re-arrange unit test building

COMBINE-lab · Mar 5, 2022 · 5df4227 · 5df4227
1 parent b540e04
commit 5df4227
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Showing 7 changed files with 42 additions and 17 deletions.
diff --git a/include/SalmonConfig.hpp b/include/SalmonConfig.hpp
@@ -1,6 +1,6 @@
 /**
 >HEADER
-    Copyright (c) 2014-2021 Rob Patro rob@cs.umd.edu
+    Copyright (c) 2014-2022 Rob Patro rob@cs.umd.edu
 
     This file is part of Salmon.
 
@@ -26,9 +26,9 @@
 
 namespace salmon {
 constexpr char majorVersion[] = "1";
-constexpr char minorVersion[] = "7";
+constexpr char minorVersion[] = "8";
 constexpr char patchVersion[] = "0";
-constexpr char version[] = "1.7.0";
+constexpr char version[] = "1.8.0";
 constexpr uint32_t indexVersion = 5;
 constexpr char requiredQuasiIndexVersion[] = "p7";
 } // namespace salmon

diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh
@@ -24,7 +24,7 @@ if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then
 fi
 
 #SVER=salmon-v1.7.0
-SVER=onetbb
+SVER=develop
 #SVER=sketch-mode
 
 EXPECTED_SHA256=5894fabbf6829a3d4a627135edc8326e931eb07fc792bfff3a0714e8fee8bb8b

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -97,10 +97,17 @@ if(HAS_IPO AND (NOT NO_IPO))
   set_property(TARGET ksw2pp PROPERTY INTERPROCEDURAL_OPTIMIZATION True)
 endif()
 
-set ( UNIT_TESTS_SRCS
+set (UNIT_TESTS_ENTRY_SRCS
     ${GAT_SOURCE_DIR}/tests/UnitTests.cpp
-    FragmentLengthDistribution.cpp
-    ${GAT_SOURCE_DIR}/external/install/src/pufferfish/rank9b.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
 )
 
 
@@ -190,8 +197,9 @@ if(HAS_IPO AND (NOT NO_IPO))
   set_property(TARGET salmon PROPERTY INTERPROCEDURAL_OPTIMIZATION True)
 endif()
 
-add_executable(unitTests ${UNIT_TESTS_SRCS})
+add_library(UnitTestsMain STATIC ${UNIT_TESTS_ENTRY_SRCS} ${GAT_SOURCE_DIR}/tests/catch.hpp)
 
+add_executable(unitTests ${UNIT_TESTS_INDIVIDUAL_SRCS} ${GAT_SOURCE_DIR}/tests/catch.hpp)
 target_compile_options(unitTests PUBLIC "$<$<CONFIG:DEBUG>:${TGT_DEBUG_FLAGS}>")
 target_compile_options(unitTests PUBLIC "$<$<CONFIG:RELEASE>:${TGT_RELEASE_FLAGS}>")
 
@@ -219,7 +227,7 @@ add_dependencies(salmon alevin_core)
 if(TBB_RECONFIGURE OR TBB_TARGET_EXISTED)
 # Link the executable
 target_link_libraries(salmon
-    Threads::Threads
+    Threads::Threads 
     puffer 
     salmon_core
     twopaco
@@ -249,19 +257,22 @@ endif()
 # dependencies for unitTests
 add_dependencies(salmon salmon_core)
 add_dependencies(salmon alevin_core)
+add_dependencies(unitTests UnitTestsMain)
 #add_dependencies(salmon puffer)
 #add_dependencies(salmon twopaco)
 #add_dependencies(salmon graphdump)
 #add_dependencies(salmon ntcard)
 #add_dependencies(salmon ksw2pp)
 
 if(TBB_RECONFIGURE OR TBB_TARGET_EXISTED)
+
 target_link_libraries(unitTests
     Threads::Threads
 ## PUFF_INTEGRATION
     salmon_core
     alevin_core
     gff
+    UnitTestsMain
     ${STADEN_LIBRARIES} 
     ${Boost_LIBRARIES}
     ${ICU_LIBS}

diff --git a/tests/GCSampleTests.cpp b/tests/GCSampleTests.cpp
@@ -1,4 +1,12 @@
+#include "catch.hpp"
 #include <random>
+#include <unordered_map>
+#include <iostream>
+#include "LibraryFormat.hpp"
+#include "SalmonUtils.hpp"
+#include "Transcript.hpp"
+#include "UtilityFunctions.hpp"
+
 
 std::string generateRandomSequence(size_t length, std::uniform_int_distribution<>& dis, std::mt19937& gen) {
   char nucs[] =  {'A', 'C', 'G', 'T'};
@@ -44,6 +52,7 @@ SCENARIO("GC sampling works properly") {
 
       THEN("Sampled is the same as unsampled : ") {
         for (size_t tn = 0; tn < 1000; ++tn) {
+
           auto l = txpsSampled[tn].RefLength;
           for (size_t i = 0; i < l; ++i) {
             REQUIRE(txpsSampled[tn].gcAt(i) == txpsUnSampled[tn].gcAt(i));

diff --git a/tests/KmerHistTests.cpp b/tests/KmerHistTests.cpp
@@ -1,3 +1,4 @@
+#include "catch.hpp"
 #include "UtilityFunctions.hpp"
 
 // from http://stackoverflow.com/questions/2380962/generate-all-combinations-of-arbitrary-alphabet-up-to-arbitrary-length

diff --git a/tests/LibraryTypeTests.cpp b/tests/LibraryTypeTests.cpp
@@ -1,3 +1,13 @@
+#include "catch.hpp"
+#include <random>
+#include <unordered_map>
+#include <iostream>
+#include "LibraryFormat.hpp"
+#include "SalmonUtils.hpp"
+#include "Transcript.hpp"
+#include "UtilityFunctions.hpp"
+
+
 SCENARIO("Library types are encoded/decoded properly") {
 
     GIVEN("A collection of library formats") {

diff --git a/tests/UnitTests.cpp b/tests/UnitTests.cpp
@@ -1,14 +1,8 @@
 #define CATCH_CONFIG_MAIN  // This tells Catch to provide a main() - only do this in one cpp file
-#include <unordered_map>
-#include <iostream>
 #include "catch.hpp"
-#include "LibraryFormat.hpp"
-#include "SalmonUtils.hpp"
-#include "Transcript.hpp"
-#include "UtilityFunctions.hpp"
 
 bool verbose=false; // Apparently, we *need* this (OSX)
-#include "GCSampleTests.cpp"
-#include "LibraryTypeTests.cpp"
+//#include "GCSampleTests.cpp"
+//#include "LibraryTypeTests.cpp"
 //#include "KmerHistTests.cpp"