Skip to content

Commit

Permalink
Update genesis
Browse files Browse the repository at this point in the history
  • Loading branch information
lczech committed Oct 23, 2024
1 parent d2cd10c commit 55ac134
Show file tree
Hide file tree
Showing 2 changed files with 6 additions and 3 deletions.
7 changes: 5 additions & 2 deletions CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -168,7 +168,7 @@ include( "${CMAKE_CURRENT_LIST_DIR}/tools/cmake/DownloadDependency.cmake" )
# These are replaced by tools/cmake/update_dependencies.sh to the hashes that are currently checked out.
# Thus, do not replace the hashes manually!
SET( CLI11_COMMIT_HASH "5cb3efabce007c3a0230e4cc2e27da491c646b6c" ) #CLI11_COMMIT_HASH#
SET( genesis_COMMIT_HASH "059e5b50a33c2826edd931435c11661c7a5b0985" ) #genesis_COMMIT_HASH#
SET( genesis_COMMIT_HASH "f1a5fb82d4b59706e8dbf60d41d094b88022fc94" ) #genesis_COMMIT_HASH#

# Call the github download function, which takes four arguments:
# - LIBPATH : Path to the libracy dir where dependencies are stored.
Expand All @@ -188,7 +188,10 @@ endif (APPLE)
# Dependencies Settings
# --------------------------------------------------------------------------------------------------

# Force to set te options used for genesis. Bit cumbersome in cmake...
# Force to set the options used for genesis. Bit cumbersome in cmake...
# For now, grenedalf is always compiled with C++11, so we deactivate
# the genesis auto detection of the highest available C++ standard here.
set(GENESIS_CPP_STANDARD "11" CACHE BOOL "Use OpenMP." FORCE)
set(GENESIS_USE_OPENMP OFF CACHE BOOL "Use OpenMP." FORCE)

# Add Genesis as dependency.
Expand Down
2 changes: 1 addition & 1 deletion libs/genesis
Submodule genesis updated 51 files
+46 −7 .github/workflows/ci.yaml
+21 −10 CMakeLists.txt
+9 −2 lib/genesis/placement/simulator/distributions.cpp
+9 −8 lib/genesis/population/function/fst_pool_functions.hpp
+4 −3 lib/genesis/population/function/genome_locus.hpp
+3 −2 lib/genesis/sequence/formats/fastq_writer.cpp
+4 −4 lib/genesis/sequence/formats/fastq_writer.hpp
+4 −3 lib/genesis/sequence/formats/fastx_input_view_stream.hpp
+6 −6 lib/genesis/sequence/formats/fastx_output_stream.hpp
+3 −2 lib/genesis/sequence/kmer/bitfield.hpp
+46 −0 lib/genesis/sequence/kmer/canonical_encoding.cpp
+42 −43 lib/genesis/sequence/kmer/canonical_encoding.hpp
+84 −43 lib/genesis/sequence/kmer/extractor.hpp
+38 −50 lib/genesis/sequence/kmer/function.hpp
+22 −64 lib/genesis/sequence/kmer/kmer.hpp
+15 −19 lib/genesis/sequence/kmer/microvariant_scanner.hpp
+267 −0 lib/genesis/taxonomy/accession_lookup.hpp
+356 −0 lib/genesis/taxonomy/formats/accession_lookup_reader.hpp
+174 −58 lib/genesis/taxonomy/formats/ncbi.cpp
+82 −22 lib/genesis/taxonomy/formats/ncbi.hpp
+7 −5 lib/genesis/taxonomy/formats/taxonomy_reader.cpp
+5 −5 lib/genesis/taxonomy/formats/taxopath_generator.cpp
+19 −7 lib/genesis/taxonomy/functions/taxonomy.cpp
+11 −10 lib/genesis/taxonomy/functions/taxonomy.hpp
+42 −12 lib/genesis/taxonomy/printers/nested.cpp
+17 −7 lib/genesis/taxonomy/printers/nested.hpp
+0 −224 lib/genesis/taxonomy/taxon.cpp
+157 −67 lib/genesis/taxonomy/taxon.hpp
+76 −208 lib/genesis/taxonomy/taxonomy.cpp
+186 −64 lib/genesis/taxonomy/taxonomy.hpp
+1 −0 lib/genesis/utils.hpp
+8 −4 lib/genesis/utils/containers/function_cache.hpp
+7 −6 lib/genesis/utils/containers/interval_tree/functions.hpp
+17 −4 lib/genesis/utils/containers/interval_tree/interval.hpp
+10 −15 lib/genesis/utils/containers/optional.hpp
+7 −6 lib/genesis/utils/containers/transform_iterator.hpp
+8 −5 lib/genesis/utils/core/info.cpp
+2 −2 lib/genesis/utils/core/info.hpp
+109 −0 lib/genesis/utils/core/std.hpp
+19 −4 lib/genesis/utils/formats/csv/input_iterator.hpp
+19 −9 lib/genesis/utils/formats/json/document.hpp
+2 −2 lib/genesis/utils/formats/json/iterator.hpp
+3 −2 lib/genesis/utils/io/input_stream.cpp
+5 −4 lib/genesis/utils/io/input_stream.hpp
+16 −10 lib/genesis/utils/io/parser.cpp
+239 −0 lib/genesis/utils/threading/concurrent_vector_guard.hpp
+3 −1 lib/genesis/utils/threading/thread_functions.hpp
+13 −4 lib/genesis/utils/threading/thread_pool.hpp
+81 −78 test/src/sequence/kmer.cpp
+91 −0 test/src/utils/threading/concurrent_vector_guard.cpp
+142 −0 tools/cmake/DetectCppVersion.cmake

0 comments on commit 55ac134

Please sign in to comment.