GEOS-DEV · alexbenedicto · Apr 15, 2025 · Mar 26, 2025 · Mar 26, 2025 · Apr 2, 2025
diff --git a/.gitignore b/.gitignore
@@ -162,4 +162,7 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+#.idea/
+
+# VSCode
+.vscode
diff --git a/README.md b/README.md
@@ -128,7 +128,11 @@ Installation
     python -m pytest ./<PACKAGE_NAME>
     ```
 
-**NOTE: geos-pv package cannot be build alone, but together with Paraview ([see Paraview compilation guide](https://gitlab.kitware.com/paraview/paraview/-/blob/master/Documentation/dev/build.md)). It is recommended to use Paraview v5.12+, which is based on python 3.10+. Alternatively, plugins from geos-pv/PVplugins can be manually loaded into Paraview ([see documentation](https://docs.paraview.org/en/latest/ReferenceManual/pythonProgrammableFilter.html#python-algorithm)).**
+  [!WARNING]
+  Due to local package conflicts with `pip install`, it is recommended either to build the packages one by one, or to inlude only top-level packages (see dependency tree hereabove) in the build list.
+
+  [!NOTE]
+  geos-pv package cannot be build alone, but together with Paraview ([see Paraview compilation guide](https://gitlab.kitware.com/paraview/paraview/-/blob/master/Documentation/dev/build.md)). It is recommended to use Paraview v5.12+, which is based on python 3.10+. Alternatively, plugins from geos-pv/PVplugins can be manually loaded into Paraview ([see documentation](https://docs.paraview.org/en/latest/ReferenceManual/pythonProgrammableFilter.html#python-algorithm)).
 
 
 Contributions
@@ -141,8 +145,8 @@ If you would like to report a bug, please submit an [issue](https://github.com/G
 If you would like to contribute to GEOS Python packages, please respect the following guidelines:
 
 1. Create a new branch named from this template: `[CONTRIBUTOR]/[TYPE]/[TITLE]` where CONTRIBUTOR is the name of the contributor, TYPE is the type of contribution among 'feature', 'refactor', 'doc', 'ci', TITLE is a short title for the branch.
-1. Add your code trying to integrate into the current code architecture.
-1. Push the branch, open a new PR, and add reviewers
+2. Add your code trying to integrate into the current code architecture.
+3. Push the branch, open a new PR respecting naming [semantics](https://gist.github.com/joshbuchea/6f47e86d2510bce28f8e7f42ae84c716), and add reviewers
 
 If you do not have the rights to push the code and open new PRs, consider opening a new issue to explain what you want to do and ask for the dev rights.
 
@@ -170,6 +174,9 @@ dependencies = [
 ]
 ```
 
+[!IMPORTANT]
+geos-pv dependencies are managed using a requirements.txt (together with the setup.py) file where all internal (and external if needed) dependencies are present. It ensures that internal dependency paths are correctly set when plugins are manually loaded into Paraview.
+
 Release
 -------
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -17,7 +17,8 @@
 
 # Add python modules to be documented
 python_root = '..'
-python_modules = ( 'geos-ats', 'geos-geomechanics', 'geos-mesh', 'geos-posp', 'geos-timehistory', 'geos-utils', 'geos-xml-tools', 'geos-xml-viewer', 'hdf5-wrapper', 'pygeos-tools' )
+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' )
+
 
 for m in python_modules:
     sys.path.insert( 0, os.path.abspath( os.path.join( python_root, m, 'src' ) ) )
@@ -48,7 +49,7 @@
 ]
 
 autoclass_content = 'both'
-autodoc_mock_imports = [ "ats", "colorcet", "h5py", "lxml", "meshio", "mpi4py", "scipy", "paraview", "pygeosx", "pylvarray", "vtk", "xmlschema", "xsdata" ]
+autodoc_mock_imports = [ "ats", "colorcet", "h5py", "lxml", "matplotlib", "meshio", "mpi4py", "scipy", "pandas", "paraview", "pygeosx", "pylvarray", "vtk", "xmlschema", "xsdata", ]
 autodoc_typehints = 'none'
 autodoc_typehints_format = 'short'
 suppress_warnings = [ "autodoc.mocked_object" ]

diff --git a/docs/geos-pv.rst b/docs/geos-pv.rst
@@ -0,0 +1,12 @@
+GEOS Paraview plugins
+=====================
+
+.. toctree::
+   :maxdepth: 5
+   :caption: Contents:
+
+   ./geos_pv_docs/home.rst
+
+   ./geos_pv_docs/modules.rst
+
+   ./geos_pv_docs/readers.rst
diff --git a/docs/geos_posp_docs/PVplugins.rst b/docs/geos_posp_docs/PVplugins.rst
@@ -75,14 +75,7 @@ PVGeomechanicsWorkflowVolumeWell plugin
 
 .. automodule:: PVplugins.PVGeomechanicsWorkflowVolumeWell
 
-
-PVGeosLogReader plugin
---------------------------------
-
-.. automodule:: PVplugins.PVGeosLogReader
-
-
-PVMergeBlocksEnhanced plugin
+PVplugins.PVMergeBlocksEnhanced module
 --------------------------------------
 
 .. automodule:: PVplugins.PVMergeBlocksEnhanced
@@ -93,14 +86,7 @@ PVMohrCirclePlot plugin
 
 .. automodule:: PVplugins.PVMohrCirclePlot
 
-
-PVPythonViewConfigurator plugin
------------------------------------------
-
-.. automodule:: PVplugins.PVPythonViewConfigurator
-
-
-PVSurfaceGeomechanics plugin
+PVplugins.PVSurfaceGeomechanics module
 --------------------------------------
 
 .. automodule:: PVplugins.PVSurfaceGeomechanics

diff --git a/docs/geos_posp_docs/modules.rst b/docs/geos_posp_docs/modules.rst
@@ -6,8 +6,6 @@ Processing
 
    filters
 
-   readers
-
    processing
 
    pyvistaTools
diff --git a/docs/geos_posp_docs/processing.rst b/docs/geos_posp_docs/processing.rst
@@ -3,14 +3,6 @@ Processing functions
 
 This package define functions to process data.
 
-geos_posp.processing.geosLogReaderFunctions module
-------------------------------------------------------
-
-.. automodule:: geos_posp.processing.geosLogReaderFunctions
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 geos_posp.processing.multiblockInpectorTreeFunctions module
 ---------------------------------------------------------------
 

diff --git a/docs/geos_posp_docs/readers.rst b/docs/geos_posp_docs/readers.rst
diff --git a/docs/geos_posp_docs/visu.pythonViewUtils.rst b/docs/geos_posp_docs/visu.pythonViewUtils.rst
diff --git a/docs/geos_posp_docs/visu.rst b/docs/geos_posp_docs/visu.rst
@@ -9,6 +9,4 @@ This package includes visualization tools dedicated to Paraview software.
 
    visu.PVUtils
 
-   visu.mohrCircles
-
-   visu.pythonViewUtils
+   visu.mohrCircles
diff --git a/docs/geos_pv_docs/geosLogReaderUtils.rst b/docs/geos_pv_docs/geosLogReaderUtils.rst
@@ -0,0 +1,45 @@
+GeosLogReaderUtils functions
+============================
+
+This package define functions dedicated to the GeosLogReader.
+
+
+geos.pv.geosLogReaderUtils.GeosLogReaderAquifers module
+-------------------------------------------------------------------
+
+.. automodule:: geos.pv.geosLogReaderUtils.GeosLogReaderAquifers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+geos.pv.geosLogReaderUtils.geosLogReaderConvergence module
+---------------------------------------------------------------------
+
+.. automodule:: geos.pv.geosLogReaderUtils.GeosLogReaderConvergence
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+geos.pv.geosLogReaderUtils.GeosLogReaderFlow module
+---------------------------------------------------------------
+
+.. automodule:: geos.pv.geosLogReaderUtils.GeosLogReaderFlow
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+geos.pv.geosLogReaderUtils.GeosLogReaderFunctions module
+--------------------------------------------------------------------
+
+.. automodule:: geos.pv.geosLogReaderUtils.geosLogReaderFunctions
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+geos.pv.geosLogReaderUtils.GeosLogReaderWells module
+--------------------------------------------------------------------
+
+.. automodule:: geos.pv.geosLogReaderUtils.GeosLogReaderWells
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/geos_pv_docs/home.rst b/docs/geos_pv_docs/home.rst
@@ -0,0 +1,18 @@
+Home
+====
+
+**geos-pv** is a Python package that gathers `Paraview <https://www.paraview.org/>`_ plugins of GEOS python tools. 
+
+It includes:
+
+* Paraview readers allowing to load data;
+* generic tools to processes meshes;
+* GEOS pre-processing tools to clean and check GEOS input mesh;
+* GEOS post-processing tools to clean GEOS output mesh, compute additional properties, or create specific plots such as Mohr's circle plot.
+
+The packages can be loaded into Paraview using the Plugin Manager from `Tools > Plugin Manager`. On success, you will 
+see the selected plugin in the `Filters`` menu (see `Paraview documentation <https://docs.paraview.org/en/latest/ReferenceManual/pythonProgrammableFilter.html>`.
+
+Alternatively, geos-pv package can be build together with Paraview ([see Paraview compilation guide](https://gitlab.kitware.com/paraview/paraview/-/blob/master/Documentation/dev/build.md)). 
+It is recommended to use Paraview v5.12+, which is based on python 3.10+. If you need to build geos-pv package with the paraview dependency, use the command:
+`pip install Path/To/geosPythonPackages/geos-pv[paraview]`
diff --git a/docs/geos_pv_docs/modules.rst b/docs/geos_pv_docs/modules.rst
@@ -0,0 +1,11 @@
+Processing
+==========
+
+.. toctree::
+   :maxdepth: 5
+
+   geosLogReaderUtils
+
+   pyplotUtils
+
+   utils
diff --git a/docs/geos_pv_docs/pyplotUtils.rst b/docs/geos_pv_docs/pyplotUtils.rst
@@ -0,0 +1,13 @@
+pyplotUtils functions
+=====================
+
+This package define options for matplotlib.
+
+
+geos.pv.pyplotUtils.matplotlibOptions module
+---------------------------------------------
+
+.. automodule:: geos.pv.pyplotUtils.matplotlibOptions
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/geos_pv_docs/readers.rst b/docs/geos_pv_docs/readers.rst
@@ -0,0 +1,7 @@
+Paraview readers
+================
+
+readers.PVGeosLogReader module
+----------------------------------
+
+.. automodule:: readers.PVGeosLogReader
diff --git a/docs/geos_pv_docs/utils.rst b/docs/geos_pv_docs/utils.rst
@@ -0,0 +1,29 @@
+Utilities
+=========
+
+This package defines utilities for Paraview plugins.
+
+
+geos.pv.utils.checkboxFunction module
+---------------------------------------------
+
+.. automodule:: geos.pv.utils.checkboxFunction
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+geos.pv.utils.DisplayOrganizationParaview module
+-------------------------------------------------
+
+.. automodule:: geos.pv.utils.DisplayOrganizationParaview
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+geos.pv.utils.paraviewTreatments module
+---------------------------------------------
+
+.. automodule:: geos.pv.utils.paraviewTreatments
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/index.rst b/docs/index.rst
@@ -80,11 +80,13 @@ Packages
 
     geos-ats
 
+    geos-geomechanics
+
     geos-mesh
 
     geos-posp
-
-    geos-geomechanics
+    
+    geos-pv
 
     geos-timehistory
 

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,19 +1,19 @@
-sphinx >= 7.4.7
-sphinx_rtd_theme
-sphinx-argparse >= 0.5.2
-sphinx-autodoc-typehints
-sphinx-design
+sphinx >= 8.2
+sphinx_rtd_theme >= 3.0
+sphinx-argparse >= 0.5
+sphinx-autodoc-typehints >= 3.1
+sphinx-design >= 0.6
 # Running CLI programs and capture outputs
-sphinxcontrib-programoutput>=0.17
+sphinxcontrib-programoutput >= 0.17
 # Installing all package requirements to be able to load all the modules and run the help.
-vtk >= 9.1
+vtk >= 9.3
 networkx >= 2.4
-tqdm
-numpy
-pandas
-typing_extensions
+tqdm >= 4.67
+numpy >= 2.2
+pandas >= 2.2
+typing_extensions > 4.12
 matplotlib>=3.9.4
-h5py
-lxml>=4.5.0
-parameterized
-pyvista
+h5py >= 3.12
+lxml >= 4.5.0
+parameterized >= 0.9
+pyvista >= 0.44
-Original file line number
+Diff line change
@@ Expand Up / @@ -6,8 +6,6 @@ Processing @@
        filters
-       readers
        processing
        pyvistaTools