refactor: move pyvista tools

.github/workflows/README.md

@@ -22,7 +22,7 @@ Tests each Python package independently to ensure:
 - `geos-ats` - Automated Testing System for GEOS
 - `geos-geomechanics` - Geomechanics analysis tools
 - `geos-mesh` - Mesh conversion and validation tools
-- `geos-posp` - Post-processing utilities
+- `geos-processing` - Post-processing utilities
 - `geos-timehistory` - Time history analysis
 - `geos-trame` - Trame-based visualization
 - `geos-utils` - Utility functions
@@ -62,7 +62,7 @@ build:
 ```yaml
 check_integration_label:
   - Checks for 'test-geos-integration' label
-  
+
 check_force_integration_label:
   - Checks for 'force-geos-integration' label
 ```
@@ -141,7 +141,7 @@ Tests that geosPythonPackages integrates correctly with GEOS by:
   - Patches script to search `/usr/local/bin/` for pip-installed tools
   - Installs Python packages via the GEOS setup script
   - Creates symlinks to tools in `bin_direct/`
-- **Validates**: 
+- **Validates**:
   - ✅ Python packages install correctly
   - ✅ Scripts are findable and linkable
   - ✅ All required tools are available
@@ -262,7 +262,7 @@ Tests are automatically skipped when changes only affect:
 
 #### Non-Integrated Packages
 - `geos-geomechanics/` - Standalone geomechanics tools
-- `geos-posp/` - Post-processing utilities
+- `geos-processing/` - Post-processing utilities
 - `geos-pv/` - ParaView utilities
 - `geos-timehistory/` - Time history analysis
 - `geos-trame/` - Trame visualization

.github/workflows/python-package.yml

@@ -58,12 +58,11 @@ jobs:
       max-parallel: 3
       matrix:
         python-version: ["3.10","3.11","3.12"]
-        package-name: 
+        package-name:
           - geos-ats
           - geos-utils
           - geos-geomechanics
           - geos-mesh
-          - geos-posp
           - geos-processing
           - geos-timehistory
           - geos-trame
@@ -78,8 +77,6 @@ jobs:
             dependencies: "geos-utils geos-geomechanics"
           - 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
@@ -92,11 +89,11 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
-    
+
     - name: Install OSMesa and GL
       run: |
         sudo apt-get update
-        sudo apt-get install -y libosmesa6      
+        sudo apt-get install -y libosmesa6
         sudo apt-get install -y \
             libegl1-mesa-dev \
             libgles2-mesa-dev \
@@ -151,7 +148,7 @@ jobs:
             echo "Label '${{ env.LABEL_TEST_GEOS_INTEGRATION }}' found"
           fi
           echo "has_label=$LABEL_FOUND" >> $GITHUB_OUTPUT
-  
+
   check_force_integration_label:
     runs-on: ubuntu-latest
     needs: [build]
@@ -281,11 +278,11 @@ jobs:
           echo "required=false" >> "$GITHUB_OUTPUT"
           echo "skip_reason=no-geos-integrated-changes" >> "$GITHUB_OUTPUT"
         fi
-  
+
   geos_ci_dispatch:
     name: Dispatch cases of GEOS CI
     runs-on: ubuntu-latest
-    outputs: 
+    outputs:
       is_GEOS_CI_skipped: ${{ steps.dispatch.outputs.skipped }}
       fwd_geos_integration_required: ${{ steps.dispatch.outputs.fwd_geos_integration_required }}
       fwd_skip_reason: ${{ steps.dispatch.outputs.skip_reason }}
@@ -298,31 +295,31 @@ jobs:
           HAS_TEST_LABEL="${{ needs.check_integration_label.outputs.has_geos_integration_label }}"
           HAS_FORCE_LABEL="${{ needs.check_force_integration_label.outputs.has_geos_integration_force_label }}"
           SKIP_REASON="${{ needs.check_geos_integration_required.outputs.skip_reason }}"
-          
+
           echo "fwd_geos_integration_required=${GEOS_REQUIRED}" >> "$GITHUB_OUTPUT"
           echo "fwd_skip_reason=${SKIP_REASON}" >> "$GITHUB_OUTPUT"
-          
+
           echo "=== GEOS Integration Dispatch ==="
           echo "GEOS Required (by file changes): ${GEOS_REQUIRED}"
           echo "Has '${{ env.LABEL_TEST_GEOS_INTEGRATION }}' label: ${HAS_TEST_LABEL}"
           echo "Has '${{ env.LABEL_FORCE_GEOS_INTEGRATION }}' label: ${HAS_FORCE_LABEL}"
           echo ""
-          
+
           # Case 1: Force label - always run tests
           if [[ "$HAS_FORCE_LABEL" == "true" ]]; then
             echo "✓ '${{ env.LABEL_FORCE_GEOS_INTEGRATION }}' label present - forcing GEOS integration tests"
             echo "skipped=false" >> "$GITHUB_OUTPUT"
             exit 0
           fi
-          
+
           # Case 2: GEOS required AND test label present - run tests
           if [[ "$GEOS_REQUIRED" == "true" && "$HAS_TEST_LABEL" == "true" ]]; then
             echo "✓ GEOS integration required and '${{ env.LABEL_TEST_GEOS_INTEGRATION }}' label present"
             echo "  Will proceed with GEOS integration tests"
             echo "skipped=false" >> "$GITHUB_OUTPUT"
             exit 0
           fi
-          
+
           # Case 3: GEOS required BUT test label missing - ERROR
           if [[ "$GEOS_REQUIRED" == "true" && "$HAS_TEST_LABEL" == "false" ]]; then
             echo "✗ ERROR: GEOS integration is required but '${{ env.LABEL_TEST_GEOS_INTEGRATION }}' label is missing"
@@ -334,7 +331,7 @@ jobs:
             echo "Action required: Add the '${{ env.LABEL_TEST_GEOS_INTEGRATION }}' label to this PR"
             exit 1
           fi
-          
+
           # Case 4: GEOS NOT required BUT test label present - SKIP TESTS
           if [[ "$GEOS_REQUIRED" == "false" && "$HAS_TEST_LABEL" == "true" ]]; then
             echo "⊘ SKIPPED: '${{ env.LABEL_TEST_GEOS_INTEGRATION }}' label present but GEOS integration is not required"
@@ -348,7 +345,7 @@ jobs:
             echo "skipped=true" >> "$GITHUB_OUTPUT"
             exit 0
           fi
-          
+
           # Case 5: GEOS NOT required AND no labels - SKIP TESTS
           if [[ "$GEOS_REQUIRED" == "false" && "$HAS_TEST_LABEL" == "false" ]]; then
             echo "⊘ GEOS integration not required and no labels present"
@@ -357,7 +354,7 @@ jobs:
             echo "skipped=true" >> "$GITHUB_OUTPUT"
             exit 0
           fi
-          
+
           # Should never reach here
           echo "✗ ERROR: Unexpected state in dispatch logic"
           exit 1
@@ -383,7 +380,7 @@ jobs:
 
         GEOS_REQUIRED="${{ needs.geos_ci_dispatch.outputs.fwd_geos_integration_required }}"
         SKIP_REASON="${{ needs.geos_ci_dispatch.outputs.fwd_skip_reason }}"
-       
+
         GEOS_RESULT="${{ needs.geos_integration_test.result }}"
 
         if [[ "$GEOS_REQUIRED" == "true" ]]; then

.github/workflows/typing-check.yml

@@ -16,7 +16,7 @@ jobs:
       max-parallel: 3
       matrix:
         # add packages to check typing
-        package-name: ["geos-geomechanics", "geos-posp", "geos-processing", "geos-timehistory", "geos-utils", "geos-trame", "geos-xml-tools", "hdf5-wrapper"]
+        package-name: ["geos-geomechanics", "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-processing', 'geos-pv', 'geos-timehistory',
+python_modules = ( 'geos-ats', 'geos-geomechanics', 'geos-mesh', 'geos-processing', 'geos-pv', 'geos-timehistory',
                    'geos-utils', 'geos-xml-tools', 'geos-xml-viewer', 'hdf5-wrapper', 'pygeos-tools' )
 
 

docs/geos_mesh_docs/utils.rst

@@ -46,4 +46,14 @@ geos.mesh.utils.multiblockModifiers module
 .. automodule:: geos.mesh.utils.multiblockModifiers
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:
+
+
+
+geos.mesh.utils.pyvistaTools module
+-----------------------------------------------
+
+.. automodule:: geos.mesh.utils.pyvistaTools
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/index.rst

@@ -86,8 +86,6 @@ Packages
 
     geos-mesh
 
-    geos-posp
-
     geos-processing
 
     geos-pv

geos-posp/src/geos_posp/pyvistaTools/pyvistaUtils.py → geos-mesh/src/geos/mesh/utils/pyvistaTools.py

@@ -1,7 +1,7 @@
 # SPDX-License-Identifier: Apache-2.0
 # SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
 # SPDX-FileContributor: Martin Lemay
-from typing import Optional, Union, cast
+from typing import Optional, Union
 
 import numpy as np
 import numpy.typing as npt
@@ -16,9 +16,8 @@
 from geos.mesh.utils.arrayHelpers import ( getAttributeValuesAsDF, computeCellCenterCoordinates )
 from geos.mesh.utils.arrayModifiers import transferPointDataToCellData
 
-__doc__ = r"""
+__doc__ = """
 This module contains utilities to process meshes using pyvista.
-
 """
 
 
@@ -31,46 +30,51 @@ def loadDataSet(
     """Load the data using pyvista and extract properties from horizontal slice.
 
     Args:
-        reader (pv.PVDReader): pyvista pvd reader
-        timeStepIndexes (list[int]): list of time step indexes to load.
-        elevation (float): elevation (m) of horizontal slice
-        properties (tuple[str]): list of properties to extract
+        reader (pv.PVDReader): Pyvista pvd reader.
+        timeStepIndexes (list[int]): List of time step indexes to load.
+        elevation (float): Elevation (m) of horizontal slice.
+        properties (tuple[str]): List of properties to extract.
 
     Returns:
-        tuple[dict[str, pd.DataFrame], npt.NDArray[np.float64]]: tuple containing
-            a dictionnary with times as keys and dataframe with properties as
+        tuple[dict[str, pd.DataFrame], npt.NDArray[np.float64]]: Tuple containing
+            a dictionary with times as keys and dataframe with properties as
             values, and an array with cell center coordinates of the slice.
 
     """
     timeToPropertyMap: dict[ str, pd.DataFrame ] = {}
     surface: vtkPolyData
     timeValues: list[ float ] = reader.time_values
     for index in timeStepIndexes:
-        assert index < len( timeValues ), "Time step index is out of range."
+        if index >= len( timeValues ):
+            raise IndexError( "Time step index is out of range." )
 
         time: float = timeValues[ index ]
         reader.set_active_time_value( time )
         inputMesh: pv.Multiblock = reader.read()
 
         volMesh: Optional[ Union[ pv.MultiBlock, pv.UnstructuredGrid ] ] = getBlockByName(
             inputMesh, GeosDomainNameEnum.VOLUME_DOMAIN_NAME.value )
-        assert volMesh is not None, "Volumic mesh was not found."
+        if not volMesh:
+            raise AttributeError( "Volumic mesh was not found." )
 
         # Merge volume block
         mergedMesh: pv.UnstructuredGrid = volMesh.combine(
             merge_points=True ) if isinstance( volMesh, pv.MultiBlock ) else volMesh
-        assert mergedMesh is not None, "Merged mesh is undefined."
+        if not mergedMesh:
+            raise ValueError( "Merged mesh is undefined." )
 
-        # extract data
+        # Extract data
         surface = extractSurfaceFromElevation( mergedMesh, elevation )
-        # transfer point data to cell center
-        surface = cast( vtkPolyData, transferPointDataToCellData( surface ) )
+        # Transfer point data to cell center
+        surface = vtkPolyData.SafeDownCast( transferPointDataToCellData( surface ) )
         timeToPropertyMap[ str( time ) ] = getAttributeValuesAsDF( surface, properties )
 
-    # get cell center coordinates
-    assert surface is not None, "Surface are undefined."
+    # Get cell center coordinates
+    if not surface:
+        raise ValueError( "Surface are undefined." )
     pointsCoords: vtkDataArray = computeCellCenterCoordinates( surface )
-    assert pointsCoords is not None, "Cell center are undefined."
+    if not pointsCoords:
+        raise ValueError( "Cell center are undefined." )
     pointsCoordsNp: npt.NDArray[ np.float64 ] = vnp.vtk_to_numpy( pointsCoords )
     return ( timeToPropertyMap, pointsCoordsNp )
 
@@ -93,14 +97,14 @@ def getBlockByName( multiBlockMesh: Union[ pv.MultiBlock, pv.UnstructuredGrid ],
 
     mesh: Optional[ Union[ pv.MultiBlock, pv.UnstructuredGrid ] ]
     for i, mbMesh in enumerate( multiBlockMesh ):
-        # if one of the block of multiBlockMesh is the volumic mesh,
+        # If one of the block of multiBlockMesh is the volumic mesh,
         # then save the mesh and break
         if multiBlockMesh.get_block_name( i ) == blockName:
             mesh = mbMesh
             break
-        # else look at its internal mesh(es)
+        # Else look at its internal mesh(es)
         mesh = getBlockByName( mbMesh, blockName )
-        # if mesh is not None, it is the searched one
+        # If mesh is not None, it is the searched one
         if mesh is not None:
             break
     return mesh