Merge branch 'develop'

Author: Rob Patro

scripts/fetchPufferfish.sh

@@ -23,11 +23,11 @@ if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then
     rm -fr ${INSTALL_DIR}/src/pufferfish
 fi
 
-#SVER=salmon-v1.8.0
-SVER=develop
+SVER=salmon-v1.9.0
+#SVER=develop
 #SVER=sketch-mode
 
-EXPECTED_SHA256=9c415bf431629929153625b354d8bc96828da2a236e99b5d1e6624311b3e0ad5
+EXPECTED_SHA256=2a862daeff95a19c9b188bc26a5d02fc0ecc5b9c9ae5523a67c9d14e62551c5d
 
 mkdir -p ${EXTERNAL_DIR}
 curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip

src/CMakeLists.txt

@@ -99,15 +99,13 @@ endif()
 
 set (UNIT_TESTS_ENTRY_SRCS
     ${GAT_SOURCE_DIR}/tests/UnitTests.cpp
-    ${GAT_SOURCE_DIR}/tests/catch.hpp
 )
 
 set (UNIT_TESTS_INDIVIDUAL_SRCS
   ${GAT_SOURCE_DIR}/src/FragmentLengthDistribution.cpp
   ${GAT_SOURCE_DIR}/external/install/src/pufferfish/rank9b.cpp
   ${GAT_SOURCE_DIR}/tests/GCSampleTests.cpp
   ${GAT_SOURCE_DIR}/tests/LibraryTypeTests.cpp
-  # ${GAT_SOURCE_DIR}/tests/KmerHistTests.cpp
 )
 
 
@@ -197,7 +195,9 @@ if(HAS_IPO AND (NOT NO_IPO))
   set_property(TARGET salmon PROPERTY INTERPROCEDURAL_OPTIMIZATION True)
 endif()
 
-add_library(UnitTestsMain STATIC ${UNIT_TESTS_ENTRY_SRCS} ${GAT_SOURCE_DIR}/tests/catch.hpp)
+add_library(UnitTestsMain STATIC ${UNIT_TESTS_ENTRY_SRCS})
+target_compile_options(UnitTestsMain PUBLIC "$<$<CONFIG:DEBUG>:${TGT_DEBUG_FLAGS}>")
+target_compile_options(UnitTestsMain PUBLIC "$<$<CONFIG:RELEASE>:${TGT_RELEASE_FLAGS}>")
 
 add_executable(unitTests ${UNIT_TESTS_INDIVIDUAL_SRCS} ${GAT_SOURCE_DIR}/tests/catch.hpp)
 target_compile_options(unitTests PUBLIC "$<$<CONFIG:DEBUG>:${TGT_DEBUG_FLAGS}>")

tests/catch.hpp

@@ -1,6 +1,6 @@
 /*
- *  Catch v2.13.8
- *  Generated: 2022-01-03 21:20:09.589503
+ *  Catch v2.13.9
+ *  Generated: 2022-04-12 22:37:23.260201
  *  ----------------------------------------------------------
  *  This file has been merged from multiple headers. Please don't edit it directly
  *  Copyright (c) 2022 Two Blue Cubes Ltd. All rights reserved.
@@ -15,7 +15,7 @@
 
 #define CATCH_VERSION_MAJOR 2
 #define CATCH_VERSION_MINOR 13
-#define CATCH_VERSION_PATCH 8
+#define CATCH_VERSION_PATCH 9
 
 #ifdef __clang__
 #    pragma clang system_header
@@ -13392,6 +13392,10 @@ namespace Catch {
                     filename.erase(0, lastSlash);
                     filename[0] = '#';
                 }
+                else
+                {
+                    filename.insert(0, "#");
+                }
 
                 auto lastDot = filename.find_last_of('.');
                 if (lastDot != std::string::npos) {
@@ -15387,7 +15391,7 @@ namespace Catch {
     }
 
     Version const& libraryVersion() {
-        static Version version( 2, 13, 8, "", 0 );
+        static Version version( 2, 13, 9, "", 0 );
         return version;
     }
 
@@ -17890,7 +17894,7 @@ using Catch::Detail::Approx;
 #define INFO( msg ) (void)(0)
 #define UNSCOPED_INFO( msg ) (void)(0)
 #define WARN( msg ) (void)(0)
-#define CAPTURE( msg ) (void)(0)
+#define CAPTURE( ... ) (void)(0)
 
 #define TEST_CASE( ... )  INTERNAL_CATCH_TESTCASE_NO_REGISTRATION(INTERNAL_CATCH_UNIQUE_NAME( C_A_T_C_H_T_E_S_T_ ))
 #define TEST_CASE_METHOD( className, ... ) INTERNAL_CATCH_TESTCASE_NO_REGISTRATION(INTERNAL_CATCH_UNIQUE_NAME( C_A_T_C_H_T_E_S_T_ ))