Merge branch 'master' into welsh_powell_coloring

.github/workflows/benchmark.yml

@@ -37,7 +37,7 @@ jobs:
       # Build your program with the given configuration
         run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}} -j
       - name: Download previous benchmark data
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ./cache
           key: ${{ runner.os }}-benchmark

.github/workflows/benchmark_pr.yml

@@ -36,7 +36,7 @@ jobs:
       # Build your program with the given configuration
         run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}} -j
       - name: Download previous benchmark data
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ./cache
           key: ${{ runner.os }}-benchmark

.github/workflows/clang_format.yml

@@ -0,0 +1,26 @@
+name: clang-format Check
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  formatting-check:
+    name: Formatting Check
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        path:
+          - 'benchmark'
+          - 'examples'
+          - 'include/CXXGraph'
+          - 'test'
+    steps:
+    - uses: actions/checkout@v4
+    - name: Run clang-format style check
+      uses: jidicula/[email protected]
+      with:
+        clang-format-version: '16'
+        check-path: ${{ matrix.path }}

.github/workflows/codacy.yml

@@ -56,6 +56,6 @@ jobs:
 
       # Upload the SARIF file generated in the previous step
       - name: Upload SARIF results file
-        uses: github/codeql-action/upload-sarif@v2
+        uses: github/codeql-action/upload-sarif@v3
         with:
           sarif_file: results.sarif

.github/workflows/codeql.yml

@@ -44,7 +44,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -80,6 +80,6 @@ jobs:
     #     ./location_of_script_within_repo/buildscript.sh
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3
       with:
         category: "/language:${{matrix.language}}"

.github/workflows/flawfinder.yml

@@ -33,6 +33,6 @@ jobs:
           output: 'flawfinder_results.sarif'
 
       - name: Upload analysis results to GitHub Security tab
-        uses: github/codeql-action/upload-sarif@v2
+        uses: github/codeql-action/upload-sarif@v3
         with:
           sarif_file: ${{github.workspace}}/flawfinder_results.sarif

.github/workflows/label.yml

@@ -13,6 +13,6 @@ jobs:
   triage:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/labeler@v4
+    - uses: actions/labeler@v5
       with:
         repo-token: "${{ secrets.GITHUB_TOKEN }}"

CMakeLists.txt

@@ -1,7 +1,7 @@
 cmake_minimum_required(VERSION 3.9)
 
 # set the project name and version
-project(CXXGraph VERSION 3.0.0)
+project(CXXGraph VERSION 3.1.0)
 
 configure_file(CXXGraphConfig.h.in ${PROJECT_SOURCE_DIR}/include/CXXGraph/CXXGraphConfig.h)
 

README.md

@@ -44,6 +44,7 @@ If you are interested, please contact us at [email protected] or contribute to
 | :heavy_check_mark: | Release 1.1.0 | May 8, 2023 |
 | :heavy_check_mark: | Stable Release 2.0.0 | Jun 1, 2023 |
 | :heavy_check_mark: | Stable Release 3.0.0 | Nov 3, 2023 |
+| :heavy_check_mark: | Release 3.1.0 | Jan 9, 2023 |
 | :memo: | Introduce Hypergraph [#122](https://github.com/ZigRazor/CXXGraph/issues/122) | TBD |
 | :memo: | Stable Release 4.0.0 | TBD |
 

benchmark/BellmanFord_BM.cpp

@@ -30,4 +30,4 @@ static void BellmanFord_FromReadedCitHep(benchmark::State &state) {
   }
 }
 
-BENCHMARK(BellmanFord_FromReadedCitHep);
+BENCHMARK(BellmanFord_FromReadedCitHep);

benchmark/Boruvka_BM.cpp

@@ -26,4 +26,4 @@ static void Boruvka_FromReadedCitHep(benchmark::State &state) {
   }
 }
 
-BENCHMARK(Boruvka_FromReadedCitHep);
+BENCHMARK(Boruvka_FromReadedCitHep);

benchmark/Connectivity_BM.cpp

@@ -53,4 +53,4 @@ static void StrongConnectivity_FromReadedCitHep(benchmark::State &state) {
   }
 }
 
-BENCHMARK(StrongConnectivity_FromReadedCitHep);
+BENCHMARK(StrongConnectivity_FromReadedCitHep);

benchmark/CycleCheck_BM.cpp

@@ -53,4 +53,4 @@ static void CycleCheckDFS_FromReadedCitHep(benchmark::State &state) {
   }
 }
 
-BENCHMARK(CycleCheckDFS_FromReadedCitHep);
+BENCHMARK(CycleCheckDFS_FromReadedCitHep);

benchmark/Dial_BM.cpp

@@ -27,4 +27,4 @@ static void Dial_FromReadedCitHep(benchmark::State &state) {
   }
 }
 
-BENCHMARK(Dial_FromReadedCitHep);
+BENCHMARK(Dial_FromReadedCitHep);

benchmark/Edge_BM.cpp

@@ -47,4 +47,4 @@ static void NodeGetNodePair(benchmark::State &state) {
     e.getNodePair();
   }
 }
-BENCHMARK(NodeGetNodePair);
+BENCHMARK(NodeGetNodePair);

benchmark/FloydWarshall_BM.cpp

@@ -1,4 +1,5 @@
 #include <benchmark/benchmark.h>
+
 #include <memory>
 
 #include "CXXGraph/CXXGraph.hpp"

benchmark/FordFulkerson_BM.cpp

@@ -31,4 +31,4 @@ static void FordFulkerson_FromReadedCitHep(benchmark::State &state) {
   }
 }
 
-BENCHMARK(FordFulkerson_FromReadedCitHep);
+BENCHMARK(FordFulkerson_FromReadedCitHep);

benchmark/Kruskal_BM.cpp

@@ -26,4 +26,4 @@ static void Kruskal_FromReadedCitHep(benchmark::State &state) {
   }
 }
 
-BENCHMARK(Kruskal_FromReadedCitHep);
+BENCHMARK(Kruskal_FromReadedCitHep);

benchmark/Node_BM.cpp

@@ -33,4 +33,4 @@ static void NodeGetData(benchmark::State &state) {
     n1.getData();
   }
 }
-BENCHMARK(NodeGetData);
+BENCHMARK(NodeGetData);

benchmark/Partition_BM.cpp

@@ -113,4 +113,4 @@ static void PartitionEBV_FromReadedCitHep(benchmark::State &state) {
   }
 }
 
-BENCHMARK(PartitionEBV_FromReadedCitHep);
+BENCHMARK(PartitionEBV_FromReadedCitHep);

benchmark/Prim_BM.cpp

@@ -26,4 +26,4 @@ static void Prim_FromReadedCitHep(benchmark::State &state) {
   }
 }
 
-BENCHMARK(Prim_FromReadedCitHep);
+BENCHMARK(Prim_FromReadedCitHep);

benchmark/main.cpp

@@ -1,3 +1,3 @@
 #include <benchmark/benchmark.h>
 
-BENCHMARK_MAIN();
+BENCHMARK_MAIN();

examples/CMakeLists.txt

@@ -5,5 +5,7 @@ add_subdirectory(DialExample)
 add_subdirectory(DijkstraExample)
 add_subdirectory(NetworkDynamicsExample)
 add_subdirectory(PartitionExample)
+add_subdirectory(PrimExample)
+add_subdirectory(FloydWarshallExample)
 
 endif(EXAMPLES)

examples/DialExample/dial_example.cpp

@@ -1,7 +1,7 @@
 #include <math.h>
-#include <memory>
 
 #include <CXXGraph/CXXGraph.hpp>
+#include <memory>
 
 using std::make_shared;
 

examples/DijkstraExample/dijkstra_example.cpp

@@ -1,5 +1,4 @@
 #include <CXXGraph/CXXGraph.hpp>
-
 #include <memory>
 
 using std::make_shared;

examples/FloydWarshallExample/CMakeLists.txt

@@ -0,0 +1,17 @@
+cmake_minimum_required(VERSION 3.9)
+project(floydWarshallExample)
+
+# specify the C++ standard
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED True)
+
+set(CMAKE_CXX_IMPLICIT_LINK_DIRECTORIES /usr/local/lib ${CMAKE_CXX_IMPLICIT_LINK_DIRECTORIES})
+
+add_executable(floyd_warshall floyd_warshall.cpp)
+target_include_directories(floyd_warshall PUBLIC "${CMAKE_SOURCE_DIR}/include")
+
+target_link_libraries(floyd_warshall
+                        pthread
+                        ssl
+                        crypto
+                        z)

examples/FloydWarshallExample/floyd_warshall.cpp

@@ -0,0 +1,45 @@
+#include <CXXGraph/CXXGraph.hpp>
+#include <memory>
+
+using std::make_shared;
+// example taken from
+// https://www.youtube.com/watch?v=B06q2yjr-Cc
+int main() {
+  CXXGraph::Node<int> node0("0", 0);
+  CXXGraph::Node<int> node1("1", 1);
+  CXXGraph::Node<int> node2("2", 2);
+  CXXGraph::Node<int> node3("3", 3);
+  CXXGraph::Node<int> node4("4", 4);
+
+  CXXGraph::UndirectedWeightedEdge<int> edge1(1, node0, node1, 1);
+  CXXGraph::UndirectedWeightedEdge<int> edge2(2, node0, node2, 2);
+  CXXGraph::UndirectedWeightedEdge<int> edge3(3, node1, node2, 6);
+  CXXGraph::UndirectedWeightedEdge<int> edge4(4, node1, node3, 4);
+  CXXGraph::UndirectedWeightedEdge<int> edge5(5, node2, node3, 5);
+  CXXGraph::UndirectedWeightedEdge<int> edge6(6, node3, node4, 3);
+
+  CXXGraph::T_EdgeSet<int> edgeSet;
+  edgeSet.insert(make_shared<CXXGraph::UndirectedWeightedEdge<int>>(edge1));
+  edgeSet.insert(make_shared<CXXGraph::UndirectedWeightedEdge<int>>(edge2));
+  edgeSet.insert(make_shared<CXXGraph::UndirectedWeightedEdge<int>>(edge3));
+  edgeSet.insert(make_shared<CXXGraph::UndirectedWeightedEdge<int>>(edge4));
+  edgeSet.insert(make_shared<CXXGraph::UndirectedWeightedEdge<int>>(edge5));
+  edgeSet.insert(make_shared<CXXGraph::UndirectedWeightedEdge<int>>(edge6));
+  // Can print out the edges for debugging
+  std::cout << edge1 << "\n";
+  std::cout << edge2 << "\n";
+  std::cout << edge3 << "\n";
+  std::cout << edge4 << "\n";
+  std::cout << edge5 << "\n";
+  std::cout << edge6 << "\n";
+
+  CXXGraph::Graph<int> graph(edgeSet);
+  CXXGraph::FWResult res = graph.floydWarshall();
+  std::cout << "floyd Warshall Result: "
+            << "\n";
+  for (auto i : res.result) {
+    std::cout << "distance of: " << i.first.first << " " << i.first.second
+              << " = " << i.second << "\n";
+  }
+  return 0;
+}

examples/NetworkDynamicsExample/network_dynamics_example.cpp

@@ -1,7 +1,7 @@
-#include "CXXGraph/CXXGraph.hpp"
-
 #include <memory>
 
+#include "CXXGraph/CXXGraph.hpp"
+
 using std::make_shared;
 
 int main() {
@@ -25,23 +25,26 @@ int main() {
 
   auto degreeMatrix = graph.getDegreeMatrix();
   for (const auto& nodePair : *degreeMatrix) {
-        const CXXGraph::shared<const CXXGraph::Node<int>>& node = nodePair.first;
-        const std::vector<int>& degrees = nodePair.second;
+    const CXXGraph::shared<const CXXGraph::Node<int>>& node = nodePair.first;
+    const std::vector<int>& degrees = nodePair.second;
 
-        std::cout << "Node: " << node->getId() << ", Degree: " << degrees[0] << "\n";
-    }
+    std::cout << "Node: " << node->getId() << ", Degree: " << degrees[0]
+              << "\n";
+  }
   auto laplacianMatrix = graph.getLaplacianMatrix();
   for (const auto& nodePair : *laplacianMatrix) {
     const auto& node = nodePair.first;
     const auto& neighbors = nodePair.second;
 
     std::cout << "Node " << node->getId() << " connected to:" << std::endl;
     for (const auto& neighbor : neighbors) {
-        if (neighbor.first == node) {
-            std::cout << "  -> Itself" << std::endl;
-        } else {
-            std::cout << "  -> Node " << neighbor.first->getId() << " with Edge ID " << (neighbor.second ? neighbor.second->getId() : -1) << std::endl;
-        }
+      if (neighbor.first == node) {
+        std::cout << "  -> Itself" << std::endl;
+      } else {
+        std::cout << "  -> Node " << neighbor.first->getId() << " with Edge ID "
+                  << (neighbor.second ? neighbor.second->getId() : -1)
+                  << std::endl;
+      }
     }
     std::cout << std::endl;
   }
@@ -53,7 +56,8 @@ int main() {
 
     std::cout << "Transitions from Node " << node->getId() << ":" << std::endl;
     for (const auto& transition : transitions) {
-        std::cout << "  -> To Node " << transition.first->getId() << " with Probability " << transition.second << std::endl;
+      std::cout << "  -> To Node " << transition.first->getId()
+                << " with Probability " << transition.second << std::endl;
     }
     std::cout << std::endl;
   }

examples/PartitionExample/partition_example.cpp

@@ -19,14 +19,17 @@ int main() {
   // std::cout << *cit_graph_ptr << std::endl;
   std::cout << cit_graph_ptr->getEdgeSet().size() << std::endl;
   std::cout << cit_graph_ptr->getNodeSet().size() << std::endl;
-  auto partitionedTwo = cit_graph_ptr->partitionGraph(
-      CXXGraph::Partitioning::HDRF_ALG, 2, 1, 1, 1, 4);
+  auto partitionedTwo =
+      CXXGraph::Partitioning::Partitioner<int>::partitionGraph(
+          *cit_graph_ptr, CXXGraph::Partitioning::HDRF_ALG, 2, 1, 1, 1, 4);
   std::cout << "end partition two" << std::endl;
-  auto partitionedFour = cit_graph_ptr->partitionGraph(
-      CXXGraph::Partitioning::HDRF_ALG, 4, 1, 1, 1, 4);
+  auto partitionedFour =
+      CXXGraph::Partitioning::Partitioner<int>::partitionGraph(
+          *cit_graph_ptr, CXXGraph::Partitioning::HDRF_ALG, 4, 1, 1, 1, 4);
   std::cout << "end partition four" << std::endl;
-  auto partitionedEight = cit_graph_ptr->partitionGraph(
-      CXXGraph::Partitioning::HDRF_ALG, 8, 1, 1, 1, 4);
+  auto partitionedEight =
+      CXXGraph::Partitioning::Partitioner<int>::partitionGraph(
+          *cit_graph_ptr, CXXGraph::Partitioning::HDRF_ALG, 8, 1, 1, 1, 4);
   std::cout << "end partition eight" << std::endl;
   auto statsTwo = CXXGraph::Partitioning::getPartitionStats(partitionedTwo);
   auto statsFour = CXXGraph::Partitioning::getPartitionStats(partitionedFour);

examples/PrimExample/CMakeLists.txt

@@ -0,0 +1,17 @@
+cmake_minimum_required(VERSION 3.9)
+project(PrimExample)
+
+# specify the C++ standard
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED True)
+
+set(CMAKE_CXX_IMPLICIT_LINK_DIRECTORIES /usr/local/lib ${CMAKE_CXX_IMPLICIT_LINK_DIRECTORIES})
+
+add_executable(prim_example prim_example.cpp)
+target_include_directories(prim_example PUBLIC "${CMAKE_SOURCE_DIR}/include")
+
+target_link_libraries(prim_example
+                        pthread
+                        ssl
+                        crypto
+                        z)