DOC: Updates to python docs (#1039)

* DOC: Updates to python docs * Python Plugin updates * Added python release notes --------- Signed-off-by: Michael Jackson <[email protected]>
BlueQuartzSoftware · Aug 8, 2024 · 6137b7b · 6137b7b
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diff --git a/src/Plugins/SimplnxCore/docs/DBSCANFilter.md b/src/Plugins/SimplnxCore/docs/DBSCANFilter.md
@@ -6,7 +6,7 @@ DREAM3D Review (Clustering)
 
 ## Description
 
-This **Filter** applies the DBSCAN (density-based spatial clustering of applications with noise) algorithm to an **Attribute Array**.  DBSCAN is a _clustering algorithm_ that assigns to each point of the **Attribute Array** a _cluster Id_; points that have the same cluster Id are grouped together more densely (in the sense that the _distance_ between them is small) in the data space (i.e., points that have many nearest neighbors will belong to the same cluster).  The user may select from a number of options to use as the distance metric.  Points that are in sparse regions of the data space are considered "outliers"; these points will belong to cluster Id 0.  Additionally, the user may opt to use a mask to ignore certain points; where the mask is _false_, the points will be categorized as outliers and placed in cluster 0.  The algorithm requires two parameters: a _neighborbood region_, called epsilon; and the minimum number of points needed to form a cluster.  The algorithm, in pseudocode, proceeds as follows:
+This **Filter** applies the DBSCAN (density-based spatial clustering of applications with noise) algorithm to an **Attribute Array**.  DBSCAN is a *clustering algorithm* that assigns to each point of the **Attribute Array** a *cluster Id*; points that have the same cluster Id are grouped together more densely (in the sense that the _distance_ between them is small) in the data space (i.e., points that have many nearest neighbors will belong to the same cluster).  The user may select from a number of options to use as the distance metric.  Points that are in sparse regions of the data space are considered "outliers"; these points will belong to cluster Id 0.  Additionally, the user may opt to use a mask to ignore certain points; where the mask is *false*, the points will be categorized as outliers and placed in cluster 0.  The algorithm requires two parameters: a *neighborbood region*, called epsilon; and the minimum number of points needed to form a cluster.  The algorithm, in pseudocode, proceeds as follows:
 
     for each point p in dataset
     {

diff --git a/src/Plugins/SimplnxCore/docs/RemoveFlaggedVerticesFilter.md b/src/Plugins/SimplnxCore/docs/RemoveFlaggedVerticesFilter.md
@@ -6,7 +6,7 @@ Data Cleanup (Geometry)
 
 ## Description
 
-This **Filter** removes **Vertices** from the supplied **Vertex Geometry** that are flagged as **TRUE** by a boolean mask array. A new reduced **Vertex Geometry** is created that contains all the remaining **Vertices**. It is unknown until run time how many **Vertices** will be removed from the **Geometry**. Therefore, this **Filter** requires that a new **Data Container** be created to contain the reduced **Vertex Geometry**. This new **Vertex Geometry** will contain copies of any **Feature** or **Ensemble** **Attribute Matrices** from the original **Data Container**. Additionally, _all **Vertex** data will be copied_, with tuples *removed* for any **Vertices** removed by the **Filter**. The user must supply a name for the reduced **Vertex Geometry**, but all other copied objects (**Attribute Matrices** and **Attribute Arrays**) will retain the same names as the original source.
+This **Filter** removes **Vertices** from the supplied **Vertex Geometry** that are flagged as **TRUE** by a boolean mask array. A new reduced **Vertex Geometry** is created that contains all the remaining **Vertices**. It is unknown until run time how many **Vertices** will be removed from the **Geometry**. Therefore, this **Filter** requires that a new **Data Container** be created to contain the reduced **Vertex Geometry**. This new **Vertex Geometry** will contain copies of any **Feature** or **Ensemble** **Attribute Matrices** from the original **Data Container**. Additionally, *all **Vertex** data will be copied*, with tuples *removed* for any **Vertices** removed by the **Filter**. The user must supply a name for the reduced **Vertex Geometry**, but all other copied objects (**Attribute Matrices** and **Attribute Arrays**) will retain the same names as the original source.
 
 *Note:* Since it cannot be known before run time how many **Vertices** will be removed, the new **Vertex Geometry** and all associated **Vertex** data to be copied will be initialized to have size 0. Any **Feature** or **Ensemble** information will retain the same dimensions and size.
 

diff --git a/wrapping/python/docs/index_template.rst b/wrapping/python/docs/index_template.rst
@@ -2,7 +2,7 @@
    compiling additional plugins, and you want the python docs
    generated, you will need to add those to the list below
 
-DREAM3D-NX Python Docs (v24.06.05)
+DREAM3D-NX Python Docs (v24.08.03)
 ===================================
 
 Installation
@@ -85,15 +85,16 @@ How to use SIMPLNX from Python
    :maxdepth: 1
    :caption: Release Notes
 
-   ReleaseNotes_240605
-   ReleaseNotes_130
-   ReleaseNotes_127
-   ReleaseNotes_126
-   ReleaseNotes_124
-   ReleaseNotes_123
-   ReleaseNotes_121
-   ReleaseNotes_120
-   ReleaseNotes_110
+   release_notes/ReleaseNotes_240803
+   release_notes/ReleaseNotes_240605
+   release_notes/ReleaseNotes_130
+   release_notes/ReleaseNotes_127
+   release_notes/ReleaseNotes_126
+   release_notes/ReleaseNotes_124
+   release_notes/ReleaseNotes_123
+   release_notes/ReleaseNotes_121
+   release_notes/ReleaseNotes_120
+   release_notes/ReleaseNotes_110
 
 Indices and tables
 ==================

diff --git a/wrapping/python/docs/source/Installation.rst b/wrapping/python/docs/source/Installation.rst
@@ -1,28 +1,17 @@
 Installation
 ============
 
-Latest Version: 24.06.05
+Latest Version: 24.08.03
 -------------------------
 
 The *simplnx* library can be installed through an Anaconda packages from the *BlueQuartzSoftware* channel. This can be achieved
 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
-
-    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 simplnx
-
+    Intel based MacOS machines can *ONLY* install up to Python 3.11. Due to dependecies from
+    conda-forge, Python 3.12 is not possible as of AUG 2024.
 
 
 Full DREAM3D-NX Installation
@@ -36,7 +25,6 @@ Full DREAM3D-NX Installation
 
     conda config --add channels conda-forge
     conda config --set channel_priority strict
-    conda create -n nxpython python=3.10
+    conda create -n nxpython python=3.12
     conda activate nxpython
     conda install -c bluequartzsoftware dream3dnx
-
diff --git a/wrapping/python/docs/source/Tutorial_3.rst b/wrapping/python/docs/source/Tutorial_3.rst
@@ -35,7 +35,7 @@ When Creating a New Plugin (**Use Existing Plugin** is unchecked)
 - **Filter Names (comma-separated)**: This field allows you to specify the programmatic names of the filters you want to create. Each filter name should be separated by a comma.  For example, `FirstFilter,SecondFilter`.
 
 When Using an Existing Plugin (**Use Existing Plugin** is checked)
-*****************************************************************
+*******************************************************************
 
 - **Existing Plugin Location**: This specifies the directory of the existing plugin to which you want to add new filters. You can select the directory by clicking the `Browse` button.
 

diff --git a/wrapping/python/docs/source/User_API.rst b/wrapping/python/docs/source/User_API.rst
@@ -36,7 +36,7 @@ Error & Warning Reporting
          print(f"{filter.name()} :: No errors running the filter")
 
 Creating Geometries
-------------------
+--------------------
 
 All the `simplnx` geometries can be created in Python using the following helper methods:
 

diff --git a/wrapping/python/docs/source/conf.py b/wrapping/python/docs/source/conf.py
@@ -9,7 +9,7 @@
 project = 'SIMPLNX Python Docs'
 copyright = '2024, BlueQuartz Software, LLC'
 author = 'BlueQuartz Software, LLC'
-release = '1.3.0'
+release = '24.08.03'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

diff --git a/...g/python/docs/source/ReleaseNotes_110.rst → ...source/release_notes/ReleaseNotes_110.rst b/...g/python/docs/source/ReleaseNotes_110.rst → ...source/release_notes/ReleaseNotes_110.rst
diff --git a/...g/python/docs/source/ReleaseNotes_120.rst → ...source/release_notes/ReleaseNotes_120.rst b/...g/python/docs/source/ReleaseNotes_120.rst → ...source/release_notes/ReleaseNotes_120.rst
diff --git a/...g/python/docs/source/ReleaseNotes_121.rst → ...source/release_notes/ReleaseNotes_121.rst b/...g/python/docs/source/ReleaseNotes_121.rst → ...source/release_notes/ReleaseNotes_121.rst
diff --git a/...g/python/docs/source/ReleaseNotes_123.rst → ...source/release_notes/ReleaseNotes_123.rst b/...g/python/docs/source/ReleaseNotes_123.rst → ...source/release_notes/ReleaseNotes_123.rst
diff --git a/...g/python/docs/source/ReleaseNotes_124.rst → ...source/release_notes/ReleaseNotes_124.rst b/...g/python/docs/source/ReleaseNotes_124.rst → ...source/release_notes/ReleaseNotes_124.rst
diff --git a/...g/python/docs/source/ReleaseNotes_126.rst → ...source/release_notes/ReleaseNotes_126.rst b/...g/python/docs/source/ReleaseNotes_126.rst → ...source/release_notes/ReleaseNotes_126.rst
diff --git a/...g/python/docs/source/ReleaseNotes_127.rst → ...source/release_notes/ReleaseNotes_127.rst b/...g/python/docs/source/ReleaseNotes_127.rst → ...source/release_notes/ReleaseNotes_127.rst
diff --git a/...g/python/docs/source/ReleaseNotes_130.rst → ...source/release_notes/ReleaseNotes_130.rst b/...g/python/docs/source/ReleaseNotes_130.rst → ...source/release_notes/ReleaseNotes_130.rst
diff --git a/...ython/docs/source/ReleaseNotes_240605.rst → ...rce/release_notes/ReleaseNotes_240605.rst b/...ython/docs/source/ReleaseNotes_240605.rst → ...rce/release_notes/ReleaseNotes_240605.rst
diff --git a/wrapping/python/docs/source/release_notes/ReleaseNotes_240803.rst b/wrapping/python/docs/source/release_notes/ReleaseNotes_240803.rst
@@ -0,0 +1,57 @@
+Release Notes 24.08.03
+======================
+
+With this release we are moving towards a YYMMDD style of versioning. The `simplnx` library is
+under activate development and while we strive to maintain a stable API bugs are
+found that necessitate the changing of the API.
+
+Version 24.08.03
+-----------------
+
+
+API Changes & Additions 24.08.03
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+- No major changes/additions to note
+
+Change Log 24.08.03
+^^^^^^^^^^^^^^^^^^^^
+
+- ENH: Fix compile warnings in FilterUtilities. Init array in DataStore when resizing (#1026) [d534b18d]
+- ENH: Update NXRunner error messages to provide instructions for .json files (#1032) [5aa8dd5f]
+- ENH: Combine and Write STL Files - Allow user to select a Part Number Index to use for numbering. (#1024) [24a870f9]
+- CI: Fixed python tests on asan CI (#1031) [8eccc1bf]
+- CI: Updated nightly ASAN CI to use clang 14 (#1029) [37c3df57]
+- CI: Update GitHub CI to newer GCC & Clang versions. (#1028) [f05b3781]
+- BUG FIX: PeregrineHDF5Reader file system path and Array Type Fixes (#1025) [0332e709]
+- ENH: Allow Crop Image Geometry to only crop a specific dimension (#1021) [c3be139e]
+- BUG FIX: Remove Python plugin import error handling. (#1019) [b9d47447]
+- BUG: Fix Reading Shift File in AlignSectionsList (#1018) [ed04c3ac]
+- ENH: Various ReadPeregrineHDF5File Improvements (#1016) [8346cd36]
+- Fixed C++20 issue with template id in constructor starting in gcc 11 (#1015) [c62fa7f8]
+- ENH: Update required standard to C++20 (#1004) [31406a49]
+- PERF: Inline Keyword and Anonymous Namespace Cleanup (#1013) [639460e9]
+- DOC: ConvertHexGridToSquareGrid Doc Updates (#1014) [37e1159a]
+- COMP: Fix compiler warnings in ComputeSurfaceFeaturesTest (#1003) [8bc16916]
+- BUG: Fix out of core preferences file save bug (#1012) [5f1e159f]
+- BUG: KAM messages should only be printed at 1 a second. (#1008) [a6324cac]
+- FILTERS: Adding MeshIO reader and writers. (#1009) [74a06a32]
+- Remove submodule for geometry creation helper methods. (#1007) [3af3fd55]
+- ENH: Add the ability to resample images as they are read in as an image stack. (#1011) [a2aaa4cb]
+- ENH: Renaming DataAnalysisToolkit to NXDataAnalysisToolkit. (#1010) [1d9a483a]
+- FILTER: Add RemoveFlaggedEdges filter. Update other RemoveFlaggedXXX filters (#986) [d7190167]
+- ENH: Include additional geometry examples and tests. (#1006) [365acfd8]
+- FILTER: SliceTriangleGeometry & CreateAMScanPaths (#984) [8f241745]
+- ENH: More explicit details when a parameter does not validate. (#1005) [34a1c054]
+- ENH: Added a benchmark utility executable (#1002) [90feefba]
+- ENH: Adjust warning text for 0 step value in InitializeDataArray (#999) [cec98fca]
+- BUG: Update geometry find element functions to use static casting (#1000) [d86dbbdc]
+- FILTER/ENH: DBSCAN Filter and Clustering Cleanup (#994) [e0d0cf26]
+- ENH: Update Python Plugin Generation File Structure (#989) [40512e34]
+- BUG: Update node based geometry 'findElementSizes(bool)' family of functions (#991) [baf97023]
+- ENH: Reading OEM EBSD HDF5 Files should have better error messages generated (#996) [95f41e7b]
+- ENH: Added DataStructure::getDataAsUnsafe functions (#998) [788e0736]
+- Update vcpkg baseline for HDF5 1.14.4.3 (#997) [68d0e63f]
+- DOCS: Create Python tutorial covering basic usage and filter writing (#925) [07dab90b]
+- ENH: Small fixes for DREAM3D-NX RC-12 release (#988) [5592a973]
+- ENH: Small fixes for RC-12 release [b7958b48]
diff --git a/wrapping/python/plugins/NXDataAnalysisToolkit/conda/meta.yaml b/wrapping/python/plugins/NXDataAnalysisToolkit/conda/meta.yaml
@@ -11,22 +11,25 @@ source:
 
 build:
   noarch: python
-  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  script: {{ PYTHON }} -m pip install {{ SRC_DIR }}/NXDataAnalysisToolkit -vv --no-deps --no-build-isolation
   number: 0
 
 requirements:
   build:
-    - python >=3.10
+    - python >=3.12
     - pytest
     - pip
+    - hatchling
   run:
-    - python >=3.10
+    - python >=3.12
     - matplotlib
     - numpy
     - opencv
     - scipy
     - h5py
     - pillow
+    - meshio
+    - dream3dnx
 
 test:
   imports:
@@ -35,8 +38,9 @@ test:
     - pip check
   requires:
     - pip
+
 
 about:
   home: https://www.dream3d.io/
   license: BSD
-  summary: DREAM3D-NX consists of data analysis tools (Filters) that allow for the construction of customized workflows (Pipelines) to analyze data.
+  summary: NXDataAnalysisToolkit is a python based plugin for DREAM3D-NX that adds additional filters. These filters can be used from DREAM3D-NX itself or from a python script.
-Original file line number
+Diff line change
@@ Expand Up / @@ -36,7 +36,7 @@ Error & Warning Reporting @@
              print(f"{filter.name()} :: No errors running the filter")
     Creating Geometries
-    ------------------
+    --------------------
     All the `simplnx` geometries can be created in Python using the following helper methods:
@@ Expand Down @@