Add cpp test (#3)

* Added Cpp testing structure!

* Added Test Fixture Class

* Forced the cluster to only return OTU data, and created the fix test fixture with test!

* Created all of the test for the optimatrix adapter and removed the .dll from being tracked!

* Created all the test in the testfixture for listvectors and now I am adding them to the test files.

* Created base test for listVector

* Basic test for listVector are completed!

* Created the basic structure and test fixture for cluster commands

* Cluster Testing suite being pushed up!

* Fix cluster algorithm (#2)

* Fixed a slew of issues by adding bidirection distances.

* Fixed the clustering issue, clustering should be working correctly now!

* Generated Definitions for OptiCluster Test

* Finished creating unit test of the cluster command and opticluster

* Added OptiData test fixture

* Started creating the unit test for utils

* Utils command cluster and test work as expected!!

* Removed old code from one of the testing suites.

* Added another test in utils.

* Clustor has a 89% test coverage! Everything should be tested and ready to merge back!

.gitignore

@@ -10,6 +10,7 @@ __pycache__/
 
 # Cpp Object files
 *.o
+*.dll
 
 # Distribution / packaging
 .Python
@@ -39,6 +40,9 @@ var/
 pip-log.txt
 pip-delete-this-directory.txt
 
+# CMakeCheck list via Clion
+CMakeLists.txt
+
 # Unit test / coverage reports
 htmlcov/
 .tox/
@@ -186,4 +190,5 @@ fabric.properties
 .idea/caches/build_file_checksums.ser
 
 # idea folder, uncomment if you don't need it
-# .idea
+.idea
+src/.DS_Store

.vscode/c_cpp_properties.json

@@ -0,0 +1,19 @@
+{
+    "configurations": [
+        {
+            "name": "Mac",
+            "includePath": [
+                "${workspaceFolder}/**"
+            ],
+            "defines": [],
+            "macFrameworkPath": [
+                "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/Library/Frameworks"
+            ],
+            "compilerPath": "/usr/bin/clang",
+            "cStandard": "c17",
+            "cppStandard": "c++17",
+            "intelliSenseMode": "macos-clang-arm64"
+        }
+    ],
+    "version": 4
+}

.vscode/settings.json

@@ -0,0 +1,58 @@
+{
+    "files.associations": {
+        "__bit_reference": "cpp",
+        "__config": "cpp",
+        "__hash_table": "cpp",
+        "__locale": "cpp",
+        "__node_handle": "cpp",
+        "__split_buffer": "cpp",
+        "__threading_support": "cpp",
+        "__tree": "cpp",
+        "__verbose_abort": "cpp",
+        "array": "cpp",
+        "bitset": "cpp",
+        "cctype": "cpp",
+        "clocale": "cpp",
+        "cmath": "cpp",
+        "complex": "cpp",
+        "cstdarg": "cpp",
+        "cstddef": "cpp",
+        "cstdint": "cpp",
+        "cstdio": "cpp",
+        "cstdlib": "cpp",
+        "cstring": "cpp",
+        "ctime": "cpp",
+        "cwchar": "cpp",
+        "cwctype": "cpp",
+        "execution": "cpp",
+        "fstream": "cpp",
+        "initializer_list": "cpp",
+        "iomanip": "cpp",
+        "ios": "cpp",
+        "iosfwd": "cpp",
+        "iostream": "cpp",
+        "istream": "cpp",
+        "limits": "cpp",
+        "list": "cpp",
+        "locale": "cpp",
+        "map": "cpp",
+        "mutex": "cpp",
+        "new": "cpp",
+        "optional": "cpp",
+        "ostream": "cpp",
+        "ratio": "cpp",
+        "set": "cpp",
+        "sstream": "cpp",
+        "stdexcept": "cpp",
+        "streambuf": "cpp",
+        "string": "cpp",
+        "string_view": "cpp",
+        "tuple": "cpp",
+        "typeinfo": "cpp",
+        "unordered_map": "cpp",
+        "unordered_set": "cpp",
+        "variant": "cpp",
+        "vector": "cpp",
+        "algorithm": "cpp"
+    }
+}

DESCRIPTION

@@ -9,8 +9,10 @@ Description: One paragraph description of what the package does as one
         or more full sentences.
 License: GPL (>= 2)
 Imports: Rcpp (>= 1.0.12)
-LinkingTo: Rcpp
+LinkingTo: Rcpp,
+    testthat
 Suggests: 
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0),
+    xml2
 Config/testthat/edition: 3
 RoxygenNote: 7.3.1

R/Cluster.R

@@ -18,10 +18,10 @@ OptiCluster <- function(sparse_matrix, cutoff, iterations)
   indexOneList <- sparse_matrix@i
   indexTwoList <- sparse_matrix@j
   valueList <- sparse_matrix@x
-  matrix_length <- length(indexOneList)
   clustering_output_string <- MatrixToOpiMatrixCluster(indexOneList, indexTwoList, valueList, cutoff,
-                                   matrix_length, matrix_length, iterations)
+                                   iterations)
   df <- t(read.table(text = clustering_output_string, sep = "\t", header = TRUE))
+  df <- data.frame(df[-1,])
   colnames(df)[1] <- "cluster"
-  return(data.frame(df))
-}
+  return(df)
+}

R/RcppExports.R

@@ -1,7 +1,7 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
-MatrixToOpiMatrixCluster <- function(xPosition, yPosition, data, cutoff, rowSize, colSize, iterations = 2L) {
-    .Call(`_Opticluster_MatrixToOpiMatrixCluster`, xPosition, yPosition, data, cutoff, rowSize, colSize, iterations)
+MatrixToOpiMatrixCluster <- function(xPosition, yPosition, data, cutoff, iterations = 2L) {
+    .Call(`_Opticluster_MatrixToOpiMatrixCluster`, xPosition, yPosition, data, cutoff, iterations)
 }
 

R/catch-routine-registration.R

@@ -0,0 +1,6 @@
+# This dummy function definition is included with the package to ensure that
+# 'tools::package_native_routine_registration_skeleton()' generates the required
+# registration info for the 'run_testthat_tests' symbol.
+(function() {
+  .Call("run_testthat_tests", FALSE, PACKAGE = "Opticluster")
+})

src/Adapters/OptimatrixAdapter.h

@@ -7,6 +7,7 @@
 #include <vector>
 #include <string>
 #include <set>
+#include <unordered_set>
 #include <list>
 #include "../MothurDependencies/OptiMatrix.h"
 #include <fstream>
@@ -25,12 +26,13 @@ class OptimatrixAdapter {
         this->cutoff = cutoff;
     }
     OptiMatrix* ConvertToOptimatrix(const std::vector<int>
-        &xPosition, const std::vector<int>& yPosition, const std::vector<double>& data, int rowSize, int colSize);
+        &xPosition, const std::vector<int>& yPosition, const std::vector<double>& data);
     std::vector<std::set<long long>> GetCloseness() {return closeness;}
     std::vector<std::string> GetNameList() {return nameList;}
     std::vector<std::string> GetSingletons() {return singletons;}
 private:
     double cutoff;
+    //TODO Get rid of values inside of the adapter, it should not care about them
     std::vector<std::set<long long>> closeness;
     std::vector<std::string> nameList;
     std::vector<std::string> singletons;

src/ClusterCommand.cpp

@@ -16,7 +16,11 @@ ClusterCommand::~ClusterCommand() {
 /// Bad alloctions, returns basic_string, returns emptry string, returns non-utf8 characters, etc
 /// @param optiMatrix
 /// @return
-int ClusterCommand::runOptiCluster(OptiMatrix *optiMatrix) {
+std::string ClusterCommand::runOptiCluster(OptiMatrix *optiMatrix) {
+    std::string clusterOutputData;
+    std::string sensFile;
+    std::string outStep;
+    std::string clusterMatrixOutput;
     if (!cutOffSet) {
         clusterOutputData += ("\nYou did not set a cutoff, using 0.03.\n");
         cutoff = 0.5;
@@ -122,7 +126,6 @@ int ClusterCommand::runOptiCluster(OptiMatrix *optiMatrix) {
 
         clusterOutputData += "\n\n";
         list = cluster.getList();
-        list->setLabel(std::to_string(cutoff));
         //
         if (printHeaders) {
             //only print headers the first time
@@ -138,5 +141,5 @@ int ClusterCommand::runOptiCluster(OptiMatrix *optiMatrix) {
         for (double result : results) { sensFile + std::to_string(result) + '\t'; }
     }
     delete matrix;
-    return 0;
+    return clusterMatrixOutput;
 }

src/ClusterCommandTestFixture.cpp

@@ -0,0 +1,20 @@
+//
+// Created by Gregory Johnson on 5/1/24.
+//
+
+#include "tests/ClusterCommandTestFixture.h"
+
+bool ClusterCommandTestFixture::TestSetIterationsWorksCorrectly(const int iterations, const bool expectResult) {
+    Setup();
+    const bool result = clusterCommand->SetMaxIterations(iterations);
+    TearDown();
+    return result == expectResult;
+}
+
+void ClusterCommandTestFixture::Setup() {
+    clusterCommand = std::make_unique<ClusterCommand>();
+}
+
+void ClusterCommandTestFixture::TearDown() {
+    clusterCommand.reset();
+}

src/ListVector.cpp

@@ -45,7 +45,7 @@ std::string ListVector::print(std::ostream &output, std::map<std::string, int> &
     otuTag = "Otu";
     std::string output_cluster;
     printHeaders(output_cluster, ct, true);
-    output_cluster += label + "\t" + std::to_string(numBins);
+    //output_cluster += label + "\t" + std::to_string(numBins);
     //TestHelper::Print(output_cluster);
     Utils util;
     std::vector<listCt> hold;
@@ -100,9 +100,7 @@ std::string ListVector::print(std::ostream &output) {
 void ListVector::printHeaders(std::string &output, std::map<std::string, int> &ct, bool sortPlease) {
     if (printListHeaders) {
         if (binLabels.size() == 0) { sortPlease = false; } //we are creating arbitary otuNames
-        output = "hello\n";
         std::vector<std::string> theseLabels = getLabels();
-        output = "label\tnum" + otuTag + "s";
         if (sortPlease) {
             Utils util;
             std::vector<listCt> hold;
@@ -131,7 +129,6 @@ void ListVector::printHeaders(std::string &output, std::map<std::string, int> &c
         }
 
         output += "\n";
-
         printListHeaders = false;
     }
 }

src/ListVectorTestFixture.cpp

@@ -0,0 +1,132 @@
+//
+// Created by Gregory Johnson on 5/1/24.
+//
+
+#include "tests/ListVectorTestFixture.h"
+
+bool ListVectorTestFixture::TestListVectorReturnsCorrectNumberOfBins(const std::vector<std::string>& mockListOfSequences,
+    const int expectedResult) {
+    Setup();
+    for (const auto& sequences: mockListOfSequences) {
+        listVector->push_back(sequences);
+    }
+    const bool result = listVector->getNumBins() == expectedResult;
+    TearDown();
+    return result;
+}
+
+bool ListVectorTestFixture::TestListVectorReturnsCorrectNumSeqs(const std::vector<std::string> &mockListOfSequences,
+    const int expectedResult) {
+    Setup();
+    for (const auto& sequences: mockListOfSequences) {
+        listVector->push_back(sequences);
+    }
+    const bool result = listVector->getNumSeqs() == expectedResult;
+    TearDown();
+    return result;
+}
+
+bool ListVectorTestFixture::TestListVectorReturnsCorrectMaxRank(const std::vector<std::string> &mockListOfSequences,
+    const int expectedResult) {
+    Setup();
+    for (const auto& sequences: mockListOfSequences) {
+        listVector->push_back(sequences);
+    }
+    const bool result = listVector->getMaxRank() == expectedResult;
+    TearDown();
+    return result;
+}
+
+bool ListVectorTestFixture::TestListVectorReturnsCorrectGetValue(const std::vector<std::string> &mockListOfSequences,
+    const int index, const std::string &expectedResult) {
+    Setup();
+    for (const auto& sequences: mockListOfSequences) {
+        listVector->push_back(sequences);
+    }
+    const bool result = listVector->get(index) == expectedResult;
+    TearDown();
+    return result;
+}
+
+bool ListVectorTestFixture::TestListVectorReturnsCorrectGetLabelsValue(
+    const std::vector<std::string> &mockListOfSequences, const int expectedResult) {
+    Setup();
+    for (const auto& sequences: mockListOfSequences) {
+        listVector->push_back(sequences);
+    }
+    const bool result = listVector->getLabels().size() == expectedResult;
+    TearDown();
+    return result;
+}
+
+bool ListVectorTestFixture::TestListVectorReturnsCorrectGetOtuNames(const std::vector<std::string> &mockListOfSequences,
+    const int binToTest, const std::string &expectedResult) {
+    Setup();
+    for (const auto& sequences: mockListOfSequences) {
+        listVector->push_back(sequences);
+    }
+    const bool result = listVector->getOTUName(binToTest) == expectedResult;
+    TearDown();
+    return result;
+}
+
+bool ListVectorTestFixture::TestListVectorSetsLabelsCorrectly(const std::vector<std::string> &mockListOfLabels,
+    const int expectedResult) {
+    Setup();
+    listVector->setLabels(mockListOfLabels);
+    const bool result = listVector->getLabels().size() == expectedResult;
+    TearDown();
+    return result;
+}
+
+bool ListVectorTestFixture::TestListVectorSetsPrintedLabelsCorrectly(const bool mockValue, const bool expectedResult) {
+    Setup();
+    const bool result = expectedResult == listVector->setPrintedLabels(mockValue);
+    TearDown();
+    return result;
+}
+
+bool ListVectorTestFixture::TestListVectorPushBackSetsDataCorrectly(const std::vector<std::string>& mockListOfSequences,
+        const int index, const std::string& expectedResult) {
+    Setup();
+    for (const auto& sequences: mockListOfSequences) {
+        listVector->push_back(sequences);
+    }
+    const bool result =listVector->get(index) == expectedResult;
+    TearDown();
+    return result;
+
+}
+
+bool ListVectorTestFixture::TestListVectorPrintDisplaysDataCorrectly(
+    const std::vector<std::string> &mockListOfSequences, const std::string& expectedResult) {
+    Setup();
+    std::ofstream stream;
+    for (const auto& sequences: mockListOfSequences) {
+        listVector->push_back(sequences);
+    }
+    // Get rid of ofstream in listVector
+    const bool result =listVector->print(stream) == expectedResult;
+    TearDown();
+    return result;
+}
+
+
+bool ListVectorTestFixture::TestListVectorReturnsCorrectGetOtuNamesSize(const std::vector<std::string> &mockListOfSequences,
+                                                                        const int binToTest, const int expectedResult) {
+    Setup();
+    for (const auto& sequences: mockListOfSequences) {
+        listVector->push_back(sequences);
+    }
+    const bool result = listVector->getOTUName(binToTest).size() == expectedResult;
+    TearDown();
+    return result;
+}
+
+void ListVectorTestFixture::Setup() {
+    listVector = std::make_unique<ListVector>();
+}
+
+void ListVectorTestFixture::TearDown() {
+    listVector.reset();
+}