CONDA: Various fixes to allow packaging of python bindings. (#691)

* CONDA: Various fixes to allow packaging of python bindings.
* TestOne and TestTwo can now be disabled if testing is disabled.
* .pyi files are correctly generated on Windows when generating anaconda packages
* Summary.cmake reformatted a bit to better group the cmake variables being printed.
* Remove TestOne and TestTwo from Docs. Add missing data_structure arg
* allow TOC to show each filter in the side bar.
* Use list(APPEND...) in cmake code

Co-authored-by: Jared Duffey <[email protected]>

---------

Signed-off-by: Michael Jackson <[email protected]>
Co-authored-by: Jared Duffey <[email protected]>

CMakeLists.txt

@@ -786,13 +786,18 @@ endif()
 if(COMPLEX_ENABLE_OrientationAnalysis)
   set(COMPLEX_PLUGIN_LIST ${COMPLEX_PLUGIN_LIST} OrientationAnalysis)
 endif()
+
+if(COMPLEX_BUILD_TESTS)
+  list(APPEND COMPLEX_PLUGIN_LIST TestOne TestTwo)
+endif()
+
 # Add any plugins to the list
 set(COMPLEX_PLUGIN_LIST ${COMPLEX_PLUGIN_LIST} ${COMPLEX_EXTRA_PLUGINS})
 
 
 foreach(plugin ${COMPLEX_PLUGIN_LIST})
-  if(NOT DEFINED COMPLEX_ENABLE_${plugin})
-    set(COMPLEX_ENABLE_${plugin} ON)
+  if(NOT DEFINED COMPLEX_PLUGIN_ENABLE_${plugin})
+    set(COMPLEX_PLUGIN_ENABLE_${plugin} ON)
   endif()
   complex_add_plugin(PLUGIN_NAME ${plugin})
 endforeach()

cmake/Summary.cmake

@@ -37,6 +37,12 @@ endfunction()
 #------------------------------------------------------------------------------------
 # Print out a Summary Section:
 message(STATUS "* ============= COMPLEX Configuration Summary ===============")
+set(ALL_PROJECTS complex)
+foreach(proj ${ALL_PROJECTS})
+    # cmpGitRevisionString(PROJECT_NAME ${proj})
+    get_property(githash GLOBAL PROPERTY ${proj}_GIT_HASH)
+    message(STATUS "* ${proj}: ${${proj}_SOURCE_DIR}  Git Hash: ${githash}")
+endforeach()
 message(STATUS "* BUILD_TYPE: ${CMAKE_BUILD_TYPE}")
 message(STATUS "* COMPLEX: ${complex_VERSION}")
 OSInformation()
@@ -55,36 +61,29 @@ message(STATUS "* nod (${nod_VERSION}) ${nod_DIR}")
 message(STATUS "* reproc++ (${reproc_VERSION}) ${reproc++_DIR}")
 
 message(STATUS "* -------------- Complex Configuration Options -------------------------------------")
-message(STATUS "* COMPLEX_BUILD_PYTHON: ${COMPLEX_BUILD_PYTHON}")
-message(STATUS "* Python3_EXECUTABLE: ${Python3_EXECUTABLE}")
-message(STATUS "* MKDOCS_EXECUTABLE: ${MKDOCS_EXECUTABLE}")
-
-message(STATUS "* COMPLEX_EMBED_PYTHON: ${COMPLEX_EMBED_PYTHON}")
 message(STATUS "* COMPLEX_BUILD_TESTS: ${COMPLEX_BUILD_TESTS}")
 message(STATUS "* COMPLEX_ENABLE_MULTICORE: ${COMPLEX_ENABLE_MULTICORE}")
 message(STATUS "* COMPLEX_ENABLE_COMPRESSORS: ${COMPLEX_ENABLE_COMPRESSORS}")
 message(STATUS "* COMPLEX_DOWNLOAD_TEST_FILES: ${COMPLEX_DOWNLOAD_TEST_FILES}")
 message(STATUS "* COMPLEX_WRITE_TEST_OUTPUT: ${COMPLEX_WRITE_TEST_OUTPUT}")
-
-get_property(ComplexPluginTargets GLOBAL PROPERTY ComplexPluginTargets)
-foreach(d3dPlugin ${ComplexPluginTargets})
-    message(STATUS "* COMPLEX_ENABLE_${d3dPlugin}: ${COMPLEX_ENABLE_${d3dPlugin}}")
-endforeach()
-
 message(STATUS "* COMPLEX_ENABLE_LINK_FILESYSTEM: ${COMPLEX_ENABLE_LINK_FILESYSTEM}")
 message(STATUS "* COMPLEX_ENABLE_INSTALL: ${COMPLEX_ENABLE_INSTALL}")
 message(STATUS "* COMPLEX_ENABLE_PACKAGING: ${COMPLEX_ENABLE_PACKAGING}")
 message(STATUS "* COMPLEX_BUILD_DOCS: ${COMPLEX_BUILD_DOCS}")
 message(STATUS "* DREAM3D_DATA_DIR: ${DREAM3D_DATA_DIR}")
 
-set(ALL_PROJECTS complex)
-foreach(proj ${ALL_PROJECTS})
-    # cmpGitRevisionString(PROJECT_NAME ${proj})
-    get_property(githash GLOBAL PROPERTY ${proj}_GIT_HASH)
-    message(STATUS "* ${proj}: ${${proj}_SOURCE_DIR}  Git Hash: ${githash}")
+message(STATUS "* -------------- Complex Python Configuration Options -------------------------------------")
+message(STATUS "* COMPLEX_BUILD_PYTHON: ${COMPLEX_BUILD_PYTHON}")
+message(STATUS "* COMPLEX_EMBED_PYTHON: ${COMPLEX_EMBED_PYTHON}")
+message(STATUS "* Python3_EXECUTABLE: ${Python3_EXECUTABLE}")
+message(STATUS "* MKDOCS_EXECUTABLE: ${MKDOCS_EXECUTABLE}")
+
+message(STATUS "* -------------- Known Plugins ------------------------------------------------------")
+foreach(plugin ${COMPLEX_PLUGIN_LIST})
+    message(STATUS "* COMPLEX_PLUGIN_ENABLE_${plugin}: ${COMPLEX_PLUGIN_ENABLE_${plugin}}")
 endforeach()
-message(STATUS "* -------------- Plugins ------------------------------------------------------")
 
+message(STATUS "* -------------- Active Plugins ------------------------------------------------------")
 get_property(ComplexPluginTargets GLOBAL PROPERTY ComplexPluginTargets)
 foreach(d3dPlugin ${ComplexPluginTargets})
     get_property(PluginNumFilters GLOBAL PROPERTY ${d3dPlugin}_filter_count)
@@ -93,4 +92,5 @@ foreach(d3dPlugin ${ComplexPluginTargets})
     get_property(PluginDocsEnabled GLOBAL PROPERTY ${d3dPlugin}_docs_enabled)
     message(STATUS "* ${d3dPlugin}: [${COMPLEX_PLUGIN_ENABLE_${d3dPlugin}}] ${PluginNumFilters} Filters  Docs:[${PluginDocsEnabled}]")
 endforeach()
+
 message(STATUS "* ======================================================================")

conda/bld.bat

@@ -1,6 +1,14 @@
+:: ****************************************************************************
+:: This script file builds the necessary dependencies that are not found as 
+:: part of a python environment but are needed to ultimately build the 
+:: complex python bindings.
+:: ****************************************************************************
+
 mkdir sdk
 
-rem "H5Support"
+:: ****************************************************************************
+:: Build the H5Support library
+:: ****************************************************************************
 
 mkdir h5support_build
 cd h5support_build
@@ -30,7 +38,9 @@ if errorlevel 1 exit 1
 
 cd ..
 
-rem "EbsdLib"
+:: ****************************************************************************
+:: Build the EbsdLib library
+:: ****************************************************************************
 
 mkdir ebsdlib_build
 cd ebsdlib_build
@@ -59,7 +69,9 @@ if errorlevel 1 exit 1
 
 cd ..
 
-rem "expected-lite"
+:: ****************************************************************************
+:: Build the expected-light library
+:: ****************************************************************************
 
 mkdir expected-lite_build
 cd expected-lite_build
@@ -80,7 +92,9 @@ if errorlevel 1 exit 1
 
 cd ..
 
-rem "span-lite"
+:: ****************************************************************************
+:: Build the span-light library
+:: ****************************************************************************
 
 mkdir span-lite_build
 cd span-lite_build
@@ -101,7 +115,9 @@ if errorlevel 1 exit 1
 
 cd ..
 
-rem "nod"
+:: ****************************************************************************
+:: Build the nod library
+:: ****************************************************************************
 
 mkdir nod_build
 cd nod_build
@@ -118,9 +134,25 @@ if errorlevel 1 exit 1
 cmake --build . --target install
 if errorlevel 1 exit 1
 
+
+:: ****************************************************************************
+:: Install the EbsdLibrary into the python build environment so that stubgen
+:: has access to it.
+:: ****************************************************************************
 cd ..
+cd ebsdlib_build
+
+cmake -D CMAKE_INSTALL_PREFIX:PATH="%LIBRARY_PREFIX%" .
+if errorlevel 1 exit 1
 
-rem "complex"
+cmake --build . --target install
+if errorlevel 1 exit 1
+
+cd ..
+
+:: ****************************************************************************
+:: Build the complex library
+:: ****************************************************************************
 
 mkdir build
 cd build
@@ -134,11 +166,3 @@ if errorlevel 1 exit 1
 cmake --build . --target install
 if errorlevel 1 exit 1
 
-cd ..
-cd ebsdlib_build
-
-cmake -D CMAKE_INSTALL_PREFIX:PATH="%LIBRARY_PREFIX%" .
-if errorlevel 1 exit 1
-
-cmake --build . --target install
-if errorlevel 1 exit 1

conda/recipe.yaml

@@ -42,7 +42,7 @@ requirements:
     - ninja
     - git
   host:
-    - "python {{ python }}"
+    - python
     - mypy
     - numpy >=1.16
     - boost_mp11

src/Plugins/TestOne/CMakeLists.txt

@@ -1,6 +1,8 @@
 include("${complex_SOURCE_DIR}/cmake/Plugin.cmake")
 
 set(PLUGIN_NAME "TestOne")
+set(${PLUGIN_NAME}_SOURCE_DIR ${complex_SOURCE_DIR}/src/Plugins/${PLUGIN_NAME})
+
 #------------------------------------------------------------------------------
 # These are all the filters in the plugin. All filters should be kept in the
 # PLUGIN_NAME/src/PLUGIN_NAME/Filters/ directory.
@@ -15,7 +17,7 @@ set(FilterList
 
 create_complex_plugin(NAME ${PLUGIN_NAME}
                       FILTER_LIST ${FilterList}
-                      DESCRIPTION "Plugin for Comp${PLUGIN_NAME}lexCore"
+                      DESCRIPTION "Test Plugin for ${PLUGIN_NAME}"
                       VERSION "0.1.0"
 )
 

src/Plugins/TestTwo/CMakeLists.txt

@@ -1,6 +1,8 @@
 include("${complex_SOURCE_DIR}/cmake/Plugin.cmake")
 
 set(PLUGIN_NAME "TestTwo")
+set(${PLUGIN_NAME}_SOURCE_DIR ${complex_SOURCE_DIR}/src/Plugins/${PLUGIN_NAME})
+
 #------------------------------------------------------------------------------
 # These are all the filters in the plugin. All filters should be kept in the
 # PLUGIN_NAME/src/PLUGIN_NAME/Filters/ directory.
@@ -10,7 +12,7 @@ set(FilterList
 
 create_complex_plugin(NAME ${PLUGIN_NAME}
                       FILTER_LIST ${FilterList}
-                      DESCRIPTION "Plugin for Comp${PLUGIN_NAME}lexCore"
+                      DESCRIPTION "Test Plugin for ${PLUGIN_NAME}"
                       VERSION "0.1.0"
 )
 

test/CMakeLists.txt

@@ -14,11 +14,6 @@ find_package(Catch2 CONFIG REQUIRED)
 
 include(Catch)
 
-get_property(COMPLEX_PLUGIN_COUNT GLOBAL PROPERTY COMPLEX_PLUGIN_COUNT)
-add_subdirectory(${complex_SOURCE_DIR}/src/Plugins/TestOne ${complex_BINARY_DIR}/Plugins/TestOne)
-add_subdirectory(${complex_SOURCE_DIR}/src/Plugins/TestTwo ${complex_BINARY_DIR}/Plugins/TestTwo)
-MATH(EXPR COMPLEX_PLUGIN_COUNT "${COMPLEX_PLUGIN_COUNT}+2")
-
 add_subdirectory(UnitTestCommon)
 
 add_executable(complex_test
@@ -51,9 +46,21 @@ target_link_libraries(complex_test
     complex::UnitTestCommon
 )
 
+#------------------------------------------------------------------------------
 # Require that the test plugins are built before tests because some tests
 # require loading from those plugins but don't want to link to them.
-add_dependencies(complex_test TestOne TestTwo)
+get_property(COMPLEX_PLUGIN_COUNT GLOBAL PROPERTY COMPLEX_PLUGIN_COUNT)
+
+#------------------------------------------------------------------------------
+# Create dependencies with complex_test on each of the test plugins
+#------------------------------------------------------------------------------
+if(COMPLEX_PLUGIN_ENABLE_TestOne)
+  add_dependencies(complex_test TestOne)
+endif()
+
+if(COMPLEX_PLUGIN_ENABLE_TestTwo)
+  add_dependencies(complex_test TestTwo)
+endif()
 
 set_target_properties(complex_test
   PROPERTIES

test/PluginTest.cpp

@@ -31,6 +31,16 @@ TEST_CASE("Test Loading Plugins")
   const auto& filterHandles = filterList->getFilterHandles();
   auto plugins = filterList->getLoadedPlugins();
 
+  if(plugins.size() != COMPLEX_PLUGIN_COUNT)
+  {
+    std::cout << "Incorrect number of plugins were loaded.\n"
+              << "Expected: " << COMPLEX_PLUGIN_COUNT << "\nLoaded: " << plugins.size() << "\nLoaded Plugins are:\n";
+    for(auto const& plugin : plugins)
+    {
+      std::cout << plugin->getName() << std::endl;
+    }
+  }
+
   REQUIRE(plugins.size() == COMPLEX_PLUGIN_COUNT);
   REQUIRE(filterHandles.size() >= 2);
 
@@ -62,6 +72,15 @@ TEST_CASE("Test Singleton")
   auto plugins = filterList->getLoadedPlugins();
 
   // Check plugins were loaded
+  if(plugins.size() != COMPLEX_PLUGIN_COUNT)
+  {
+    std::cout << "Incorrect number of plugins were loaded.\n"
+              << "Expected: " << COMPLEX_PLUGIN_COUNT << "\nLoaded: " << plugins.size() << "\nLoaded Plugins are:\n";
+    for(auto const& plugin : plugins)
+    {
+      std::cout << plugin->getName() << std::endl;
+    }
+  }
   REQUIRE(plugins.size() == COMPLEX_PLUGIN_COUNT);
 
   // Check filters loaded

wrapping/python/ReadMe.md

@@ -38,6 +38,13 @@ Create the package from the `complex` sources
     [user@host] $ cd complex/conda
     [user@host] $ conda build . 
 
+For faster environment solves mamba can also be used. 
+
+```
+conda install boa
+conda mambabuild --python 3.8|3.9|3.10 .
+```
+
 ### Uploading to Anaconda.org
 
     [user@host] $ conda login

wrapping/python/docs/generate_sphinx_docs.cpp

@@ -353,6 +353,9 @@ void GenerateRstFilterDocs()
       IFilter::UniquePointer filter = filterListPtr->createFilter(filterHandle);
       // auto plugin = filterListPtr->getPlugin(filterHandle);
 
+      rstStream << filterClassName << "\n";
+      rstStream << GenerateUnderline(filterClassName.size(), '-') << "\n\n";
+
       rstStream << ".. _" << filterClassName << ":\n";
       rstStream << ".. py:class:: " << filterClassName << "\n\n";
 
@@ -399,18 +402,16 @@ void GenerateRstFilterDocs()
       }
       rstStream << '\n';
 
-      rstStream << "   .. py:method:: Execute(";
+      rstStream << "   .. py:method:: Execute(data_structure";
 
       std::stringstream memberStream;
+      memberStream << "      :param complex.DataStructure data_structure: The DataStructure object that holds the data to be processed.\n";
 
       size_t index = 0;
       for(const auto& parameterPair : parameters)
       {
         auto const& anyParameter = parameterPair.second;
-        if(index != 0)
-        {
-          rstStream << ", ";
-        }
+        rstStream << ", ";
 
         rstStream << parameterPair.first;
         memberStream << "      :param " << s_ParameterMap[anyParameter->uuid()] << " " << anyParameter->name() << ": " << anyParameter->helpText() << "\n";
@@ -466,6 +467,10 @@ void GenerateIndexRstFile()
   for(const auto& plugin : pluginListPtr)
   {
     std::string plugName = plugin->getName();
+    if(plugName == "TestOne" || plugName == "TestTwo")
+    {
+      continue;
+    }
     const std::string pluginRootDir = fmt::format("{}", s_PluginDirMap[plugName]);
 
     if(plugName == "ComplexCore")

wrapping/python/examples/angle_conversion.py

@@ -13,7 +13,7 @@
 data_structure = cx.DataStructure()
 # Create a DataArray to copy the Euler Angles into 
 array_path = cx.DataPath(['Euler Angles'])
-result = cx.CreateDataArray.execute(data_structure,
+result = cx.CreateDataArray.execute(data_structure=data_structure,
                                     numeric_type=cx.NumericType.float32,
                                     component_count=3,
                                     tuple_dimensions=[[99]],