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mlemayTTEmlemayTTE
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Modify doc ci to return error if warnings are present
Update docs to pass the new ci Add geos-xml-viewer to the doc
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‎.github/workflows/doc-test.yml‎

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- uses: ammaraskar/sphinx-action@dev
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with:
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docs-folder: "docs/"
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build-command: "sphinx-build -b html . _build"
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build-command: "sphinx-build -b html . _build -W"

‎docs/conf.py‎

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# Add python modules to be documented
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python_root = '..'
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python_modules = ( 'geos-ats', 'geos-mesh', 'geos-posp', 'geos-timehistory', 'geos-utils', 'geos-xml-tools', 'hdf5-wrapper', 'pygeos-tools', 'geos-geomechanics' )
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python_modules = ( 'geos-ats', 'geos-geomechanics', 'geos-mesh', 'geos-posp', 'geos-timehistory', 'geos-utils', 'geos-xml-tools', 'geos-xml-viewer', 'hdf5-wrapper', 'pygeos-tools' )
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for m in python_modules:
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sys.path.insert( 0, os.path.abspath( os.path.join( python_root, m, 'src' ) ) )
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = [
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'sphinx_design', 'sphinx_rtd_theme', 'sphinxarg.ext', 'sphinxcontrib.programoutput', 'sphinx.ext.autodoc',
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'sphinx.ext.doctest', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon', 'sphinx.ext.todo', 'sphinx.ext.viewcode'
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'sphinx.ext.napoleon', 'sphinx_design', 'sphinx_rtd_theme', 'sphinxarg.ext', 'sphinxcontrib.programoutput',
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'sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.mathjax', 'sphinx.ext.todo', 'sphinx.ext.viewcode'
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]
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autoclass_content = 'both'
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autodoc_mock_imports = [ "ats", "h5py", "lxml", "paraview", "pygeosx", "pylvarray", "meshio", "mpi4py", "scipy" ]
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autodoc_mock_imports = [ "ats", "h5py", "lxml", "paraview", "pygeosx", "pylvarray", "meshio", "mpi4py", "scipy", "xmlschema", "colorcet", "xsdata" ]
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autodoc_typehints = 'none'
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autodoc_typehints_format = 'short'
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suppress_warnings = [ "" ]
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suppress_warnings = [ "autodoc.mocked_object" ]
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typehints_defaults = 'braces'
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# The suffix(es) of source filenames.

‎docs/geos-geomechanics.rst‎

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GEOS Post-Processing tools
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GEOS Geomechanics tools
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=============================
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.. toctree::

‎docs/geos-xml-viewer.rst‎

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GEOS XML VIEWER
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===============
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The `geos-xml-viewer` python package defines tools to read, process, and visualize objects from GEOS input xml file.
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See `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.
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This package defines multiple console scripts and a vtk ilter associated with a Paraview reader.
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Consol scripts
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--------------
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geos-exporter
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^^^^^^^^^^^^^
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Reads the xml file and writes a PartionedDataSetCollection file containing all the mesh objects (mesh, wells, boxes) defind in the xml.
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.. argparse::
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:module: geos_xml_viewer.bin.exporter
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:func: parsing
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:prog: geos-exporter
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geos-modifier
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^^^^^^^^^^^^^
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Rewrite wells into VTK file and modify the xml file accordingly.
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.. argparse::
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:module: geos_xml_viewer.bin.modifier
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:func: parsing
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:prog: geos-modifier
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geos-splitter
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^^^^^^^^^^^^^
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Extract Internal wells into VTK files.
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.. argparse::
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:module: geos_xml_viewer.bin.splitter
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:func: parsing
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:prog: geos-splitter
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geos-viewer
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^^^^^^^^^^^^^
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Viewer dedicated to xml mesh objects (mesh, wells, boxes).
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.. argparse::
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:module: geos_xml_viewer.bin.viewer
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:func: parsing
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:prog: geos-viewer
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WIP consol scripts
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------------------
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geos-validate
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^^^^^^^^^^^^^
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Validate xml file according to GEOS scheme.
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.. argparse::
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:module: geos_xml_viewer.bin.validate
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:func: parsing
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:prog: geos-validate
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vtk filter
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----------
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Geos deck reader
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^^^^^^^^^^^^^^^^
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Vtk reader of GEOS xml file to load or build vtk objects (mesh, wells, boxes).
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.. automodule:: geos_xml_viewer.filters.geosDeckReader
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:members:
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:undoc-members:
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:show-inheritance:
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Paraview plugin
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----------------
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Paraview plugin of Geos Deck Reader.
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.. automodule:: PVPlugins.deckReader
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:no-members:
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:no-undoc-members:
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Utilities
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---------
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.. automodule:: geos_xml_viewer.algorithms.deck
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:members:
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:undoc-members:
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.. automodule:: geos_xml_viewer.algorithms.write_wells
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:members:
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:undoc-members:

‎docs/geos_geomechanics_docs/home.rst‎

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GEOS Geomechanics Tools
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=========================
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-----------------------
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This package contains geomechanics functions and data models.

‎docs/geos_geomechanics_docs/model.rst‎

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Geomechanics models
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======================
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This
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This module defines data structures for geomechanics calculations.
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geos.geomechanics.model.MohrCircle module
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------------------------------------------

‎docs/geos_geomechanics_docs/processing.rst‎

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Processing
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============
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The processing part of `geos-geomechanics` package contains functions tools to compute geomechanical properties.
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The processing part of `geos-geomechanics` package contains the basis functions to compute geomechanical properties.
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geos.geomechanics.processing.geomechanicsCalculatorFunctions module
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---------------------------------------------------------------------

‎docs/geos_posp_docs/PVplugins.rst‎

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* Processing plugins to compute additional geomechanical properties;
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* Visualization plugins to plot Mohr's circles and cross plots using Paraview Python View.
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PVplugins.PVAttributeMapping module
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PVAttributeMapping plugin
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-----------------------------------
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.. automodule:: PVplugins.PVAttributeMapping
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:members:
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:undoc-members:
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PVplugins.PVCreateConstantAttributePerRegion module
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PVCreateConstantAttributePerRegion plugin
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---------------------------------------------------
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.. automodule:: PVplugins.PVCreateConstantAttributePerRegion
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:members:
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:undoc-members:
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PVplugins.PVExtractMergeBlocksVolume module
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PVExtractMergeBlocksVolume plugin
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.. automodule:: PVplugins.PVExtractMergeBlocksVolume
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:members:
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:undoc-members:
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PVplugins.PVExtractMergeBlocksVolumeSurface module
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PVExtractMergeBlocksVolumeSurface plugin
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--------------------------------------------------
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.. automodule:: PVplugins.PVExtractMergeBlocksVolumeSurface
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:members:
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PVplugins.PVExtractMergeBlocksVolumeSurfaceWell module
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PVExtractMergeBlocksVolumeSurfaceWell plugin
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------------------------------------------------------
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.. automodule:: PVplugins.PVExtractMergeBlocksVolumeSurfaceWell
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:members:
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PVplugins.PVExtractMergeBlocksVolumeWell module
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PVExtractMergeBlocksVolumeWell plugin
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-----------------------------------------------
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.. automodule:: PVplugins.PVExtractMergeBlocksVolumeWell
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:members:
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:undoc-members:
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PVplugins.PVGeomechanicsAnalysis module
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PVGeomechanicsAnalysis plugin
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---------------------------------------
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.. automodule:: PVplugins.PVGeomechanicsAnalysis
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:members:
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:undoc-members:
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PVplugins.PVGeomechanicsWorkflowVolume module
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PVGeomechanicsWorkflowVolume plugin
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---------------------------------------------
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.. automodule:: PVplugins.PVGeomechanicsWorkflowVolume
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:members:
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:undoc-members:
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PVplugins.PVGeomechanicsWorkflowVolumeSurface module
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PVGeomechanicsWorkflowVolumeSurface plugin
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----------------------------------------------------
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.. automodule:: PVplugins.PVGeomechanicsWorkflowVolumeSurface
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:members:
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:undoc-members:
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PVplugins.PVGeomechanicsWorkflowVolumeSurfaceWell module
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PVGeomechanicsWorkflowVolumeSurfaceWell plugin
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.. automodule:: PVplugins.PVGeomechanicsWorkflowVolumeSurfaceWell
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:members:
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:undoc-members:
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PVplugins.PVGeomechanicsWorkflowVolumeWell module
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PVGeomechanicsWorkflowVolumeWell plugin
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.. automodule:: PVplugins.PVGeomechanicsWorkflowVolumeWell
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:members:
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:undoc-members:
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PVplugins.PVGeosLogReader module
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PVGeosLogReader plugin
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:members:
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:undoc-members:
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PVplugins.PVMergeBlocksEnhanced module
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PVMergeBlocksEnhanced plugin
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.. automodule:: PVplugins.PVMergeBlocksEnhanced
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:members:
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:undoc-members:
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PVplugins.PVMohrCirclePlot module
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PVMohrCirclePlot plugin
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.. automodule:: PVplugins.PVMohrCirclePlot
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:members:
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PVplugins.PVPythonViewConfigurator module
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PVPythonViewConfigurator plugin
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PVplugins.PVSurfaceGeomechanics module
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PVSurfaceGeomechanics plugin
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PVplugins.PVTransferAttributesVolumeSurface module
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PVTransferAttributesVolumeSurface plugin
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‎docs/geos_posp_docs/home.rst‎

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Home
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====
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**Geos-posp** is a Python library to read, process and visualize GEOS simulation software outputs.
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‎docs/geos_posp_docs/processing.rst‎

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This package define functions to process data.
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geos_posp.processing.geomechanicsCalculatorFunctions module
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---------------------------------------------------------------
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.. automodule:: geos_posp.processing.geomechanicsCalculatorFunctions
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:members:
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geos_posp.processing.geosLogReaderFunctions module
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------------------------------------------------------
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:undoc-members:
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geos_posp.processing.MohrCircle module
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------------------------------------------
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.. automodule:: geos_posp.processing.MohrCircle
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geos_posp.processing.MohrCoulomb module
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geos_posp.processing.multiblockInpectorTreeFunctions module
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---------------------------------------------------------------
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