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ab45082
move GeomechnicsCalculator to geos-mesh
RomainBaville Sep 19, 2025
bfd0196
move PVGeomechanicsAnalysis in geos-pv
RomainBaville Sep 19, 2025
2836b32
move GeomechanicsCalculator in the correct folder
RomainBaville Sep 22, 2025
7cc21f7
Remove PVPythonAlgorithmBase
RomainBaville Sep 22, 2025
9ef6814
refactor computeElasticModulus functions
RomainBaville Sep 22, 2025
a88a1e7
refactor compute biot coefficient
RomainBaville Sep 22, 2025
ce526f9
refactor computeCompressibilityCoefficient function
RomainBaville Sep 22, 2025
424d76d
refactor computeRealEffectiveStressRatio
RomainBaville Sep 22, 2025
6a55e7f
refactor computeSpecificGravity
RomainBaville Sep 22, 2025
8418261
refactor computeTotalStresses
RomainBaville Sep 22, 2025
fadec20
refactor computBasicOutputs
RomainBaville Sep 22, 2025
d267ad7
refactor computeAdvence
RomainBaville Sep 22, 2025
8c5c28a
Add the function getOutput
RomainBaville Sep 23, 2025
f366704
Clean for the ci
RomainBaville Sep 23, 2025
c227278
update the doc
RomainBaville Sep 23, 2025
f54221b
Change the name to add logic
RomainBaville Sep 23, 2025
be176c9
refactor the doc
RomainBaville Sep 23, 2025
dc1934b
Refactor the paraview plugin
RomainBaville Sep 23, 2025
96e8880
clean for ci
RomainBaville Sep 23, 2025
4c9c5ce
clean the doc
RomainBaville Sep 24, 2025
62e4b23
fix the ci
RomainBaville Sep 24, 2025
9d37f5c
Update the workflow plugins using the filter
RomainBaville Sep 24, 2025
0e827b7
fix the test
RomainBaville Sep 24, 2025
26883db
fix the ci
RomainBaville Sep 24, 2025
afa427f
Add the new folder geos-processing
RomainBaville Sep 26, 2025
f09f60d
move GeomechanicsCalculators to geos-processing
RomainBaville Sep 26, 2025
af6480f
Update to the last version of the main
RomainBaville Sep 26, 2025
5188921
Apply suggestions from Paloma's review
RomainBaville Oct 7, 2025
2629ad2
Keep the old way to load the file, this update is for another pr
RomainBaville Oct 7, 2025
45d49c8
fix the ci
RomainBaville Oct 7, 2025
5022f88
Factorize the checkMandatoryAttributesFunction and add docs
RomainBaville Oct 7, 2025
0858294
Merge branch 'main' into RomainBaville/refactor/movegeomechanicscalcu…
RomainBaville Oct 8, 2025
44766fd
update import
RomainBaville Oct 8, 2025
35c3541
fix Install packages
RomainBaville Oct 8, 2025
7da5168
fix ci
RomainBaville Oct 8, 2025
795d6d9
fix geos-post build
RomainBaville Oct 8, 2025
1902c77
Apply Jacques suggestion with dataclass
RomainBaville Oct 14, 2025
989c5ec
update dataclass
RomainBaville Oct 14, 2025
f95b50c
fix ruff
RomainBaville Oct 14, 2025
b723d15
Merge branch 'main' into RomainBaville/refactor/movegeomechanicscalcu…
RomainBaville Oct 14, 2025
b90dc80
Merge branch 'main' into RomainBaville/refactor/movegeomechanicscalcu…
RomainBaville Oct 15, 2025
1bb88c6
update the doc
RomainBaville Oct 15, 2025
452d5cc
Apply suggestions from Paloma's review
RomainBaville Oct 15, 2025
b40cb80
Fix dataclass default value
RomainBaville Oct 20, 2025
4beafcc
Merge branch 'main' into RomainBaville/refactor/movegeomechanicscalcu…
RomainBaville Oct 20, 2025
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5 changes: 4 additions & 1 deletion .github/workflows/python-package.yml
Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,7 @@ jobs:
- geos-geomechanics
- geos-mesh
- geos-posp
- geos-processing
- geos-timehistory
- geos-trame
- geos-xml-tools
Expand All @@ -57,8 +58,10 @@ 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
Expand Down
4 changes: 2 additions & 2 deletions .github/workflows/typing-check.yml
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
name: "Pull Request Typing Check"
on:
on:
- pull_request

# Cancels in-progress workflows for a PR when updated
Expand All @@ -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
Expand Down
4 changes: 2 additions & 2 deletions docs/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -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' )


Expand Down Expand Up @@ -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'
]

Expand Down
13 changes: 13 additions & 0 deletions docs/geos-processing.rst
Original file line number Diff line number Diff line change
@@ -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
1 change: 0 additions & 1 deletion docs/geos_mesh_docs/processing.rst
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,6 @@ geos.mesh.processing.FillPartialArrays filter
:undoc-members:
:show-inheritance:


geos.mesh.processing.meshQualityMetricHelpers module
-----------------------------------------------------

Expand Down
7 changes: 0 additions & 7 deletions docs/geos_posp_docs/PVplugins.rst
Original file line number Diff line number Diff line change
Expand Up @@ -34,13 +34,6 @@ PVExtractMergeBlocksVolumeWell plugin

.. automodule:: PVplugins.PVExtractMergeBlocksVolumeWell


PVGeomechanicsAnalysis plugin
---------------------------------------

.. automodule:: PVplugins.PVGeomechanicsAnalysis


PVGeomechanicsWorkflowVolume plugin
---------------------------------------------

Expand Down
8 changes: 0 additions & 8 deletions docs/geos_posp_docs/filters.rst
Original file line number Diff line number Diff line change
Expand Up @@ -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
-----------------------------------------------

Expand Down
4 changes: 4 additions & 0 deletions docs/geos_processing_docs/generic_processing_tools.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
Generic processing filters
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

In progress..
15 changes: 15 additions & 0 deletions docs/geos_processing_docs/post_processing.rst
Original file line number Diff line number Diff line change
@@ -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:
4 changes: 4 additions & 0 deletions docs/geos_processing_docs/pre_processing.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
Pre-processing filters
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

In progress..
7 changes: 7 additions & 0 deletions docs/geos_pv_docs/processing.rst
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@ PVAttributeMapping

.. automodule:: geos.pv.plugins.PVAttributeMapping


PVCreateConstantAttributePerRegion
-----------------------------------

Expand All @@ -18,6 +19,12 @@ PVFillPartialArrays
.. automodule:: geos.pv.plugins.PVFillPartialArrays


PVGeomechanicsCalculator plugin
---------------------------------------

.. automodule:: geos.pv.plugins.PVGeomechanicsCalculator


PVSplitMesh
----------------------------------

Expand Down
6 changes: 4 additions & 2 deletions docs/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ To do this, you can clone a copy of the geosPythonPackages repository and instal
cd geosPythonPackages/
python -m pip install --upgrade geos-ats
.. note::
To upgrade an existing installation, the python executable in the above command should correspond to the version you indicated in your host config. If you have previously built the tools, this version will be linked in the build directory: `build_dir/bin/python`.

Expand Down Expand Up @@ -87,7 +87,9 @@ Packages
geos-mesh

geos-posp


geos-processing

geos-pv

geos-timehistory
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -506,8 +506,7 @@ def reservoirStressPathReal( deltaStress: npt.NDArray[ np.float64 ],
den: npt.NDArray[ np.float64 ] = np.copy( deltaPressure )
den[ mask ] = 1.0
# use -1 to agree with Geos convention (i.e., compression with negative stress)
# take the xx, yy, and zz components only
rsp: npt.NDArray[ np.float64 ] = np.copy( deltaStress[ :, :3 ] )
rsp: npt.NDArray[ np.float64 ] = np.copy( deltaStress[ :, : ] )
for j in range( rsp.shape[ 1 ] ):
rsp[ :, j ] /= den
rsp[ mask, j ] = np.nan
Expand Down
10 changes: 5 additions & 5 deletions geos-geomechanics/tests/testsFunctionsGeomechanicsCalculator.py
Original file line number Diff line number Diff line change
Expand Up @@ -181,11 +181,11 @@ def test_ReservoirStressPathReal( self: Self ) -> None:
deltaPressure: npt.NDArray[ np.float64 ] = 0.2 * pressure
obtained: npt.NDArray[ np.float64 ] = fcts.reservoirStressPathReal( deltaStress, deltaPressure )
expected: npt.NDArray[ np.float64 ] = np.array( [
[ 8.0, 12.5, 9.0 ],
[ 0.32, 0.46, 0.34 ],
[ np.nan, np.nan, np.nan ],
[ 1.38, 1.81, 1.38 ],
[ 1.30, 1.55, 1.15 ],
[ 8.0, 12.5, 9.0, np.nan, 10.0, 9.5 ],
[ 0.32, 0.46, 0.34, np.nan, 0.39, 0.38 ],
[ np.nan, np.nan, np.nan, np.nan, np.nan, np.nan ],
[ 1.38, 1.81, 1.38, np.nan, 1.56, 1.56 ],
[ 1.30, 1.55, 1.15, np.nan, 1.45, 1.35 ],
] )
self.assertTrue( np.array_equal( np.round( obtained, 2 ), np.round( expected, 2 ), equal_nan=True ) )

Expand Down
1 change: 1 addition & 0 deletions geos-posp/pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,7 @@ dependencies = [
"geos-geomechanics",
"geos-utils",
"geos-mesh",
"geos-processing",
"vtk >= 9.3",
"numpy >= 2.2",
"pandas >= 2.2",
Expand Down
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