refactor: Move PVGeomechanicsAnalysis to geos-pv and GeomechanicsCalculator to geos-processing (#140)

* move GeomechnicsCalculator to geos-mesh

* move PVGeomechanicsAnalysis in geos-pv

* move GeomechanicsCalculator in the correct folder

* Remove PVPythonAlgorithmBase

* refactor computeElasticModulus functions

* refactor compute biot coefficient

* refactor computeCompressibilityCoefficient function

* refactor computeRealEffectiveStressRatio

* refactor computeSpecificGravity

* refactor computeTotalStresses

* refactor computBasicOutputs

* refactor computeAdvence

* Add the function getOutput

* Clean for the ci

* update the doc

* Change the name to add logic

* refactor the doc

* Refactor the paraview plugin

* clean for ci

* clean the doc

* fix the ci

* Update the workflow plugins using the filter

* fix the test

* fix the ci

* Add the new folder geos-processing

* move GeomechanicsCalculators to geos-processing

* Apply suggestions from Paloma's review

Co-authored-by: paloma-martinez <104762252+paloma-martinez@users.noreply.github.com>

* Keep the old way to load the file, this update is for another pr

* fix the ci

* Factorize the checkMandatoryAttributesFunction and add docs

* update import

* fix Install packages

* fix ci

* fix geos-post build

* Apply Jacques suggestion with dataclass

* update dataclass

* fix ruff

* update the doc

* Apply suggestions from Paloma's review

Co-authored-by: paloma-martinez <104762252+paloma-martinez@users.noreply.github.com>

* Fix dataclass default value

---------

Co-authored-by: paloma-martinez <104762252+paloma-martinez@users.noreply.github.com>

Author: RomainBaville

.github/workflows/python-package.yml

@@ -61,6 +61,7 @@ jobs:
           - geos-geomechanics
           - geos-mesh
           - geos-posp
+          - geos-processing
           - geos-timehistory
           - geos-trame
           - geos-xml-tools
@@ -72,8 +73,10 @@ jobs:
             dependencies: "geos-utils"
           - package-name: geos-mesh
             dependencies: "geos-utils geos-geomechanics"
-          - package-name: geos-posp
+          - package-name: geos-processing
             dependencies: "geos-utils geos-mesh geos-geomechanics"
+          - package-name: geos-posp
+            dependencies: "geos-utils geos-mesh geos-geomechanics geos-processing"
           - package-name: pygeos-tools
             dependencies: "geos-utils geos-mesh"
           - package-name: geos-timehistory

.github/workflows/typing-check.yml

@@ -1,5 +1,5 @@
 name: "Pull Request Typing Check"
-on: 
+on:
 - pull_request
 
 # Cancels in-progress workflows for a PR when updated
@@ -16,7 +16,7 @@ jobs:
       max-parallel: 3
       matrix:
         # add packages to check typing
-        package-name: ["geos-geomechanics", "geos-posp", "geos-timehistory", "geos-utils", "geos-trame", "geos-xml-tools", "hdf5-wrapper"]
+        package-name: ["geos-geomechanics", "geos-posp", "geos-processing", "geos-timehistory", "geos-utils", "geos-trame", "geos-xml-tools", "hdf5-wrapper"]
 
     steps:
     - uses: actions/checkout@v4

docs/conf.py

@@ -17,7 +17,7 @@
 
 # Add python modules to be documented
 python_root = '..'
-python_modules = ( 'geos-ats', 'geos-geomechanics', 'geos-mesh', 'geos-posp', 'geos-pv', 'geos-timehistory',
+python_modules = ( 'geos-ats', 'geos-geomechanics', 'geos-mesh', 'geos-posp', 'geos-processing', 'geos-pv', 'geos-timehistory',
                    'geos-utils', 'geos-xml-tools', 'geos-xml-viewer', 'hdf5-wrapper', 'pygeos-tools' )
 
 
@@ -45,7 +45,7 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.napoleon', 'sphinx_design', 'sphinx_rtd_theme', 'sphinxarg.ext', 'sphinxcontrib.programoutput', 
+    'sphinx.ext.napoleon', 'sphinx_design', 'sphinx_rtd_theme', 'sphinxarg.ext', 'sphinxcontrib.programoutput',
     'sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.mathjax', 'sphinx.ext.todo', 'sphinx.ext.viewcode'
 ]
 

docs/geos-processing.rst

@@ -0,0 +1,13 @@
+GEOS Processing tools
+========================
+
+
+.. toctree::
+    :maxdepth: 5
+    :caption: Contents:
+
+    ./geos_processing_docs/post_processing.rst
+
+    ./geos_processing_docs/pre_processing.rst
+
+    ./geos_processing_docs/generic_processing_tools.rst

docs/geos_mesh_docs/processing.rst

@@ -27,7 +27,6 @@ geos.mesh.processing.FillPartialArrays filter
     :undoc-members:
     :show-inheritance:
 
-
 geos.mesh.processing.meshQualityMetricHelpers module
 -----------------------------------------------------
 

docs/geos_posp_docs/PVplugins.rst

@@ -34,13 +34,6 @@ PVExtractMergeBlocksVolumeWell plugin
 
 .. automodule:: PVplugins.PVExtractMergeBlocksVolumeWell
 
-
-PVGeomechanicsAnalysis plugin
----------------------------------------
-
-.. automodule:: PVplugins.PVGeomechanicsAnalysis
-
-
 PVGeomechanicsWorkflowVolume plugin
 ---------------------------------------------
 

docs/geos_posp_docs/filters.rst

@@ -3,14 +3,6 @@ vtk Filters
 
 This package defines vtk filters that allows to process Geos outputs.
 
-geos_posp.filters.GeomechanicsCalculator module
----------------------------------------------------
-
-.. automodule:: geos_posp.filters.GeomechanicsCalculator
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 geos_posp.filters.GeosBlockExtractor module
 -----------------------------------------------
 

docs/geos_processing_docs/generic_processing_tools.rst

@@ -0,0 +1,4 @@
+Generic processing filters
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+In progress..

docs/geos_processing_docs/post_processing.rst

@@ -0,0 +1,15 @@
+Post-processing filters
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This module contains GEOS post-processing tools.
+
+Geomechanics post-processing tools
+=====================================
+
+geos.processing.post_processing.GeomechanicsCalculator module
+--------------------------------------------------------------
+
+.. automodule:: geos.processing.post_processing.GeomechanicsCalculator
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/geos_processing_docs/pre_processing.rst

@@ -0,0 +1,4 @@
+Pre-processing filters
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+In progress..