diff --git a/_repos/github/Griffan/VerifyBamID/CMakeLists.txt b/_repos/github/Griffan/VerifyBamID/CMakeLists.txt index 26c35b50..de845dda 100644 --- a/_repos/github/Griffan/VerifyBamID/CMakeLists.txt +++ b/_repos/github/Griffan/VerifyBamID/CMakeLists.txt @@ -66,6 +66,16 @@ enable_testing() add_test(NAME myTest1 WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND VerifyBamID --DisableSanityCheck --BamFile resource/test/test.bam --SVDPrefix resource/test/hapmap_3.3.b37.dat --Reference resource/test/chr20.fa.gz --NumPC 2) -#add_test( NAME myTest2 +add_test(NAME myTest2 + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} + COMMAND sh -c "diff resource/test/expected/result.Ancestry result.Ancestry && rm result.Ancestry result.selfSM") +add_test(NAME myTest3 + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} + COMMAND VerifyBamID --DisableSanityCheck --PileupFile resource/test/expected/result.Pileup --SVDPrefix resource/test/hapmap_3.3.b37.dat --Reference resource/test/chr20.fa.gz --NumPC 2) +add_test(NAME myTest4 + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} + COMMAND sh -c "diff resource/test/expected/result.Ancestry result.Ancestry && rm result.Ancestry result.selfSM") + +#add_test( NAME myTestPlot # WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} # COMMAND sh ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/run.plot.sh -i ${CMAKE_CURRENT_SOURCE_DIR}/resource/test/hapmap_3.3.b37.dat.V -o ${CMAKE_CURRENT_SOURCE_DIR}/resource/test/hapmap -r 1000g -g grey) diff --git a/_repos/github/PDB-REDO/libcifpp/CMakeLists.txt b/_repos/github/PDB-REDO/libcifpp/CMakeLists.txt index 04cb0ca7..b19a4ea8 100644 --- a/_repos/github/PDB-REDO/libcifpp/CMakeLists.txt +++ b/_repos/github/PDB-REDO/libcifpp/CMakeLists.txt @@ -27,7 +27,7 @@ cmake_minimum_required(VERSION 3.16) # set the project name project( libcifpp - VERSION 6.1.0 + VERSION 7.0.0 LANGUAGES CXX) list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake") @@ -546,55 +546,7 @@ if(NOT PROJECT_IS_TOP_LEVEL) endif() if(BUILD_TESTING) - # We're using the older version 2 of Catch2 - FetchContent_Declare( - Catch2 - GIT_REPOSITORY https://github.com/catchorg/Catch2.git - GIT_TAG v2.13.9) - - FetchContent_MakeAvailable(Catch2) - - list( - APPEND - CIFPP_tests - unit-v2 - unit-3d - format - model - rename-compound - sugar - spinner - validate-pdbx) - - foreach(CIFPP_TEST IN LISTS CIFPP_tests) - set(CIFPP_TEST "${CIFPP_TEST}-test") - set(CIFPP_TEST_SOURCE "${CMAKE_CURRENT_SOURCE_DIR}/test/${CIFPP_TEST}.cpp") - - add_executable( - ${CIFPP_TEST} ${CIFPP_TEST_SOURCE} - "${CMAKE_CURRENT_SOURCE_DIR}/test/test-main.cpp") - - target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp::cifpp - Catch2::Catch2) - target_include_directories(${CIFPP_TEST} PRIVATE "${EIGEN_INCLUDE_DIR}") - - if(MSVC) - # Specify unwind semantics so that MSVC knowns how to handle exceptions - target_compile_options(${CIFPP_TEST} PRIVATE /EHsc) - endif() - - add_custom_target( - "run-${CIFPP_TEST}" - DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/Run${CIFPP_TEST}.touch ${CIFPP_TEST}) - - add_custom_command( - OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/Run${CIFPP_TEST}.touch - COMMAND $ --data-dir - ${CMAKE_CURRENT_SOURCE_DIR}/test) - - add_test(NAME ${CIFPP_TEST} COMMAND $ --data-dir - ${CMAKE_CURRENT_SOURCE_DIR}/test) - endforeach() + add_subdirectory(test) endif() # Optionally install the update scripts for CCD and dictionary files diff --git a/_repos/github/fogellab/multiWGCNA/DESCRIPTION b/_repos/github/fogellab/multiWGCNA/DESCRIPTION index f334ffb0..9372dfae 100644 --- a/_repos/github/fogellab/multiWGCNA/DESCRIPTION +++ b/_repos/github/fogellab/multiWGCNA/DESCRIPTION @@ -1,7 +1,7 @@ Package: multiWGCNA Type: Package Title: multiWGCNA -Version: 1.1.3 +Version: 1.1.4 Authors@R: c( person("Dario", "Tommasini", email="dtommasini0@gmail.com", role = c("aut","cre"), diff --git a/_repos/github/markheckmann/OpenRepGrid.ic/DESCRIPTION b/_repos/github/markheckmann/OpenRepGrid.ic/DESCRIPTION index 71537508..737ed25a 100644 --- a/_repos/github/markheckmann/OpenRepGrid.ic/DESCRIPTION +++ b/_repos/github/markheckmann/OpenRepGrid.ic/DESCRIPTION @@ -21,8 +21,8 @@ Authors@R: c(person( Description: Shiny UI to identify cliques of related constructs in repertory grid data. See Burr, King, & Heckmann (2020) for a description of the interpretive clustering (IC) method. -Version: 0.6.1 -Date: 2022-10-25 +Version: 0.6.2 +Date: 2024-02-18 Imports: graphics, grDevices, @@ -59,4 +59,4 @@ Suggests: Encoding: UTF-8 URL: https://github.com/markheckmann/OpenRepGrid.ic BugReports: https://github.com/markheckmann/OpenRepGrid.ic/issues -RoxygenNote: 7.2.1 +RoxygenNote: 7.3.0 diff --git a/_repos/github/mfem/mfem/CMakeLists.txt b/_repos/github/mfem/mfem/CMakeLists.txt index 6bd37563..a7098d6e 100644 --- a/_repos/github/mfem/mfem/CMakeLists.txt +++ b/_repos/github/mfem/mfem/CMakeLists.txt @@ -18,9 +18,10 @@ set(USER_CONFIG "${CMAKE_CURRENT_SOURCE_DIR}/config/user.cmake" CACHE PATH "Path to optional user configuration file.") # Require C++11 and disable compiler-specific extensions -set(CMAKE_CXX_STANDARD 11) -set(CMAKE_CXX_STANDARD_REQUIRED ON) -set(CMAKE_CXX_EXTENSIONS OFF) +set(CMAKE_CXX_STANDARD 11 CACHE STRING "C++ standard to use.") +set(CMAKE_CXX_STANDARD_REQUIRED ON CACHE BOOL + "Force the use of the chosen C++ standard.") +set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Enable C++ standard extensions.") # Load user settings before the defaults - this way the defaults will not # overwrite the user set options. If the user has not set all options, we still @@ -93,7 +94,7 @@ if ((MFEM_USE_SUNDIALS OR MFEM_USE_RAJA OR MFEM_USE_UMPIRE) AND ("${CMAKE_CXX_STANDARD}" LESS "14")) - set(CMAKE_CXX_STANDARD 14) + set(CMAKE_CXX_STANDARD 14 CACHE STRING "C++ standard to use." FORCE) endif() # Include xSDK default CMake file. @@ -104,7 +105,8 @@ enable_language(CXX) if (MINGW) # MinGW GCC does not expose the functions jn/_jn, yn/_yn (used in Example # 25/25p) unless we use '-std=gnu++11': - set(CMAKE_CXX_EXTENSIONS ON) + set(CMAKE_CXX_EXTENSIONS ON + CACHE BOOL "Enable C++ standard extensions." FORCE) endif() if (MFEM_USE_CUDA) if (MFEM_USE_HIP) @@ -115,9 +117,11 @@ if (MFEM_USE_CUDA) set(CMAKE_CUDA_HOST_COMPILER ${CMAKE_CXX_COMPILER}) endif() enable_language(CUDA) - set(CMAKE_CUDA_STANDARD ${CMAKE_CXX_STANDARD}) - set(CMAKE_CUDA_STANDARD_REQUIRED ON) - set(CMAKE_CUDA_EXTENSIONS OFF) + set(CMAKE_CUDA_STANDARD ${CMAKE_CXX_STANDARD} CACHE STRING + "CUDA standard to use.") + set(CMAKE_CUDA_STANDARD_REQUIRED ON CACHE BOOL + "Force the use of the chosen CUDA standard.") + set(CMAKE_CUDA_EXTENSIONS OFF CACHE BOOL "Enable CUDA standard extensions.") set(CUDA_FLAGS "--expt-extended-lambda") if (CMAKE_VERSION VERSION_LESS 3.18.0) set(CUDA_FLAGS "-arch=${CUDA_ARCH} ${CUDA_FLAGS}") diff --git a/_repos/github/milkschen/leviosam2/CMakeLists.txt b/_repos/github/milkschen/leviosam2/CMakeLists.txt index ce0ecc25..859f2d3b 100644 --- a/_repos/github/milkschen/leviosam2/CMakeLists.txt +++ b/_repos/github/milkschen/leviosam2/CMakeLists.txt @@ -4,9 +4,18 @@ project(leviosam2 CXX C) set(PROJECT_URL "https://github.com/milkschen/leviosam2") set(PROJECT_DESCRIPTION "leviosam2") -set(PROJECT_VER "0.4.2") set(CMAKE_CXX_STANDARD 14) +# Get the latest abbreviated commit hash of the working branch +execute_process( + COMMAND git log -1 --format=%h + WORKING_DIRECTORY ${CMAKE_CURRENT_LIST_DIR} + OUTPUT_VARIABLE GIT_HASH + OUTPUT_STRIP_TRAILING_WHITESPACE +) + +set(PROJECT_VER "0.4.2-${GIT_HASH}") + find_library(HTS_LIB hts) if(NOT HTS_LIB) message(FATAL_ERROR "htslib library not found. Please specify -D CMAKE_LIBRARY_PATH and -D CMAKE_INCLUDE_PATH in the CMake command") @@ -163,14 +172,15 @@ else() endif() -file(GLOB LIB_SOURCES src/reconcile.cpp src/lift_bed.cpp src/collate.cpp src/chain.cpp - src/leviosam_utils.cpp src/bed.cpp src/lift_bed.cpp src/aln.cpp - src/yaml.cpp +file(GLOB LIB_SOURCES src/reconcile.cpp src/lift_bed.cpp src/collate.cpp + src/chain.cpp src/leviosam_utils.cpp src/bed.cpp + src/lift_bed.cpp src/aln.cpp src/cigar.cpp src/yaml.cpp src/ksw2_extd2_sse.c src/ksw2_extz2_sse.c src/ksw2_extz.c src/bam_md.c src/bam_aux.c src/gzstream.C) file(GLOB LIB_HEADERS src/leviosam.hpp - src/reconcile.hpp src/lift_bed.hpp src/collate.hpp src/chain.hpp - src/leviosam_utils.hpp src/bed.hpp src/lift_bed.hpp src/aln.hpp + src/reconcile.hpp src/lift_bed.hpp src/collate.hpp + src/chain.hpp src/leviosam_utils.hpp src/bed.hpp + src/lift_bed.hpp src/aln.hpp src/cigar.hpp src/yaml.hpp src/rapidyaml.hpp src/ksw.h src/bam.h src/IITree.h src/gzstream.h) @@ -241,6 +251,17 @@ add_test(NAME chain_test COMMAND chain_test WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/testdata ) +# cigar_test +add_executable(cigar_test src/cigar_test.cpp) +target_link_libraries(cigar_test lvsam) +target_link_libraries(cigar_test ${HTS_LIB}) +target_link_libraries(cigar_test ${SDSL_LIB}) +target_link_libraries(cigar_test gtest gtest_main) + +add_test(NAME cigar_test COMMAND cigar_test + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/testdata +) + # bed_test add_executable(bed_test src/bed_test.cpp) target_link_libraries(bed_test lvsam) diff --git a/_repos/github/parthenon-hpc-lab/parthenon/CMakeLists.txt b/_repos/github/parthenon-hpc-lab/parthenon/CMakeLists.txt index 0f6b0695..7d0d4ab3 100644 --- a/_repos/github/parthenon-hpc-lab/parthenon/CMakeLists.txt +++ b/_repos/github/parthenon-hpc-lab/parthenon/CMakeLists.txt @@ -62,9 +62,9 @@ include(cmake/Format.cmake) include(cmake/Lint.cmake) # regression test reference data -set(REGRESSION_GOLD_STANDARD_VER 20 CACHE STRING "Version of gold standard to download and use") +set(REGRESSION_GOLD_STANDARD_VER 21 CACHE STRING "Version of gold standard to download and use") set(REGRESSION_GOLD_STANDARD_HASH - "SHA512=e5e421f3c0be01e4708965542bb8b1b79b5c96de97091e46972e375c7616588d026a9a8e29226d9c7ef75346bc859fd9af72acdc7e95e0d783b5ef29aa4630b1" + "SHA512=e16b14272915b4607965e5900961402f6da96dc13da8ea3c3d213d61f82d3a1dded08c40a9ab644aa3409d93a045bba360a90a43dc289b24f525878f9ba50890" CACHE STRING "Hash of default gold standard file to download") option(REGRESSION_GOLD_STANDARD_SYNC "Automatically sync gold standard files." ON)