Create CTest unit tests to run the Python example files.

Signed-off-by: Michael Jackson <[email protected]>

.github/workflows/linux.yml

@@ -43,7 +43,7 @@ jobs:
           sudo apt-get -y install ninja-build
       - name: Install Sphinx
         run: |
-          sudo pip install sphinx myst-parser sphinx-markdown-tables sphinx_rtd_theme
+          sudo pip install sphinx myst-parser sphinx-markdown-tables sphinx_rtd_theme numpy
       - name: Setup NuGet Credentials
         shell: bash
         run: |

.github/workflows/macos.yml

@@ -32,7 +32,7 @@ jobs:
           brew install ninja
       - name: Install Sphinx
         run: |
-          sudo pip3 install sphinx myst-parser sphinx-markdown-tables sphinx_rtd_theme
+          sudo pip3 install sphinx myst-parser sphinx-markdown-tables sphinx_rtd_theme numpy
       - name: Setup NuGet Credentials
         shell: bash
         run: |

.github/workflows/windows.yml

@@ -49,7 +49,7 @@ jobs:
           -source "https://nuget.pkg.github.com/BlueQuartzSoftware/index.json"
       - name: Install Sphinx
         run: |
-          pip install sphinx myst-parser sphinx-markdown-tables sphinx_rtd_theme
+          pip install sphinx myst-parser sphinx-markdown-tables sphinx_rtd_theme numpy
       - name: Configure
         run: |
           cmake --preset ci-windows-${{matrix.toolset}} ${{github.workspace}} -T ${{matrix.toolset}}

CMakeLists.txt

@@ -63,7 +63,7 @@ option(COMPLEX_ENABLE_INSTALL "Enables COMPLEX install rules" ON)
 file(TO_CMAKE_PATH "${CMAKE_COMMAND}" CMAKE_COMMAND_NORM)
 
 project(complex
-  VERSION 1.2.0
+  VERSION 1.2.1
   DESCRIPTION "SIMPL Redesign"
   HOMEPAGE_URL "https://github.com/BlueQuartzSoftware/complex"
   LANGUAGES CXX

CMakePresets.json

@@ -33,6 +33,10 @@
           "type": "BOOL",
           "value": "ON"
         },
+        "COMPLEX_ENABLE_PYTHON_TESTS": {
+          "type": "BOOL",
+          "value": "ON"
+        },
         "COMPLEX_EMBED_PYTHON": {
           "type": "BOOL",
           "value": "OFF"

cmake/Utility.cmake

@@ -460,3 +460,86 @@ function(cmpBuildDateRevisionString)
   endif()
 
 endfunction()
+
+
+#-------------------------------------------------------------------------------
+# @Brief function AddPythonTest
+# @ NAME
+# @ FILE
+# @ PYTHONPATH
+#-------------------------------------------------------------------------------
+function(AddPythonTest)
+  set(options )
+  set(oneValueArgs NAME FILE)
+  set(multiValueArgs PYTHONPATH)
+  cmake_parse_arguments(ARGS "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+  if(COMPLEX_BUILD_PYTHON)
+    if(WIN32)
+      add_test(NAME ${ARGS_NAME}
+        COMMAND ${complex_SOURCE_DIR}/wrapping/python/testing/anaconda_test.bat
+      )
+
+      set_property(TEST ${ARGS_NAME}
+        PROPERTY
+          ENVIRONMENT
+            "PYTHON_TEST_FILE=${ARGS_FILE}"
+      )
+    else()
+      add_test(NAME ${ARGS_NAME}
+        COMMAND ${complex_SOURCE_DIR}/wrapping/python/testing/anaconda_test.sh
+      )
+
+      set_property(TEST ${ARGS_NAME}
+        PROPERTY
+          ENVIRONMENT
+            "PYTHON_TEST_FILE=${ARGS_FILE}"
+      )
+    endif()
+  else()
+    add_test(NAME ${ARGS_NAME}
+      COMMAND ${PYTHON_EXECUTABLE} ${ARGS_FILE}
+    )
+  endif()
+
+  if(WIN32)
+    string(REPLACE ";" "\\;" ARGS_PYTHONPATH "${ARGS_PYTHONPATH}")
+  else()
+    string(REPLACE ";" ":" ARGS_PYTHONPATH "${ARGS_PYTHONPATH}")
+  endif()
+
+  set_property(TEST ${ARGS_NAME}
+    APPEND
+    PROPERTY
+      ENVIRONMENT
+      "PYTHONPATH=${ARGS_PYTHONPATH}"
+      "${complex_PYTHON_TEST_ENV}"
+  )
+endfunction()
+
+#-------------------------------------------------------------------------------
+# @Brief function CreatePythonTests
+# @ PREFIX
+# @ INPUT_DIR
+# @ TEST_NAMES
+#-------------------------------------------------------------------------------
+function(CreatePythonTests)
+  set(options)
+  set(oneValueArgs PREFIX INPUT_DIR)
+  set(multiValueArgs TEST_NAMES)
+  cmake_parse_arguments(ARGS "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+  set(TESTS_PYTHONPATH
+    "$<TARGET_FILE_DIR:complex>"
+  )
+
+  foreach(test ${ARGS_TEST_NAMES})
+    string(REPLACE "/" "_" test_name ${test})
+    set(PY_TEST_NAME ${ARGS_PREFIX}_${test_name})
+
+    AddPythonTest(NAME ${PY_TEST_NAME}
+      FILE ${ARGS_INPUT_DIR}/${test}.py
+      PYTHONPATH ${TESTS_PYTHONPATH}
+    )
+  endforeach()
+endfunction()

conda/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "complex" %}
-{% set version = "1.2.0" %}
+{% set version = "1.2.1" %}
 
 package:
   name: {{ name|lower }}

conda/recipe.yaml

@@ -1,5 +1,5 @@
 context:
-  version: "1.2.0"
+  version: "1.2.1"
   name: complex
 
 package:

src/Plugins/ComplexCore/src/ComplexCore/Filters/CreateDataArray.cpp

@@ -134,7 +134,8 @@ IFilter::PreflightResult CreateDataArray::preflightImpl(const DataStructure& dat
     if(!useDims)
     {
       return MakePreflightErrorResult(
-          -78602, "The DataArray to be created is not within an AttributeMatrix, so the dimensions cannot be determined implicitly. Check Set Tuple Dimensions to set the dimensions");
+          -78602, fmt::format("The DataArray to be created '{}'is not within an AttributeMatrix, so the dimensions cannot be determined implicitly. Check Set Tuple Dimensions to set the dimensions",
+                              dataArrayPath.toString()));
     }
     else
     {

src/Plugins/ComplexCore/src/ComplexCore/Filters/ReadTextDataArrayFilter.cpp

@@ -106,7 +106,8 @@ IFilter::PreflightResult ReadTextDataArrayFilter::preflightImpl(const DataStruct
     if(!useDims)
     {
       return MakePreflightErrorResult(
-          -77602, "The DataArray to be created is not within an AttributeMatrix, so the dimensions cannot be determined implicitly. Check Set Tuple Dimensions to set the dimensions");
+          -78602, fmt::format("The DataArray to be created '{}'is not within an AttributeMatrix, so the dimensions cannot be determined implicitly. Check Set Tuple Dimensions to set the dimensions",
+                              arrayPath.toString()));
     }
     else
     {

src/Plugins/ComplexCore/wrapping/python/complexpy.cpp

@@ -10,7 +10,6 @@
 #include "ComplexCore/ComplexCoreFilterBinding.hpp"
 
 #include <ComplexCore/ComplexCorePlugin.hpp>
-
 #include <complex/DataStructure/AttributeMatrix.hpp>
 #include <complex/DataStructure/DataArray.hpp>
 #include <complex/DataStructure/DataGroup.hpp>
@@ -80,6 +79,7 @@
 #include <complex/Pipeline/AbstractPipelineNode.hpp>
 #include <complex/Pipeline/Pipeline.hpp>
 #include <complex/Pipeline/PipelineFilter.hpp>
+#include <complex/Utilities/DataGroupUtilities.hpp>
 
 #include <fmt/ranges.h>
 
@@ -510,6 +510,37 @@ PYBIND11_MODULE(complex, mod)
   dataStructure.def_property_readonly("size", &DataStructure::getSize);
   dataStructure.def("__len__", &DataStructure::getSize);
   dataStructure.def("remove", py::overload_cast<const DataPath&>(&DataStructure::removeData));
+  dataStructure.def("hierarchy_to_str", [](DataStructure& self) {
+    std::stringstream ss;
+    self.exportHierarchyAsText(ss);
+    return ss.str();
+  });
+  dataStructure.def("hierarchy_to_graphviz", [](DataStructure& self) {
+    std::stringstream ss;
+    self.exportHierarchyAsGraphViz(ss);
+    return ss.str();
+  });
+  dataStructure.def("get_children", [](DataStructure& self, complex::DataPath& parentPath) {
+    if(parentPath.empty())
+    {
+      std::vector<DataPath> outputPaths;
+      for(const auto* object : self.getTopLevelData())
+      {
+        auto topLevelPath = DataPath::FromString(object->getDataPaths()[0].getTargetName()).value();
+        outputPaths.push_back(topLevelPath);
+      }
+      return outputPaths;
+    }
+    else
+    {
+      auto result = complex::GetAllChildDataPaths(self, parentPath);
+      if(result)
+      {
+        return result.value();
+      }
+      return std::vector<DataPath>{};
+    }
+  });
 
   py::class_<BaseGroup, DataObject, std::shared_ptr<BaseGroup>> baseGroup(mod, "BaseGroup");
   baseGroup.def("contains", py::overload_cast<const std::string&>(&BaseGroup::contains, py::const_));

src/complex/DataStructure/DataStructure.cpp

@@ -870,72 +870,77 @@ void DataStructure::resetIds(DataObject::IdType startingId)
   m_RootGroup.updateIds(updatedIds);
 }
 
-void DataStructure::exportHeirarchyAsGraphViz(std::ostream& outputStream) const
+void DataStructure::exportHierarchyAsGraphViz(std::ostream& outputStream) const
 {
   // initialize dot file
   outputStream << "digraph DataGraph {\n"
                << "\tlabelloc =\"t\"\n"
-               << "\trankdir=LR;\n\n";
-
+               << "\trankdir=LR;\n"
+               << "\tlabel=\"DataStructure Hierarchy\"\n"
+               << "\tlabelloc=\"t\"\n"
+               << "\tfontcolor=\"#FFFFFA\"\n"
+               << "\tfontsize=12\n"
+               << "\tgraph [splines=true bgcolor=\"#242627\"]\n"
+               << "\tnode [shape=record style=\"filled\" fillcolor=\"#1D7ECD\" fontsize=12 fontcolor=\"#FFFFFA\"]\n"
+               << "\tedge [dir=front arrowtail=empty style=\"\" color=\"#FFFFFA\"]\n\n";
   // set base case
   for(const auto* object : getTopLevelData())
   {
     auto topLevelPath = DataPath::FromString(object->getDataPaths()[0].getTargetName()).value();
     auto optionalDataPaths = GetAllChildDataPaths(*this, topLevelPath);
+    outputStream << "\n/* Top level DataObject: " << topLevelPath.getTargetName() << " */\n\"" << topLevelPath.getTargetName() << "\";\n";
 
-    if(!optionalDataPaths.has_value() || optionalDataPaths.value().size() == 0)
+    if(optionalDataPaths.has_value() && !optionalDataPaths.value().empty())
     {
-      outputStream << "\"" << topLevelPath.getTargetName() << "\";\n\n";
+      // Begin recursion
+      recurseHierarchyToGraphViz(outputStream, optionalDataPaths.value(), topLevelPath.getTargetName());
     }
-
-    // Begin recursion
-    recurseHeirarchyToGraphViz(outputStream, optionalDataPaths.value(), topLevelPath.getTargetName());
   }
 
   // close dot file
   outputStream << "}" << std::endl; // for readability
 }
 
-void DataStructure::recurseHeirarchyToGraphViz(std::ostream& outputStream, const std::vector<DataPath> paths, const std::string& parent) const
+void DataStructure::exportHierarchyAsText(std::ostream& outputStream) const
 {
-  for(const auto& path : paths)
+  // set base case
+  for(const auto* object : getTopLevelData())
   {
-    // Output parent node, child node, and edge connecting them in .dot format
-    outputStream << "\"" << parent << "\" -> \"" << path.getTargetName() << "\"\n";
+    auto topLevelPath = DataPath::FromString(object->getDataPaths()[0].getTargetName()).value();
+    outputStream << k_Delimiter << topLevelPath.getTargetName() << "\n";
+    auto optionalDataPaths = GetAllChildDataPaths(*this, topLevelPath);
 
-    // pull child paths or skip to next iteration
-    auto optionalChildPaths = GetAllChildDataPaths(*this, path);
-    if(!optionalChildPaths.has_value() || optionalChildPaths.value().size() == 0)
+    if(optionalDataPaths.has_value() && !optionalDataPaths.value().empty())
     {
-      continue;
+      // Begin recursion
+      recurseHierarchyToText(outputStream, optionalDataPaths.value(), "");
     }
-
-    // recurse
-    recurseHeirarchyToGraphViz(outputStream, optionalChildPaths.value(), path.getTargetName());
   }
-  outputStream << "\n"; // for readability
+  outputStream << std::endl; // for readability
 }
 
-void DataStructure::exportHeirarchyAsText(std::ostream& outputStream) const
+void DataStructure::recurseHierarchyToGraphViz(std::ostream& outputStream, const std::vector<DataPath> paths, const std::string& parent) const
 {
-  // set base case
-  for(const auto* object : getTopLevelData())
+  for(const auto& path : paths)
   {
-    auto topLevelPath = DataPath::FromString(object->getDataPaths()[0].getTargetName()).value();
-    auto optionalDataPaths = GetAllChildDataPaths(*this, topLevelPath);
-
-    outputStream << k_Delimiter << topLevelPath.getTargetName() << "\n";
+    auto* dataObjectPtr = getData(path);
+    // Output parent node, child node, and edge connecting them in .dot format
+    outputStream << "\"" << parent << "\" -> \"" << path.getTargetName() << "\"\n";
 
-    if(optionalDataPaths.has_value() || optionalDataPaths.value().size() != 0)
+    // pull child paths or skip to next iteration
+    auto optionalChildPaths = GetAllChildDataPaths(*this, path);
+    if(!optionalChildPaths.has_value() || optionalChildPaths.value().empty())
     {
-      // Begin recursion
-      recurseHeirarchyToText(outputStream, optionalDataPaths.value(), "");
+      continue;
     }
+
+    // recurse
+    recurseHierarchyToGraphViz(outputStream, optionalChildPaths.value(), path.getTargetName());
   }
-  outputStream << std::endl; // for readability
+  // outputStream << "\n"; // for readability
 }
 
-void DataStructure::recurseHeirarchyToText(std::ostream& outputStream, const std::vector<DataPath> paths, std::string indent) const
+void DataStructure::recurseHierarchyToText(std::ostream& outputStream, const std::vector<DataPath> paths, std::string indent) const
 {
   indent += "  ";
 
@@ -946,13 +951,13 @@ void DataStructure::recurseHeirarchyToText(std::ostream& outputStream, const std
 
     // pull child paths or skip to next iteration
     auto optionalChildPaths = GetAllChildDataPaths(*this, path);
-    if(!optionalChildPaths.has_value() || optionalChildPaths.value().size() == 0)
+    if(!optionalChildPaths.has_value() || optionalChildPaths.value().empty())
     {
       continue;
     }
 
     // recurse
-    recurseHeirarchyToText(outputStream, optionalChildPaths.value(), indent);
+    recurseHierarchyToText(outputStream, optionalChildPaths.value(), indent);
   }
 }
 

src/complex/DataStructure/DataStructure.hpp

@@ -665,14 +665,14 @@ class COMPLEX_EXPORT DataStructure
    * @param outputStream the child class of ostream to output dot syntax to
    * @return
    */
-  void exportHeirarchyAsGraphViz(std::ostream& outputStream) const;
+  void exportHierarchyAsGraphViz(std::ostream& outputStream) const;
 
   /**
    * @brief Outputs data graph in console readable format
    * @param outputStream the child class of ostream to output to
    * @return
    */
-  void exportHeirarchyAsText(std::ostream& outputStream) const;
+  void exportHierarchyAsText(std::ostream& outputStream) const;
 
   /**
    * @brief Copy assignment operator. The copied DataStructure's observers are not retained.
@@ -800,7 +800,7 @@ class COMPLEX_EXPORT DataStructure
    * @param parent name of the calling parent to output
    * @return
    */
-  void recurseHeirarchyToGraphViz(std::ostream& outputStream, const std::vector<DataPath> paths, const std::string& parent) const;
+  void recurseHierarchyToGraphViz(std::ostream& outputStream, const std::vector<DataPath> paths, const std::string& parent) const;
 
   /**
    * @brief The recursive function to parse graph and dump names to and output stream in
@@ -810,7 +810,7 @@ class COMPLEX_EXPORT DataStructure
    * @param indent the indent for the heirarchy
    * @return
    */
-  void recurseHeirarchyToText(std::ostream& outputStream, const std::vector<DataPath> paths, std::string indent) const;
+  void recurseHierarchyToText(std::ostream& outputStream, const std::vector<DataPath> paths, std::string indent) const;
 
   /**
    * @brief Notifies observers to the provided message.