GEOS-DEV · alexbenedicto · Apr 15, 2025 · Mar 26, 2025 · Mar 26, 2025 · Apr 2, 2025
diff --git a/README.md b/README.md
@@ -142,7 +142,7 @@ If you would like to contribute to GEOS Python packages, please respect the foll
 
 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
+1. 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.
 
@@ -186,6 +186,19 @@ The *setup.py* file is optional. It is required if the package depends on anothe
   )
   ```
 
+If you want to add new Paraview plugins, create the plugins in the `geos-pv/src/PVplugins` directory. 
+If the plugin depends on another GEOS python package, add the package name to `geos-pv/requirements.txt` and the following lines to the top of your plugin:
+
+```
+import sys
+from pathlib import Path
+# update sys.path to load all GEOS Python Package dependencies
+geos_pv_path: Path = Path( __file__ ).parent.parent.parent
+sys.path.insert( 0, str(geos_pv_path / "src") )
+from geos.pv.utils.config import update_paths
+update_paths()
+```
+
 
 Release
 -------

diff --git a/docs/conf.py b/docs/conf.py
@@ -17,8 +17,8 @@
 
 # Add python modules to be documented
 python_root = '..'
-python_modules = ( 'geos-ats', 'geos-mesh', 'geos-posp', 'geos-timehistory', 'geos-utils', 'geos-xml-tools', 'hdf5-wrapper',
-                   'pygeos-tools', 'geos-geomechanics' )
+python_modules = ( 'geos-ats', 'geos-geomechanics', 'geos-mesh', 'geos-posp', 'geos-pv', 'geos-timehistory', 'geos-utils', 'geos-xml-tools', 'hdf5-wrapper', 'pygeos-tools' )
+
 for m in python_modules:
     sys.path.insert( 0, os.path.abspath( os.path.join( python_root, m, 'src' ) ) )
 
@@ -47,7 +47,7 @@
                'sphinx.ext.todo', 'sphinx.ext.viewcode' ]
 
 autoclass_content = 'both'
-autodoc_mock_imports = [ "ats", "h5py", "lxml", "paraview", "pygeosx", "pylvarray", "meshio", "mpi4py", "scipy" ]
+autodoc_mock_imports = [ "ats", "h5py", "lxml", "paraview", "pygeosx", "pylvarray", "meshio", "mpi4py", "scipy", "pandas", "matplotlib" ]
 autodoc_typehints = 'none'
 autodoc_typehints_format = 'short'
 suppress_warnings = [""]

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/PVplugins.rst
diff --git a/docs/geos_posp_docs/PVplugins.rst b/docs/geos_posp_docs/PVplugins.rst
@@ -87,13 +87,6 @@ PVplugins.PVGeomechanicsWorkflowVolumeWell module
    :members:
    :undoc-members:
 
-PVplugins.PVGeosLogReader module
---------------------------------
-
-.. automodule:: PVplugins.PVGeosLogReader
-   :members:
-   :undoc-members:
-
 PVplugins.PVMergeBlocksEnhanced module
 --------------------------------------
 
@@ -108,13 +101,6 @@ PVplugins.PVMohrCirclePlot module
    :members:
    :undoc-members:
 
-PVplugins.PVPythonViewConfigurator module
------------------------------------------
-
-.. automodule:: PVplugins.PVPythonViewConfigurator
-   :members:
-   :undoc-members:
-
 PVplugins.PVSurfaceGeomechanics module
 --------------------------------------
 

diff --git a/docs/geos_pv_docs/PVplugins.rst b/docs/geos_pv_docs/PVplugins.rst
@@ -0,0 +1,12 @@
+Paraview plugins
+================
+
+This package contains Paraview plugins that can be loaded in Paraview.
+
+PVplugins.PVGeosLogReader module
+---------------------------------------------
+
+.. automodule:: PVplugins.PVGeosLogReader
+   :members:
+   :undoc-members:
+   :show-inheritance:
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 +1,19 @@
+Home
+====
+
+**geos-pv** is a Python package that gathers `Paraview <https://www.paraview.org/>`_ plugins of GEOS python tools. 
+
+It includes:
+
+* a reader able to parse the GEOS output log (before commit version #9365098) to collect data and display them as tables;
+* tools to clean and check GEOS input mesh;
+* tools to clean GEOS output mesh;
+* tools to compute additional geomechanical properties from GEOS outputs;
+* tools to display Mohr's circles at a given time step and the evolution through time from GEOS outputs.
+
+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/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/geos-posp/setup.py b/geos-posp/setup.py
@@ -2,16 +2,14 @@
 from setuptools import setup
 
 # This is where you add any fancy path resolution to the local lib:
-geos_geomecha_path: str = (Path(__file__).parent.parent / "geos-geomechanics").as_uri()
-geos_utils_path: str = (Path(__file__).parent.parent / "geos-utils").as_uri()
+geos_utils_path: str = ( Path( __file__ ).parent.parent / "geos-utils" ).as_uri()
+geos_geomeca_path: str = ( Path( __file__ ).parent.parent / "geos-geomechanics" ).as_uri()
 
-setup(
-    install_requires=[
-        "vtk >= 9.3",
-        "numpy >= 1.26",
-        "pandas >= 2.2",
-        "typing_extensions >= 4.12",
-        f"geos-geomechanics @ {geos_geomecha_path}",
-        f"geos-utils @ {geos_utils_path}",
-    ]
-)
+setup( install_requires=[
+    "vtk >= 9.3",
+    "numpy >= 1.26",
+    "pandas >= 2.2",
+    "typing_extensions >= 4.12",
+    f"geos-utils @ {geos_utils_path}",
+    f"geos-geomechanics @ {geos_geomeca_path}",
+] )