src/compact.cpp
--  ${CMAKE_SOURCE_DIR}/src/dna.cpp
--  ${CMAKE_SOURCE_DIR}/src/gfa.cpp
--  ${CMAKE_SOURCE_DIR}/src/vgp.cpp
--  ${CMAKE_SOURCE_DIR}/src/exists.cpp
--  ${CMAKE_SOURCE_DIR}/src/time.cpp
--  ${CMAKE_SOURCE_DIR}/src/mmap.cpp
-   ${CMAKE_SOURCE_DIR}/src/version.cpp
-   )
- add_dependencies(seqwish tayweeargs)
-@@ -252,6 +354,11 @@ target_include_directories(seqwish PUBLIC
-   "${ska_INCLUDE}"
-   "${paryfor_INCLUDE}"
-   "${mio_INCLUDE}")
-+if( SEQWISH_LINK_SHARED_LIBRARY )
-+    target_link_libraries( seqwish libseqwish )
-+else()
-+    target_link_libraries( seqwish libseqwish_static )
-+endif()
- target_link_libraries(seqwish
-   "${sdsl-lite_LIB}/libsdsl.a"
-   "${sdsl-lite-divsufsort_LIB}/libdivsufsort.a"
-@@ -269,4 +376,6 @@ endif()
- file(MAKE_DIRECTORY ${CMAKE_SOURCE_DIR}/include)
- execute_process(COMMAND bash ${CMAKE_SOURCE_DIR}/scripts/generate_git_version.sh ${CMAKE_SOURCE_DIR}/include)
- 
--install(TARGETS seqwish DESTINATION bin)
-+install(TARGETS seqwish DESTINATION "${CMAKE_INSTALL_BIDIR}")
-+install(TARGETS libseqwish LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}")
-+install(TARGETS libseqwish_static ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}")
diff --git a/tux02-guix-substitutions-public-key.txt b/tux02-guix-substitutions-public-key.txt
deleted file mode 100644
index ee65299..0000000
--- a/tux02-guix-substitutions-public-key.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-(public-key 
- (ecc 
-  (curve Ed25519)
-  (q #9F56EAB5CE37AA15693C31F451140588240F259676C137E31C0CA70EC4D1B534#)
-  )
- )
-