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
@@ -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.
 

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-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' ) ) )
@@ -48,7 +49,7 @@
 ]
 
 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/readers.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_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
@@ -3,39 +3,6 @@ Processing functions
 
 This package define functions to process data.
 
-
-geos_posp.processing.geomechanicsCalculatorFunctions module
----------------------------------------------------------------
-
-.. automodule:: geos_posp.processing.geomechanicsCalculatorFunctions
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-geos_posp.processing.geosLogReaderFunctions module
-------------------------------------------------------
-
-.. automodule:: geos_posp.processing.geosLogReaderFunctions
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-geos_posp.processing.MohrCircle module
-------------------------------------------
-
-.. automodule:: geos_posp.processing.MohrCircle
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-geos_posp.processing.MohrCoulomb module
--------------------------------------------
-
-.. automodule:: geos_posp.processing.MohrCoulomb
-   :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 +1,10 @@
+Paraview readers
+================
+
+readers.PVGeosLogReader module
+----------------------------------
+
+.. automodule:: readers.PVGeosLogReader
+   :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/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/geos-geomechanics/src/geos/geomechanics/model/MohrCircle.py b/geos-geomechanics/src/geos/geomechanics/model/MohrCircle.py
@@ -5,7 +5,7 @@
 import numpy.typing as npt
 from typing_extensions import Self
 
-from geos_posp.processing.geomechanicsCalculatorFunctions import (
+from geos.geomechanics.processing.geomechanicsCalculatorFunctions import (
     computeStressPrincipalComponentsFromStressVector, )
 
 __doc__ = """

diff --git a/geos-geomechanics/src/geos/geomechanics/processing/geomechanicsCalculatorFunctions.py b/geos-geomechanics/src/geos/geomechanics/processing/geomechanicsCalculatorFunctions.py
@@ -5,7 +5,7 @@
 import numpy as np
 import numpy.typing as npt
 
-from geos_posp.processing.MohrCoulomb import MohrCoulomb
+from geos.geomechanics.model.MohrCoulomb import MohrCoulomb
 from geos.utils.algebraFunctions import getAttributeMatrixFromVector
 from geos.utils.PhysicalConstants import (
     EPSILON, )

diff --git a/geos-posp/src/PVplugins/PVAttributeMapping.py b/geos-posp/src/PVplugins/PVAttributeMapping.py
@@ -13,6 +13,8 @@
 if parent_dir_path not in sys.path:
     sys.path.append( parent_dir_path )
 
+import PVplugins  # noqa: F401
+
 from geos.utils.Logger import Logger, getLogger
 from geos_posp.filters.AttributeMappingFromCellCoords import (
     AttributeMappingFromCellCoords, )
@@ -211,6 +213,7 @@ def RequestData(
                                   "Use either vtkUnstructuredGrid or vtkMultiBlockDataSet" )
 
             outData.Modified()
+
             mess: str = "Attributes were successfully transferred ."
             self.m_logger.info( mess )
         except AssertionError as e:

diff --git a/geos-posp/src/PVplugins/PVCreateConstantAttributePerRegion.py b/geos-posp/src/PVplugins/PVCreateConstantAttributePerRegion.py
@@ -15,6 +15,8 @@
 if parent_dir_path not in sys.path:
     sys.path.append( parent_dir_path )
 
+import PVplugins  # noqa: F401
+
 import vtkmodules.util.numpy_support as vnp
 from geos.utils.Logger import Logger, getLogger
 from geos_posp.processing.multiblockInpectorTreeFunctions import (
-Original file line number
+Diff line change
@@ Expand Up / @@ -6,8 +6,6 @@ Processing @@
        filters
-       readers
        processing
        pyvistaTools