GEOS-DEV · alexbenedicto · Jul 3, 2025 · Jul 10, 2025 · Jul 11, 2025 · Jul 11, 2025
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -49,7 +49,6 @@ jobs:
           - geos-trame
           - geos-utils
           - geos-xml-tools
-          - geos-xml-viewer
           - hdf5-wrapper
           - pygeos-tools
         include:

diff --git a/README.md b/README.md
@@ -38,7 +38,6 @@ The following packages define hands-on executables that can be used through the
 
 * `mesh-doctor`: GEOS pre-processing application
 * `time-history`: load and plot hdf5 files
-* `geos-xml-viewer`: load GEOS xml file and display geometrical objects (mesh, boxes, wells)
 * `geos-trame`: web interface to check, display objects, and edit GEOS xml file (see [Trame documentation](https://kitware.github.io/trame/guide/tutorial/))
 
 
@@ -60,6 +59,7 @@ GEOS Python packages dependency tree (inter-dependency and main external depende
 │
 ├── geos-xml-tools
 │   ├── lxml
+│   ├── pyvista
 │
 ├── geos-mesh
 │   ├── geos-utils
@@ -86,11 +86,6 @@ GEOS Python packages dependency tree (inter-dependency and main external depende
 │   ├── pyvista
 │   ├── trame
 │
-├── geos-xml-viewer
-│   ├── geos-xml-tools
-│   ├── geos-mesh
-│   ├── pyvista
-│
 ├── geos-pv
     ├── geos-prep
     ├── geos-posp

diff --git a/docs/conf.py b/docs/conf.py
@@ -18,7 +18,7 @@
 # Add python modules to be documented
 python_root = '..'
 python_modules = ( 'geos-ats', 'geos-geomechanics', 'geos-mesh', 'geos-posp', 'geos-pv', 'geos-timehistory',
-                   'geos-utils', 'geos-xml-tools', 'geos-xml-viewer', 'hdf5-wrapper', 'pygeos-tools' )
+                   'geos-utils', 'geos-xml-tools', 'hdf5-wrapper', 'pygeos-tools' )
 
 
 for m in python_modules:
@@ -45,7 +45,7 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.napoleon', 'sphinx_design', 'sphinx_rtd_theme', 'sphinxarg.ext', 'sphinxcontrib.programoutput', 
+    'sphinx.ext.napoleon', 'sphinx_design', 'sphinx_rtd_theme', 'sphinxarg.ext', 'sphinxcontrib.programoutput',
     'sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.mathjax', 'sphinx.ext.todo', 'sphinx.ext.viewcode'
 ]
 

diff --git a/docs/geos-xml-tools.rst b/docs/geos-xml-tools.rst
@@ -1,82 +1,24 @@
-
-.. _XMLToolsPackage:
-
 GEOS XML Tools
---------------------------
-
-The `geos-xml-tools` python package adds a set of advanced features to the GEOS xml format: units, parameters, and symbolic expressions.
-See :ref:`PythonToolsSetup` for details on setup instructions, and `Advanced XML Features <https://geosx-geosx.readthedocs-hosted.com/en/latest/coreComponents/fileIO/doc/InputXMLFiles.html#advanced-xml-features>`_ for a detailed description of the input format.
-The available console scripts for this package and its API are described below.
-
-
-convert_abaqus
-^^^^^^^^^^^^^^
-
-Convert an abaqus format mesh file to gmsh or vtk format.
-
-.. argparse::
-   :module: geos.xml_tools.command_line_parsers
-   :func: build_preprocessor_input_parser
-   :prog: preprocess_xml
-
-
-format_xml
-^^^^^^^^^^^^^^
-
-Formats an xml file.
-
-.. argparse::
-   :module: geos.xml_tools.command_line_parsers
-   :func: build_xml_formatter_input_parser
-   :prog: format_xml
-
-
-check_xml_attribute_coverage
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Checks xml attribute coverage for files in the GEOS repository.
-
-.. argparse::
-   :module: geos.xml_tools.command_line_parsers
-   :func: build_attribute_coverage_input_parser
-   :prog: check_xml_attribute_coverage
-
-
-check_xml_redundancy
-^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Checks for redundant attribute definitions in an xml file, such as those that duplicate the default value.
-
-.. argparse::
-   :module: geos.xml_tools.command_line_parsers
-   :func: build_xml_redundancy_input_parser
-   :prog: check_xml_redundancy
-
+====================
 
-API
-^^^
+**geos-xml-tools** is a Python package that adds advanced features to the GEOS XML format, including units, parameters, and symbolic expressions.
 
-.. automodule:: geos.xml_tools.main
-    :members:
+See :ref:`PythonToolsSetup` for setup instructions, and `Advanced XML Features <https://geosx-geosx.readthedocs-hosted.com/en/latest/coreComponents/fileIO/doc/InputXMLFiles.html#advanced-xml-features>`_ for a detailed description of the input format. 
 
-.. automodule:: geos.xml_tools.xml_processor
-    :members:
+.. toctree::
+    :maxdepth: 1
+    :caption: Contents:
 
-.. automodule:: geos.xml_tools.xml_formatter
-    :members:
+    ./geos_xml_tools_docs/command_line_interface
 
-.. automodule:: geos.xml_tools.unit_manager
-    :members:
+    ./geos_xml_tools_docs/preprocess
 
-.. automodule:: geos.xml_tools.regex_tools
-    :members:
+    ./geos_xml_tools_docs/format_xml
 
-.. automodule:: geos.xml_tools.xml_redundancy_check
-    :members:
+    ./geos_xml_tools_docs/check_xml_attribute_coverage
 
-.. automodule:: geos.xml_tools.attribute_coverage
-    :members:
+    ./geos_xml_tools_docs/check_xml_redundancy
 
-.. automodule:: geos.xml_tools.table_generator
-    :members:
+    ./geos_xml_tools_docs/vtk_builder
 
+    ./geos_xml_tools_docs/api
diff --git a/docs/geos-xml-viewer.rst b/docs/geos-xml-viewer.rst
diff --git a/docs/geos_pv_docs/PVGeosDeckReader.rst b/docs/geos_pv_docs/PVGeosDeckReader.rst
@@ -0,0 +1,39 @@
+PVGeosDeckReader
+================
+
+Overview
+--------
+- `PVGeosDeckReader` is a Python-based Paraview reader that allows users to open GEOS XML files and create mesh objects for visualization and analysis.
+- The plugin is implemented in `PVGeosDeckReader.py` and registered as `PythonGeosDeckReader` in Paraview.
+- It outputs a `vtkPartitionedDataSetCollection` representing the mesh and associated regions as defined in the XML file.
+
+Key Features
+------------
+- **Direct XML loading**: Open GEOS XML input files (`.xml`) in Paraview as native datasets.
+- **Region support**: The reader uses the `Region` attribute (or a user-specified attribute) to organize mesh data.
+- **Integration with GEOS workflows**: Enables direct inspection and analysis of simulation input decks without conversion steps.
+
+How to Use
+----------
+1. Install the geos-pv package and ensure Paraview is set up to use Python plugins.
+2. In Paraview, load the plugin (typically via the Python Plugin Manager or by specifying the path to `PVGeosDeckReader.py`).
+3. Use the "Open" dialog in Paraview to select a GEOS XML file. Choose the `PythonGeosDeckReader` when prompted.
+4. The mesh and regions defined in the XML will be loaded as a multi-block dataset for visualization and further processing.
+
+Technical Details
+-----------------
+- The plugin is implemented as a subclass of `VTKPythonAlgorithmBase` and uses the `create_vtk_deck` function from geos-xml-tools to build the VTK data structure.
+- The plugin exposes a `FileName` property for selecting the XML file and can be extended to support additional attributes or options.
+
+Example
+-------
+.. code-block:: console
+
+    paraview --python-script=path/to/PVGeosDeckReader.py
+    # Or load via the Paraview GUI
+
+    # In Paraview:
+    # File > Open > select input.xml > choose PythonGeosDeckReader
+
+.. note::
+    This plugin is intended for users who want to inspect or debug GEOS input decks visually, or to prepare data for further Paraview-based workflows. 
diff --git a/docs/geos_pv_docs/readers.rst b/docs/geos_pv_docs/readers.rst
@@ -1,6 +1,13 @@
 Paraview readers
 ================
 
+.. toctree::
+   :maxdepth: 1
+   :caption: Contents:
+
+   ./PVGeosDeckReader.rst
+
+
 readers.PVGeosLogReader module
 ----------------------------------
 

diff --git a/docs/geos_xml_tools_docs/api.rst b/docs/geos_xml_tools_docs/api.rst
@@ -0,0 +1,26 @@
+API
+===
+
+.. automodule:: geos.xml_tools.main
+    :members:
+
+.. automodule:: geos.xml_tools.xml_processor
+    :members:
+
+.. automodule:: geos.xml_tools.xml_formatter
+    :members:
+
+.. automodule:: geos.xml_tools.unit_manager
+    :members:
+
+.. automodule:: geos.xml_tools.regex_tools
+    :members:
+
+.. automodule:: geos.xml_tools.xml_redundancy_check
+    :members:
+
+.. automodule:: geos.xml_tools.attribute_coverage
+    :members:
+
+.. automodule:: geos.xml_tools.table_generator
+    :members: 
diff --git a/docs/geos_xml_tools_docs/check_xml_attribute_coverage.rst b/docs/geos_xml_tools_docs/check_xml_attribute_coverage.rst
@@ -0,0 +1,19 @@
+Check for attribute coverage
+============================
+
+Analyzes how well a project's XML files cover the possibilities defined in an XML Schema Definition (.xsd) file.
+
+This tool parses the schema, scans XML files in the specified directory, and generates a report showing which attributes are used, their values, and their default values from the schema.
+Useful for identifying missing or underused attributes in a codebase.
+
+Example
+-------
+.. code-block:: console
+
+    geos-xml-tools coverage -r /path/to/geos/root -o coverage_report.xml
+
+
+.. argparse::
+   :module: geos.xml_tools.command_line_parsers
+   :func: build_attribute_coverage_input_parser
+   :prog: check_xml_attribute_coverage 
diff --git a/docs/geos_xml_tools_docs/check_xml_redundancy.rst b/docs/geos_xml_tools_docs/check_xml_redundancy.rst
@@ -0,0 +1,18 @@
+Check redundancy
+================
+
+Checks for redundant attribute definitions in XML files, such as those that duplicate default values or are otherwise unnecessary.
+
+This tool scans XML files in the specified directory and reports attributes that are defined but do not differ from their defaults, helping to clean up and simplify XML configurations.
+
+Example
+-------
+.. code-block:: console
+
+    geos-xml-tools redundancy -r /path/to/geos/root
+
+
+.. argparse::
+   :module: geos.xml_tools.command_line_parsers
+   :func: build_xml_redundancy_input_parser
+   :prog: check_xml_redundancy