Merge pull request #727 from UWB-Biocomputing/master

Back merge of master into development to bring development completely up-to-date

Author: stiber

.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

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;