DOC: Update Python documentation with improved navigation (#895)

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

src/simplnx/Core/Application.cpp

@@ -215,6 +215,11 @@ std::vector<Uuid> Application::getSimplUuid(const Uuid& simplnxUuid)
 
 void Application::loadPlugins(const std::filesystem::path& pluginDir, bool verbose)
 {
+  if(!std::filesystem::exists(pluginDir) && verbose)
+  {
+    fmt::print("Plugin Directory {} does not exist. Skipping", pluginDir.string());
+    return;
+  }
   if(verbose)
   {
     fmt::print("Loading Plugins from {}\n", pluginDir.string());

wrapping/python/docs/generate_sphinx_docs.cpp

@@ -28,7 +28,7 @@ namespace
 std::map<nx::core::Uuid, std::string> s_ParameterMap;
 
 const std::string k_WebServerAddress = "http://www.dream3d.io/nx_reference_manual";
-const std::string k_WebServerFilterFolder = "Filters";
+const std::string k_WebServerFilterFolder = "html";
 } // namespace
 
 #define ADD_PARAMETER_TRAIT(thing1, thing2)                                                                                                                                                            \
@@ -748,7 +748,7 @@ void GeneratePythonRstFiles()
       rstStream << "   " << rstDescription << "\n\n";
 
       // Tack on the link to the web address for the full documentation
-      const std::string webAddress = fmt::format("{}/{}/{}", k_WebServerAddress, k_WebServerFilterFolder, filterClassName);
+      const std::string webAddress = fmt::format("{}/{}/{}/{}.html", k_WebServerAddress, k_WebServerFilterFolder, plugName, filterClassName);
       rstStream << "   `Link to the full online documentation for " << filterClassName << " <" << webAddress << ">`_ \n\n";
 
       const auto& parameters = filter->parameters();

wrapping/python/docs/index_template.rst

@@ -5,7 +5,7 @@
 DREAM3D-NX Python Docs
 =======================
 
-Latest Version: 1.2.6
+Latest Version: 1.2.7
 ---------------------
 
 The *simplnx* library can be installed through an Anaconda packages from the *BlueQuartzSoftware* channel. This can be achieved
@@ -21,24 +21,45 @@ by creating a new virtual environment
 
 .. toctree::
    :maxdepth: 3
-   :caption: Contents:
+   :caption: Conceptual
 
    Installation
    Overview
    DataObjects
    Geometry
-   User_API
-   Developer_API
+
+.. toctree::
+   :maxdepth: 3
+   :caption: Using SIMPLNX
+
    Python_Introduction
-   Writing_A_New_Python_Filter
+   User_API
    Reference_Frame_Notes
+
+.. toctree::
+   :maxdepth: 3
+   :caption: Filter Writers
+
+   Writing_A_New_Python_Filter
+   Developer_API
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Filter API/Docs
+
+@PLUGIN_LIST@
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Release Notes
+
    ReleaseNotes_110
    ReleaseNotes_120
    ReleaseNotes_121
    ReleaseNotes_123
    ReleaseNotes_124
    ReleaseNotes_126
-@PLUGIN_LIST@
+   ReleaseNotes_127
 
 Indices and tables
 ==================

wrapping/python/docs/source/Developer_API.rst

@@ -1,5 +1,5 @@
-API for Developers
-===================
+SIMPLNX Filter Writing API
+==========================
 
 General Parameters 
 ------------------

wrapping/python/docs/source/Installation.rst

@@ -1,11 +1,19 @@
 Installation
 ============
 
-Latest Version: 1.2.6
+Latest Version: 1.2.7
 ---------------------
 
 The *simplnx* library can be installed through an Anaconda packages from the *BlueQuartzSoftware* channel. This can be achieved
-by creating a new virtual environment
+by creating a new virtual environment and installing SIMPLNX into that environment.
+
+
+SIMPLNX Installation
+^^^^^^^^^^^^^^^^^^^^
+
+.. attention::
+
+    This kind of installation will allow you to utilize the SIMPLNX library through python. 
 
 .. code:: shell
 
@@ -15,3 +23,20 @@ by creating a new virtual environment
     conda activate nxpython
     conda install -c bluequartzsoftware simplnx
 
+
+
+Full DREAM3D-NX Installation
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. attention::
+
+    This kind of installation will allow you to utilize the full DREAM3D-NX application
+
+.. code:: shell
+
+    conda config --add channels conda-forge
+    conda config --set channel_priority strict
+    conda create -n nxpython python=3.10
+    conda activate nxpython
+    conda install -c bluequartzsoftware dream3dnx
+

wrapping/python/docs/source/Python_Introduction.rst

@@ -303,7 +303,20 @@ Interoperating with Numpy
     This will hopefully be addressed in a future update.
 
 
-This code example shows how to create a simplnx DataArray and then use that array 
+SIMPLNX DataArray objects are exposed to python through the use of a numpy view into the Data Array. This means that any modifications
+to the numpy view are immediately reflected in the DataArray itself. This kind of interaction opens up many 3rd party libraries that
+operate on numpy arrays and views such as numpy itself, pillow (for image processing), scipy and others.
+
+Once the DataStructure has a DataArray allocated into it through the use of a filter, the user can get a view of that
+DataArray through the following:
+
+.. code:: python
+
+    output_array_path = nx.DataPath(["Image Geometry/Cell Data/RGB"])
+    rgb_np_view = data_structure[output_array_path].npview()
+
+
+The following code examples show how to create a simplnx DataArray and then use that array 
 as a numpy view.
 
 The next code section was take from `basic_arrays.py <https://github.com/bluequartzsoftware/simplnx/tree/develop/wrapping/python/examples/basic_arrays.py>`__
@@ -345,7 +358,8 @@ The next code section was take from `basic_arrays.py <https://github.com/bluequa
                                     tuple_dimensions=[[99]],
                                     output_data_array=array_path,
                                     initialization_value='0')
-    npdata = data_structure[array_path].store.npview()
+    # Get the new numpy view
+    npdata = data_structure[array_path].npview()
     # Read the CSV file into the DataArray using the numpy view
     file_path = 'angles.csv'
     npdata[:] = np.loadtxt(file_path, delimiter=',')
@@ -356,6 +370,7 @@ The next code section was take from `basic_arrays.py <https://github.com/bluequa
                                             input_type=0,
                                             output_orientation_array_name='Quaternions',
                                             output_type=2)
+    
     # Get the new numpy view and then print the data
-    npdata = data_structure['Quaternions'].store.npview()
+    npdata = data_structure['Quaternions'].npview()
     print(npdata)

wrapping/python/docs/source/User_API.rst

@@ -4,6 +4,10 @@ API for Users
 Error & Warning Reporting
 --------------------------
 
+.. _UserAPI:
+.. py:module:: nx
+
+
 .. _Result:
 .. py:class:: Result