Merge branch 'development' into issue-730-add-contributor

Author: nyeshlur

.github/pull_request_template.md

@@ -0,0 +1,26 @@
+<!-- Link to the issue and use the appropriate closing keyword (e.g., Closes, Resolves) -->
+Closes #
+
+<!-- Please provide a brief overview of the changes implemented -->
+#### Description
+
+
+<!-- Please check the boxes as applicable -->
+#### Checklist (Mandatory for new features)
+- [ ] Added Documentation 
+- [ ] Added Unit Tests 
+
+<!-- Ensure all boxes are checked before submitting the PR -->
+#### Testing (Mandatory for all changes)
+- [ ] GPU Test: `test-medium-connected.xml` Passed
+- [ ] GPU Test: `test-large-long.xml` Passed
+
+<!-- 
+PR Guidelines
+1. Ensure that your changes are merged into the `development` branch. Only merge into the `master` branch if explicitly instructed.
+     - On GitHub, at the top of the PR page, change the base branch from `master` to `development`.
+2. Assign the PR to yourself and apply the appropriate labels.
+3. Only add a reviewer after submitting the PR and confirming that all GitHub Actions have passed.
+
+Thank you for your contribution!
+-->

.github/workflows/plantUML.yml

@@ -43,11 +43,11 @@ jobs:
         run: |
           echo ${{ steps.getfile.outputs.files }}
       - name: Generate SVG Diagrams
-        uses: cloudbees/plantuml-github-action@master
+        uses: UWB-Biocomputing/plantuml-github-action@main
         with:
             args: -o "diagrams" -v -tsvg ${{ steps.getfile.outputs.files }}
       - name: Generate PNG Diagrams
-        uses: cloudbees/plantuml-github-action@master
+        uses: UWB-Biocomputing/plantuml-github-action@main
         with:
             args: -o "diagrams" -v -tpng ${{ steps.getfile.outputs.files }}
       - name: Push Local Changes

CMakeLists.txt

@@ -402,6 +402,16 @@ target_link_libraries(tests combinedLib)
 # # Link the combined library into the 'serialFileAccessTest' executable.
 # target_link_libraries(serialFileAccessTest combinedLib)
 
+add_executable(serialFileAccessTest
+        Testing/RunTests.cpp
+        Testing/UnitTesting/SerializationFileAccessTest.cpp)
+
+# Links the Googletest framework with the serialFileAccessTest executable
+target_link_libraries(serialFileAccessTest gtest gtest_main)
+
+# Link the combined library into the 'serialFileAccessTest' executable.
+target_link_libraries(serialFileAccessTest combinedLib)
+
 # Clear ENABLE_CUDA, PERFORMANCE_METRICS and GPROF from the cache so it's reset for subsequent builds
 unset(ENABLE_CUDA CACHE)
 unset(PERFORMANCE_METRICS CACHE)

Contributors.md

@@ -72,6 +72,8 @@ Natalie Gonzales
 ## 2024
 Andrzej Dawiec 
 
+Jasleen Kaur Saini
+
 ChengHao Hsu
 
 Zaina Shaikh
@@ -114,6 +116,10 @@ Victoria Jo Salvatore
 Divya Kamath    
 
 ## 2024
+Vanessa Arndorfer
+
+Xiang Li
+
 Jardi Martinez
 
 Nicholas Posey

Simulator/Connections/Connections.h

@@ -74,7 +74,7 @@ class Connections {
    virtual bool updateConnections(AllVertices &vertices);
 
    ///  Cereal serialization method
-   template <class Archive> void serialize(Archive &archive, std::uint32_t const version);
+   template <class Archive> void serialize(Archive &archive);
 
 #if defined(USE_GPU)
 public:
@@ -107,10 +107,8 @@ class Connections {
    log4cplus::Logger edgeLogger_;
 };
 
-CEREAL_CLASS_VERSION(Connections, 1);
-
 ///  Cereal serialization method
-template <class Archive> void Connections::serialize(Archive &archive, std::uint32_t const version)
+template <class Archive> void Connections::serialize(Archive &archive)
 {
    archive(cereal::make_nvp("edges", edges_),
            cereal::make_nvp("synapseIndexMap", synapseIndexMap_));

Simulator/Core/Model.h

@@ -82,7 +82,7 @@ class Model {
    virtual void updateConnections() = 0;
 
    ///  Cereal serialization method
-   template <class Archive> void serialize(Archive &archive);
+   template <class Archive> void serialize(Archive &archive, std::uint32_t const version);
 
 protected:
    // Note: This method was previously used for debugging, but it is now dead code left behind.
@@ -111,10 +111,10 @@ class Model {
       createAllVertices();   /// Populate an instance of AllVertices with an initial state for each vertex.
 };
 
-CEREAL_REGISTER_TYPE(Model);
+CEREAL_CLASS_VERSION(Model, 1);
 
 ///  Cereal serialization method
-template <class Archive> void Model::serialize(Archive &archive)
+template <class Archive> void Model::serialize(Archive &archive, std::uint32_t const version)
 {
    archive(cereal::make_nvp("connections", connections_), cereal::make_nvp("layout", layout_));
 }

Simulator/Edges/AllEdges.h

@@ -59,7 +59,7 @@ class AllEdges {
    virtual void createEdgeIndexMap(EdgeIndexMap &edgeIndexMap);
 
    ///  Cereal serialization method
-   template <class Archive> void serialize(Archive &archive, std::uint32_t const version);
+   template <class Archive> void serialize(Archive &archive);
 
 protected:
    ///  Setup the internal structure of the class (allocate memories and initialize them).
@@ -223,11 +223,9 @@ class AllEdges {
    int countVertices_;
 };
 
-CEREAL_CLASS_VERSION(AllEdges, 1);
-
 ///  Cereal serialization method
 ///  (Serializes edge weights, source vertices, and destination vertices)
-template <class Archive> void AllEdges::serialize(Archive &archive, std::uint32_t const version)
+template <class Archive> void AllEdges::serialize(Archive &archive)
 {
    // serialization
    archive(cereal::make_nvp("sourceVertexIndex", sourceVertexIndex_),

Simulator/Layouts/Layout.h

@@ -85,7 +85,7 @@ class Layout {
    BGSIZE numEndogenouslyActiveNeurons_;   ///< Number of endogenously active neurons.
 
    ///  Cereal serialization method
-   template <class Archive> void serialize(Archive &archive, std::uint32_t const version);
+   template <class Archive> void serialize(Archive &archive);
 
 protected:
    unique_ptr<AllVertices> vertices_;
@@ -95,10 +95,8 @@ class Layout {
    int numVertices_;   ///< Total number of vertices in the graph.
 };
 
-CEREAL_CLASS_VERSION(Layout, 1);
-
 ///  Cereal serialization method
-template <class Archive> void Layout::serialize(Archive &archive, std::uint32_t const version)
+template <class Archive> void Layout::serialize(Archive &archive)
 {
    archive(cereal::make_nvp("xloc", xloc_), cereal::make_nvp("yloc", yloc_),
            cereal::make_nvp("dist2", dist2_), cereal::make_nvp("dist", dist_),

Simulator/Layouts/NG911/Layout911.cpp

@@ -24,11 +24,53 @@ void Layout911::registerGraphProperties()
    GraphManager &gm = GraphManager::getInstance();
    gm.registerProperty("objectID", &VertexProperty::objectID);
    gm.registerProperty("name", &VertexProperty::name);
+   gm.registerProperty("type", &VertexProperty::type);
+   gm.registerProperty("y", &VertexProperty::y);
+   gm.registerProperty("x", &VertexProperty::x);
    gm.registerProperty("servers", &VertexProperty::servers);
    gm.registerProperty("trunks", &VertexProperty::trunks);
    gm.registerProperty("segments", &VertexProperty::segments);
 }
 
+// Loads Layout911 member variables.
+void Layout911::loadParameters()
+{
+   // Get the number of verticese from the GraphManager
+   numVertices_ = GraphManager::getInstance().numVertices();
+}
+
+// Setup the internal structure of the class.
+void Layout911::setup()
+{
+   // Base class allocates memory for: xLoc_, yLoc, dist2_, and dist_
+   // so we call its method first
+   Layout::setup();
+
+   // Loop over all vertices and set their x and y locations
+   GraphManager::VertexIterator vi, vi_end;
+   GraphManager &gm = GraphManager::getInstance();
+   for (boost::tie(vi, vi_end) = gm.vertices(); vi != vi_end; ++vi) {
+      assert(*vi < numVertices_);
+      xloc_[*vi] = gm[*vi].x;
+      yloc_[*vi] = gm[*vi].y;
+   }
+
+   // Now we cache the between each pair of vertices distances^2 into a matrix
+   for (int n = 0; n < numVertices_ - 1; n++) {
+      for (int n2 = n + 1; n2 < numVertices_; n2++) {
+         // distance^2 between two points in point-slope form
+         dist2_(n, n2) = (xloc_[n] - xloc_[n2]) * (xloc_[n] - xloc_[n2])
+                         + (yloc_[n] - yloc_[n2]) * (yloc_[n] - yloc_[n2]);
+
+         // both points are equidistant from each other
+         dist2_(n2, n) = dist2_(n, n2);
+      }
+   }
+
+   // Finally take the square root to get the distances
+   dist_ = sqrt(dist2_);
+}
+
 // Prints out all parameters to logging file.
 void Layout911::printParameters() const
 {

Simulator/Layouts/NG911/Layout911.h

@@ -52,6 +52,14 @@ class Layout911 : public Layout {
    /// Register vertex properties with the GraphManager
    virtual void registerGraphProperties() override;
 
+   /// Loads Layout911 member variables.
+   /// Registered to OperationManager as Operation::loadParameters
+   virtual void loadParameters() override;
+
+   /// Setup the internal structure of the class.
+   /// Allocate memories to store all layout state.
+   virtual void setup() override;
+
    /// Prints out all parameters to logging file.
    /// Registered to OperationManager as Operation::printParameters
    virtual void printParameters() const override;