Develop

.github/workflows/testing.yml

@@ -17,40 +17,6 @@ env:
 
 jobs:
 
-  test_win:
-    runs-on: windows-latest
-    defaults:
-      run:
-        shell: msys2 {0}
-
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          submodules: recursive
-
-      - name: MSYS2 Setup
-        uses: msys2/setup-msys2@v2
-        with:
-          msystem: MINGW64
-          update: false
-          install: mingw-w64-x86_64-gcc mingw-w64-x86_64-cmake mingw-w64-x86_64-python mingw-w64-x86_64-ninja mingw-w64-x86_64-lld
-
-      - name: Configure CMake
-        working-directory: ${{github.workspace}}
-        run: cmake -B build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_FLAGS="-fuse-ld=lld" -DRUN_TESTS=ON
-
-      - name: Build
-        working-directory: ${{github.workspace}}
-        run: cmake --build build --config ${{env.BUILD_TYPE}} -j 2
-
-      - name: Run Examples
-        working-directory: ${{github.workspace}}/build/examples
-        run: python3 run_all_examples.py
-
-      - name: Run Tests
-        working-directory: ${{github.workspace}}/build
-        run: ctest -V
-
   test_mac:
     runs-on: macos-latest
 

docs/pages/getting_started/installation_building.md

@@ -33,10 +33,10 @@ We suggest using the most recent versions when possible.
 
 ```bash
 mkdir build && cd build
-cmake -DCMAKE_BUILD_TYPE=Release -DUSE_CUDA=CUDA ..
+cmake -DCMAKE_BUILD_TYPE=Release -DUSE_CUDA=OFF ..
 make
 ```
-Where `CUDA` is `ON` if CUDA support is needed and `OFF` otherwise.
+This will build the library without CUDA support. If CUDA support is needed, then replace `-DUSE_CUDA=OFF` with `-DUSE_CUDA=ON`.
 
 ```{warning}
 If the library is installed with cuda support, the user code must be compiled using `nvcc`.

src/class_instantiation_list.json

@@ -112,6 +112,13 @@
       "folder": null,
       "exceptions": null
     },
+    {
+      "template": "class HyperGraph<$id_type, $nnz_type, $value_type>",
+      "filename": "object.inc",
+      "ifdef": null,
+      "folder": null,
+      "exceptions": null
+    },
     {
       "template": "class ConverterOrderOne<$value_type>",
       "filename": "converter_order_one.inc",
@@ -224,6 +231,27 @@
       "folder": null,
       "exceptions": null
     },
+    {
+      "template": "class MetisGraphReader<$id_type, $nnz_type, $value_type>",
+      "filename": "metis_graph_reader.inc",
+      "ifdef": null,
+      "folder": null,
+      "exceptions": null
+    },
+    {
+      "template": "class MetisGraphWriter<$id_type, $nnz_type, $value_type>",
+      "filename": "metis_graph_writer.inc",
+      "ifdef": null,
+      "folder": null,
+      "exceptions": null
+    },
+    {
+      "template": "class MTXWriter<$id_type, $nnz_type, $value_type>",
+      "filename": "mtx_writer.inc",
+      "ifdef": null,
+      "folder": null,
+      "exceptions": null
+    },
     {
       "template": "class PigoEdgeListReader<$id_type, $nnz_type, $value_type>",
       "filename": "pigo_edge_list_reader.inc",
@@ -238,6 +266,20 @@
       "folder": null,
       "exceptions": null
     },
+    {
+      "template": "class PatohReader<$id_type, $nnz_type, $value_type>",
+      "filename": "patoh_reader.inc",
+      "ifdef": null,
+      "folder": null,
+      "exceptions": null
+    },
+    {
+      "template": "class PatohWriter<$id_type, $nnz_type, $value_type>",
+      "filename": "patoh_writer.inc",
+      "ifdef": null,
+      "folder": null,
+      "exceptions": null
+    },
     {
       "template": "class BinaryReaderOrderTwo<$id_type, $nnz_type, $value_type>",
       "filename": "binary_reader_order_two.inc",
@@ -343,6 +385,13 @@
       "folder": null,
       "exceptions": null
     },
+    {
+      "template": "class Bandwidth<$id_type, $nnz_type, $value_type>",
+      "filename": "bandwidth.inc",
+      "ifdef": null,
+      "folder": null,
+      "exceptions": null
+    },
     {
       "template": "class RCMReorder<$id_type, $nnz_type, $value_type>",
       "filename": "rcm_reorder.inc",
@@ -364,6 +413,20 @@
       "folder": null,
       "exceptions": null
     },
+    {
+      "template": "class SlashburnReorder<$id_type, $nnz_type, $value_type>",
+      "filename": "slashburn_reorder.inc",
+      "ifdef": null,
+      "folder": null,
+      "exceptions": null
+    },
+    {
+      "template": "class BOBAReorder<$id_type, $nnz_type, $value_type>",
+      "filename": "boba_reorder.inc",
+      "ifdef": null,
+      "folder": null,
+      "exceptions": null
+    },
     {
       "template": "class GenericReorder<$id_type, $nnz_type, $value_type>",
       "filename": "generic_reorder.inc",
@@ -469,27 +532,97 @@
       "folder": null,
       "exceptions": null
     },
+    {
+      "template": "class MinDegreeColumn<$id_type, $nnz_type, $value_type>",
+      "filename": "min_degree_column.inc",
+      "ifdef": null,
+      "folder": null,
+      "exceptions": null
+    },
     {
       "template": "class MaxDegree<$id_type, $nnz_type, $value_type>",
       "filename": "max_degree.inc",
       "ifdef": null,
       "folder": null,
       "exceptions": null
     },
+    {
+      "template": "class MaxDegreeColumn<$id_type, $nnz_type, $value_type>",
+      "filename": "max_degree_column.inc",
+      "ifdef": null,
+      "folder": null,
+      "exceptions": null
+    },
     {
       "template": "class AvgDegree<$id_type, $nnz_type, $value_type, $float_type>",
       "filename": "avg_degree.inc",
       "ifdef": null,
       "folder": null,
       "exceptions": null
     },
+    {
+      "template": "class AvgDegreeColumn<$id_type, $nnz_type, $value_type, $float_type>",
+      "filename": "avg_degree_column.inc",
+      "ifdef": null,
+      "folder": null,
+      "exceptions": null
+    },
+    {
+      "template": "class StandardDeviationDegreeColumn<$id_type, $nnz_type, $value_type, $float_type>",
+      "filename": "standard_deviation_degree_column.inc",
+      "ifdef": null,
+      "folder": null,
+      "exceptions": null
+    },
+    {
+      "template": "class CoefficientOfVariationDegreeColumn<$id_type, $nnz_type, $value_type, $float_type>",
+      "filename": "coefficient_of_variation_degree_column.inc",
+      "ifdef": null,      
+      "folder": null,      
+      "exceptions": null
+    },
+    {
+      "template": "class GeometricAvgDegreeColumn<$id_type, $nnz_type, $value_type, $float_type>",
+      "filename": "geometric_avg_degree_column.inc",
+      "ifdef": null,
+      "folder": null,
+      "exceptions": null
+    },
     {
       "template": "class MinMaxAvgDegree<$id_type, $nnz_type, $value_type, $float_type>",
       "filename": "min_max_avg_degree.inc",
       "ifdef": null,
       "folder": null,
       "exceptions": null
     },
+    {
+      "template": "class MedianDegreeColumn<$id_type, $nnz_type, $value_type, $float_type>",
+      "filename": "median_degree_column.inc",
+      "ifdef": null,
+      "folder": null,
+      "exceptions": null
+    },
+    {
+      "template": "class OffDiagBlockNNZ<$id_type, $nnz_type, $value_type>",
+      "filename": "off_diag_block_nnz.inc",
+      "ifdef": null,
+      "folder": null,
+      "exceptions": null
+    },
+    {
+      "template": "class Profile<$id_type, $nnz_type, $value_type>",
+      "filename": "profile.inc",
+      "ifdef": null,
+      "folder": null,
+      "exceptions": null
+    },
+    {
+      "template": "class TriangleCount<$id_type, $nnz_type, $value_type>",
+      "filename": "triangle_count.inc",
+      "ifdef": null,
+      "folder": null,
+      "exceptions": null
+    },
     {
       "template": "class JaccardWeights<$id_type, $nnz_type, $value_type, $float_type>",
       "filename": "jaccard_weights.inc",

src/sparsebase/bases/iobase.h

@@ -15,6 +15,7 @@
 #include "sparsebase/io/binary_writer_order_two.h"
 #include "sparsebase/io/edge_list_reader.h"
 #include "sparsebase/io/mtx_reader.h"
+#include "sparsebase/io/mtx_writer.h"
 #include "sparsebase/io/pigo_edge_list_reader.h"
 #include "sparsebase/io/pigo_mtx_reader.h"
 #include "sparsebase/io/reader.h"
@@ -290,6 +291,102 @@ class IOBase {
     io::BinaryWriterOrderOne<ValueType> writer(filename);
     return writer.WriteArray(array);
   }
+  //! Write a CSR object to a matrix market file
+  /*!
+   * Write a CSR object to a matrix market file.
+   * @tparam IDType type to represent the number of rows and columns in the
+   * object.
+   * @tparam NNZType type to represent the number of non-zeros in the object.
+   * @tparam ValueType type to represent the data inside the matrix (vertex
+   * weights in the case of a graph).
+   * @param csr a pointer at the `CSR<IDType, NNZType, ValueType>` object to write.
+   * @param filename path to write the file.
+   * @param object is either matrix or vector.
+   * @param format is either coordinate or array.
+   * @param field is either real, double, complex, integer or pattern.
+   * @param symmetry is either general (legal for real, complex,
+    integer or pattern fields), symmetric (real, complex, integer or pattern),
+     skew-symmetric (real, complex or integer), or hermitian (complex only).
+   */
+  template <typename IDType, typename NNZType, typename ValueType>
+  static void WriteCSRToMTX(
+      format::CSR<IDType, NNZType, ValueType>* csr,
+      std::string filename,
+      std::string object = "matrix",
+      std::string format = "coordinate",
+      std::string field = "real",
+      std::string symmetry = "general") {
+    io::MTXWriter<IDType, NNZType, ValueType> writer(filename,
+                                                     object,
+                                                     format,
+                                                     field,
+                                                     symmetry);
+    return writer.WriteCSR(csr);
+  }
+  //! Write a COO object to a matrix market file
+  /*!
+   * Write a COO object to a matrix market file.
+   * @tparam IDType type to represent the number of rows and columns in the
+   * object.
+   * @tparam NNZType type to represent the number of non-zeros in the object.
+   * @tparam ValueType type to represent the data inside the matrix (vertex
+   * weights in the case of a graph).
+   * @param coo a pointer at the `COO<IDType, NNZType, ValueType>` object to write.
+   * @param filename path to write the file.
+   * @param object is either matrix or vector.
+   * @param format is either coordinate or array.
+   * @param field is either real, double, complex, integer or pattern.
+   * @param symmetry is either general (legal for real, complex,
+    integer or pattern fields), symmetric (real, complex, integer or pattern),
+     skew-symmetric (real, complex or integer), or hermitian (complex only).
+   */
+  template <typename IDType, typename NNZType, typename ValueType>
+  static void WriteCOOToMTX(
+      format::CSR<IDType, NNZType, ValueType>* coo,
+      std::string filename,
+      std::string object = "matrix",
+      std::string format = "coordinate",
+      std::string field = "real",
+      std::string symmetry = "general") {
+    io::MTXWriter<IDType, NNZType, ValueType> writer(filename,
+                                                     object,
+                                                     format,
+                                                     field,
+                                                     symmetry);
+    return writer.WriteCOO(coo);
+  }
+  //! Write an Array object to a matrix market file
+  /*!
+   * Write an Array object to a matrix market file.
+   * @tparam IDType type to represent the number of rows and columns in the
+   * object.
+   * @tparam NNZType type to represent the number of non-zeros in the object.
+   * @tparam ValueType type to represent the data inside the array (vertex
+   * weights in the case of a graph).
+   * @param arr a pointer at the `Array<ValueType>` object to write.
+   * @param filename path to write the file.
+   * @param object is either matrix or vector.
+   * @param format is either coordinate or array.
+   * @param field is either real, double, complex, integer or pattern.
+   * @param symmetry is either general (legal for real, complex,
+    integer or pattern fields), symmetric (real, complex, integer or pattern),
+     skew-symmetric (real, complex or integer), or hermitian (complex only).
+   */
+  template <typename IDType, typename NNZType, typename ValueType>
+  static void WriteArrayToMTX(
+      format::Array<ValueType>* arr,
+      std::string filename,
+      std::string object = "matrix",
+      std::string format = "coordinate",
+      std::string field = "real",
+      std::string symmetry = "general") {
+    io::MTXWriter<IDType, NNZType, ValueType> writer(filename,
+                                                     object,
+                                                     format,
+                                                     field,
+                                                     symmetry);
+    return writer.WriteArray(arr);
+  }
 };
 }  // namespace sparsebase::bases
 #endif  // SPARSEBASE_PROJECT_IOBASE_H