feat: Harmonize XML tools in repository (with geos-xml-viewer)

.github/workflows/README.md

@@ -27,7 +27,6 @@ Tests each Python package independently to ensure:
 - `geos-trame` - Trame-based visualization
 - `geos-utils` - Utility functions
 - `geos-xml-tools` - XML preprocessing and formatting
-- `geos-xml-viewer` - XML viewing tools
 - `hdf5-wrapper` - HDF5 file handling wrapper
 - `mesh-doctor` - Tools to perform checks on vtkUnstructuredGrids
 - `pygeos-tools` - GEOS Python tools
@@ -268,7 +267,6 @@ Tests are automatically skipped when changes only affect:
 - `geos-pv/` - ParaView utilities
 - `geos-timehistory/` - Time history analysis
 - `geos-trame/` - Trame visualization
-- `geos-xml-viewer/` - XML viewing tools
 
 #### Configuration Files
 - `.gitignore`, `.gitattributes` - Git configuration

.github/workflows/python-package.yml

@@ -67,7 +67,6 @@ jobs:
           - geos-timehistory
           - geos-trame
           - geos-xml-tools
-          - geos-xml-viewer
           - mesh-doctor
           - hdf5-wrapper
           - pygeos-tools
@@ -227,7 +226,6 @@ jobs:
           "^geos-pv/"
           "^geos-timehistory/"
           "^geos-trame/"
-          "^geos-xml-viewer/"
         )
 
         # Check if any changed file affects GEOS-integrated packages

docs/conf.py

@@ -19,7 +19,7 @@
 # Add python modules to be documented
 python_root = '..'
 python_modules = ( 'geos-ats', 'geos-geomechanics', 'geos-mesh', 'geos-processing', 'geos-pv', 'geos-timehistory',
-                   'geos-utils', 'geos-xml-tools', 'geos-xml-viewer', 'hdf5-wrapper', 'mesh-doctor', 'pygeos-tools' )
+                   'geos-utils', 'geos-xml-tools', 'hdf5-wrapper', 'mesh-doctor', 'pygeos-tools' )
 
 
 for m in python_modules:
@@ -77,7 +77,7 @@
                          "pyevtk", "pylvarray", "scipy", "segyio", "xmltodict", "xsdata" ]
 autodoc_typehints = 'none'
 autodoc_typehints_format = 'short'
-suppress_warnings = [ "autodoc.mocked_object" ]
+suppress_warnings = [ "autodoc", "autodoc.mocked_object" ]
 typehints_defaults = 'braces'
 
 # The suffix(es) of source filenames.

docs/geos-xml-tools.rst

@@ -1,82 +1,22 @@
-
-.. _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
-^^^
+====================
 
-.. automodule:: geos.xml_tools.main
-    :members:
+**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.xml_processor
-    :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_formatter
-    :members:
+.. toctree::
+    :maxdepth: 1
+    :caption: Contents:
 
-.. automodule:: geos.xml_tools.unit_manager
-    :members:
+    ./geos_xml_tools_docs/command_line_interface
 
-.. automodule:: geos.xml_tools.regex_tools
-    :members:
+    ./geos_xml_tools_docs/preprocess
 
-.. automodule:: geos.xml_tools.xml_redundancy_check
-    :members:
+    ./geos_xml_tools_docs/format_xml
 
-.. automodule:: geos.xml_tools.attribute_coverage
-    :members:
+    ./geos_xml_tools_docs/check_xml_attribute_coverage
 
-.. automodule:: geos.xml_tools.table_generator
-    :members:
+    ./geos_xml_tools_docs/check_xml_redundancy
 
+    ./geos_xml_tools_docs/api

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: 

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 

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