rseng · github-actions · Feb 21, 2024
diff --git 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
@@ -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 $<TARGET_FILE:${CIFPP_TEST}> --data-dir
-			${CMAKE_CURRENT_SOURCE_DIR}/test)
-
-		add_test(NAME ${CIFPP_TEST} COMMAND $<TARGET_FILE:${CIFPP_TEST}> --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
@@ -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="[email protected]",
       role = c("aut","cre"),

diff --git 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) <doi:10.1080/14780887.2020.1794088> 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
@@ -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
@@ -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
@@ -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)