@@ -1,14 +1,8 @@

-#include "Archive.h"

-#include "GapsRunner.h"

-#include "Random.h"

 #include "SIMD.h"

+#include "GapsRunner.h"

 #include <Rcpp.h>

-// used to convert defined macro values into strings

-#define STR_HELPER(x) #x

-#define STR(x) STR_HELPER(x)

-

 // [[Rcpp::export]]

 Rcpp::List cogaps_cpp(const Rcpp::NumericMatrix &D,

 const Rcpp::NumericMatrix &S, unsigned nFactor, unsigned nEquil,

@@ -36,6 +30,10 @@ unsigned nSample, const std::string &fileName, const std::string &cptFile)

     return runner.run();

 }

+// used to convert defined macro values into strings

+#define STR_HELPER(x) #x

+#define STR(x) STR_HELPER(x)

+

 // [[Rcpp::export]]

 std::string getBuildReport_cpp()

 {

@@ -20,9 +20,14 @@ enum GapsPhase

     GAPS_SAMP

 };

+// Manages all data and parameters for running CoGAPS; contains the high-level

+// algorithm logic

 class GapsRunner

 {

 private:

+#ifdef GAPS_INTERNAL_TESTS

+public:

+#endif

     Vector mChiSqEquil;

     Vector mNumAAtomsEquil;

@@ -86,4 +91,4 @@ public:

     Rcpp::List run();

 };

-#endif

\ No newline at end of file

+#endif // __COGAPS_GAPS_RUNNER_H__

\ No newline at end of file

@@ -12,6 +12,7 @@ OBJECTS =   Algorithms.o \

             test-runner.o \

             cpp_tests/testAlgorithms.o \

             cpp_tests/testAtomicDomain.o \

+            cpp_tests/testGapsRunner.o \

             cpp_tests/testGibbsSampler.o \

             cpp_tests/testMatrix.o \

             cpp_tests/testProposalQueue.o \

new file mode 100644

@@ -0,0 +1,24 @@

+#include "catch.h"

+#include "../GapsRunner.h"

+

+TEST_CASE("Test Top Level CoGAPS Call")

+{

+    Rcpp::Environment pkgEnv;

+    pkgEnv = Rcpp::Environment::namespace_env("CoGAPS");

+    Rcpp::NumericMatrix D = pkgEnv.find("SimpSim.D");

+    Rcpp::NumericMatrix S = pkgEnv.find("SimpSim.S");

+

+    GapsRunner runner(D, S, 3, 500, 100, 500, 0, 0, 0.01f, 0.01f, 100.f, 100.f,

+        123, false, false, 0, "gaps_checkpoint.out", "N",

+        Rcpp::NumericMatrix());

+    //CATCH_REQUIRE_NO_THROWS(runner.run());

+}

+

+#ifdef GAPS_INTERNAL_TESTS

+

+TEST_CASE("Test Individual Steps")

+{

+

+}

+

+#endif

\ No newline at end of file