Enable OpenMP for MacOS Builds

.circleci/config.yml

@@ -154,6 +154,10 @@ jobs:
             cd ~/SmartPeak
             export PYTHONPATH="${PWD}/tools"
             python3 -m unittest discover -s ./tools/smartpeak
+      - run:
+          name: Running SmartPeak Examples
+          command: |
+            ~/SmartPeak/.circleci/run_examples.sh ~/SmartPeak/smartpeak_release_build/bin
       - run:
           name: Packing SmartPeak
           command: |

src/tests/class_tests/smartpeak/CMakeLists.txt

@@ -6,6 +6,7 @@ project("SmartPeak_class_tests_smartpeak")
 #------------------------------------------------------------------------------
 # Configure test file to get the TEST_DATA_PATH into the tests
 set(CF_SMARTPEAK_TEST_DATA_PATH "${PROJECT_SOURCE_DIR}/data/")
+set(CF_SMARTPEAK_EXAMPLES_DATA_PATH "${PROJECT_SOURCE_DIR}/../../../examples/data/")
 set (CONFIGURED_TEST_CONFIG_H "${PROJECT_BINARY_DIR}/include/SmartPeak/test_config.h")
 configure_file(${PROJECT_SOURCE_DIR}/include/SmartPeak/test_config.h.in ${CONFIGURED_TEST_CONFIG_H})
 

src/tests/class_tests/smartpeak/include/SmartPeak/test_config.h.in

@@ -5,5 +5,7 @@
 // Macro to construct a c string containing the complete path to the test data
 #define SMARTPEAK_GET_TEST_DATA_PATH(filename) (std::string("@CF_SMARTPEAK_TEST_DATA_PATH@") + filename).c_str()
 #define SMARTPEAK_GET_TEST_DATA_PATH_MESSAGE(prefix,filename,suffix) (prefix + std::string("@CF_SMARTPEAK_TEST_DATA_PATH@") + filename + suffix).c_str()
+#define SMARTPEAK_GET_EXAMPLES_DATA_PATH(filename) (std::string("@CF_SMARTPEAK_EXAMPLES_DATA_PATH@") + filename).c_str()
+#define SMARTPEAK_GET_EXAMPLES_DATA_PATH_MESSAGE(prefix,filename,suffix) (prefix + std::string("@CF_SMARTPEAK_EXAMPLES_DATA_PATH@") + filename + suffix).c_str()
 
 #endif // SMARTPEAK_TEST_CONFIG_H

src/tests/class_tests/smartpeak/source/Task_test.cpp

@@ -246,4 +246,33 @@ TEST(Task, Task_options_change_output_dirs)
   auto er = cli::ExportReport{};
   EXPECT_TRUE(er(am));
   EXPECT_TRUE(std::filesystem::exists(report_output_dir / "FeatureDB.csv"));
+}
+
+TEST(Task, Task_run_LCMS_MRM_QCs_example_20_threads)
+{
+  namespace cli = SmartPeak::cli;
+  std::filesystem::path seq_path = SMARTPEAK_GET_EXAMPLES_DATA_PATH("LCMS_MRM_QCs");
+  std::string seq = std::string{ seq_path.lexically_normal().generic_string() };
+  std::vector<std::string> args = std::vector<std::string>{
+      "Task_test",
+          "--load-session", seq,
+          "--verbose",
+          "--allow-inconsistent",
+          "--log-dir", ".",
+          "--disable-colors",
+          "-no-pg",
+          "--parameter", "SequenceProcessor:n_thread=20"
+  };
+  auto pa = cli::Parser{ args };
+  auto as = cli::ApplicationSettings{ pa };
+  auto am = cli::ApplicationManager{ as };
+  am
+    .add(std::make_shared<cli::InitializeApplicationSettings>())
+    .add(std::make_shared<cli::LoadSession>())
+    .add(std::make_shared<cli::InitializeWorkflowResources>())
+    .add(std::make_shared<cli::InitializeWorkflowSettings>())
+    .add(std::make_shared<cli::RunIntegrityChecks>())
+    .add(std::make_shared<cli::RunWorkflow>())
+    .add(std::make_shared<cli::ExportReport>());
+  am.run();
 }