From 782c8277a32ae350853d250d407dfb9dcb26af52 Mon Sep 17 00:00:00 2001
From: Lucas Givord <lucas.givord@kitware.com>
Date: Wed, 4 Jun 2025 09:41:51 +0200
Subject: [PATCH 01/17] feat(viewer): add support for intersected cell from Box

---
 .../geos/trame/app/data_types/renderable.py   |   1 +
 .../src/geos/trame/app/ui/viewer/boxViewer.py | 111 ++++++++++++++++++
 .../src/geos/trame/app/ui/viewer/viewer.py    |  22 +++-
 geos-trame/tests/data/geosDeck/geosDeck.xml   |   4 +-
 geos-trame/tests/test_box_intersection.py     |  36 ++++++
 5 files changed, 171 insertions(+), 3 deletions(-)
 create mode 100644 geos-trame/src/geos/trame/app/ui/viewer/boxViewer.py
 create mode 100644 geos-trame/tests/test_box_intersection.py

diff --git a/geos-trame/src/geos/trame/app/data_types/renderable.py b/geos-trame/src/geos/trame/app/data_types/renderable.py
index e0312401d..af26a6253 100644
--- a/geos-trame/src/geos/trame/app/data_types/renderable.py
+++ b/geos-trame/src/geos/trame/app/data_types/renderable.py
@@ -6,6 +6,7 @@
 
 class Renderable( Enum ):
     """Enum class for renderable types and their ids."""
+    BOX = "Box"
     VTKMESH = "VTKMesh"
     INTERNALMESH = "InternalMesh"
     INTERNALWELL = "InternalWell"
diff --git a/geos-trame/src/geos/trame/app/ui/viewer/boxViewer.py b/geos-trame/src/geos/trame/app/ui/viewer/boxViewer.py
new file mode 100644
index 000000000..05b59f106
--- /dev/null
+++ b/geos-trame/src/geos/trame/app/ui/viewer/boxViewer.py
@@ -0,0 +1,111 @@
+# SPDX-License-Identifier: Apache-2.0
+# SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
+# SPDX-FileContributor: Lucas Givord - Kitware
+import pyvista as pv
+
+from geos.trame.schema_generated.schema_mod import Box
+
+import re
+
+
+class BoxViewer:
+    """A BoxViewer represents a Box and its intersected cell in a mesh.
+
+    This mesh is represented in GEOS with a Box.
+    """
+
+    def __init__( self, mesh: pv.UnstructuredGrid, box: Box ) -> None:
+        """Initialize the BoxViewer with a mesh and a box."""
+        self._mesh: pv.UnstructuredGrid = mesh
+
+        self._box: Box = box
+        self._box_polydata: pv.PolyData = None
+        self._box_polydata_actor: pv.Actor = None
+
+        self._extracted_cell: pv.UnstructuredGrid = None
+        self._extracted_cell_actor: pv.Actor = None
+
+        self._compute_box_as_polydata()
+        self._compute_intersected_cell()
+
+    def append_to_plotter( self, plotter: pv.Plotter ) -> None:
+        """Append the box and the intersected cell to the plotter.
+
+        The box is represented as a polydata with a low opacity.
+        """
+        self._box_polydata_actor = plotter.add_mesh( self._box_polydata, opacity=0.2 )
+
+        if self._extracted_cell is not None:
+            self._extracted_cell_actor = plotter.add_mesh( self._extracted_cell, show_edges=True )
+
+    def reset( self, plotter: pv.Plotter ) -> None:
+        """Reset the box viewer by removing the box and the intersected cell from the plotter."""
+        if self._box_polydata_actor is not None:
+            plotter.remove_actor( self._box_polydata_actor )
+
+        if self._extracted_cell_actor is not None:
+            plotter.remove_actor( self._extracted_cell_actor )
+
+        self._box_polydata = None
+        self._extracted_cell = None
+
+    def _compute_box_as_polydata( self ) -> None:
+        """Create a polydata reresenting a BBox using pyvista and coordinates from the Geos Box."""
+        bounding_box: list[ float ] = self._retrieve_bounding_box()
+        self._box_polydata = pv.Box( bounds=bounding_box )
+
+    def _retrieve_bounding_box( self ) -> list[ float ]:
+        """This method converts bounding box information from Box into a list of coordinates readable by pyvista.
+
+        e.g., this Box:
+
+        <Box name="box_1"
+             xMin="{ 1150, 700, 62 }"
+             xMax="{ 1250, 800, 137 }"/>
+
+        will return [1150, 1250, 700, 800, 62, 137].
+        """
+        # split str and remove brackets
+        min_point_str = re.findall( r"-?\d+\.\d+|-?\d+", self._box.x_min )
+        max_point_str = re.findall( r"-?\d+\.\d+|-?\d+", self._box.x_max )
+
+        min_point = list( map( float, min_point_str ) )
+        max_point = list( map( float, max_point_str ) )
+
+        return [
+            min_point[ 0 ],
+            max_point[ 0 ],
+            min_point[ 1 ],
+            max_point[ 1 ],
+            min_point[ 2 ],
+            max_point[ 2 ],
+        ]
+
+    def _compute_intersected_cell( self ) -> None:
+        """Extract the cells from the mesh that are inside the box."""
+        ids = self._mesh.find_cells_within_bounds( self._box_polydata.bounds )
+
+        saved_ids: list[ int ] = []
+
+        for id in ids:
+            cell: pv.vtkCell = self._mesh.GetCell( id )
+
+            is_inside = self._check_cell_inside_box( cell, self._box_polydata.bounds )
+            if is_inside:
+                saved_ids.append( id )
+
+        if len( saved_ids ) > 0:
+            self._extracted_cell = self._mesh.extract_cells( saved_ids )
+
+    def _check_cell_inside_box( self, cell: pv.Cell, box_bounds: list[ float ] ) -> bool:
+        """Check if the cell is inside the box bounds.
+
+        A cell is considered inside the box if his bounds are completely
+        inside the box bounds.
+        """
+        cell_bounds = cell.GetBounds()
+        is_inside_in_x = cell_bounds[ 0 ] >= box_bounds[ 0 ] and cell_bounds[ 1 ] <= box_bounds[ 1 ]
+        is_inside_in_y = cell_bounds[ 2 ] >= box_bounds[ 2 ] and cell_bounds[ 3 ] <= box_bounds[ 3 ]
+        is_inside_in_z = cell_bounds[ 4 ] >= box_bounds[ 4 ] and cell_bounds[ 5 ] <= box_bounds[ 5 ]
+
+        return is_inside_in_x and is_inside_in_y and is_inside_in_z
diff --git a/geos-trame/src/geos/trame/app/ui/viewer/viewer.py b/geos-trame/src/geos/trame/app/ui/viewer/viewer.py
index 80642046f..e3c06d0a7 100644
--- a/geos-trame/src/geos/trame/app/ui/viewer/viewer.py
+++ b/geos-trame/src/geos/trame/app/ui/viewer/viewer.py
@@ -11,10 +11,11 @@
 from vtkmodules.vtkRenderingCore import vtkActor
 
 from geos.trame.app.deck.tree import DeckTree
+from geos.trame.app.ui.viewer.boxViewer import BoxViewer
 from geos.trame.app.ui.viewer.perforationViewer import PerforationViewer
 from geos.trame.app.ui.viewer.regionViewer import RegionViewer
 from geos.trame.app.ui.viewer.wellViewer import WellViewer
-from geos.trame.schema_generated.schema_mod import Vtkmesh, Vtkwell, InternalWell, Perforation
+from geos.trame.schema_generated.schema_mod import Box, Vtkmesh, Vtkwell, InternalWell, Perforation
 
 pv.OFF_SCREEN = True
 
@@ -59,6 +60,7 @@ def __init__(
         self.SELECTED_DATA_ARRAY = "viewer_selected_data_array"
         self.state.change( self.SELECTED_DATA_ARRAY )( self._update_actor_array )
 
+        self.box_engine: BoxViewer | None = None
         self.region_engine = region_viewer
         self.well_engine = well_viewer
         self._perforations: dict[ str, PerforationViewer ] = {}
@@ -138,6 +140,24 @@ def update_viewer( self, active_block: BaseModel, path: str, show_obj: bool ) ->
         if isinstance( active_block, Perforation ):
             self._update_perforation( active_block, show_obj, path )
 
+        if isinstance( active_block, Box ):
+            if self.region_engine.input.number_of_cells == 0 and show_obj:
+                self.ctrl.on_add_warning(
+                    "Can't display " + active_block.name,
+                    "Please display the mesh before creating a well",
+                )
+                return
+
+            if self.box_engine is not None:
+                self.box_engine.reset( self.plotter )
+
+            if not show_obj:
+                return
+
+            box: Box = active_block
+            self.box_engine = BoxViewer( self.region_engine.input, box )
+            self.box_engine.append_to_plotter( self.plotter )
+
     def _on_clip_visibility_change( self, **kwargs: Any ) -> None:
         """Toggle cut plane visibility for all actors.
 
diff --git a/geos-trame/tests/data/geosDeck/geosDeck.xml b/geos-trame/tests/data/geosDeck/geosDeck.xml
index a4a7de8ef..efff1d45c 100644
--- a/geos-trame/tests/data/geosDeck/geosDeck.xml
+++ b/geos-trame/tests/data/geosDeck/geosDeck.xml
@@ -127,8 +127,8 @@
     <Geometry>
         <Box
         name="box_1"
-        xMin="{ 1150, 700, 62 }"
-        xMax="{ 1250, 800, 137 }"/>
+        xMin="{ 3509, 4117, -596 }"
+        xMax="{ 4482, 5041, -500 }"/>
     </Geometry>
     <!-- End Block to comment to deactivate box definition -->
 
diff --git a/geos-trame/tests/test_box_intersection.py b/geos-trame/tests/test_box_intersection.py
new file mode 100644
index 000000000..22b39f00c
--- /dev/null
+++ b/geos-trame/tests/test_box_intersection.py
@@ -0,0 +1,36 @@
+# SPDX-License-Identifier: Apache-2.0
+# SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
+# SPDX-FileContributor: Kitware
+# ruff: noqa
+from pathlib import Path
+
+from trame_server import Server
+from trame_server.state import State
+from trame_vuetify.ui.vuetify3 import VAppLayout
+
+from geos.trame.app.core import GeosTrame
+from tests.trame_fixtures import trame_state, trame_server_layout
+
+
+def test_box_intersection( trame_server_layout: tuple[ Server, VAppLayout ] ) -> None:
+    """Test box intersection."""
+    root_path = Path( __file__ ).parent.absolute().__str__()
+    file_name = root_path + "/data/geosDeck/geosDeck.xml"
+
+    app = GeosTrame( trame_server_layout[ 0 ], file_name )
+    app.state.ready()
+
+    app.deckInspector.state.object_state = [ "Problem/Mesh/0/VTKMesh/0", True ]
+    app.deckInspector.state.flush()
+
+    app.deckInspector.state.object_state = [ "Problem/Geometry/0/Box/0", True ]
+    app.deckInspector.state.flush()
+
+    box = app.deckViewer.box_engine._box
+    cells = app.deckViewer.box_engine._extracted_cell
+
+    assert box is not None
+    assert box.x_min == '{ 3509, 4117, -596 }'
+    assert box.x_max == '{ 4482, 5041, -500 }'
+    assert cells is not None
+    assert cells.number_of_cells == 1

From e261d68379c00f2ec26dd0a607d096fa74f3666a Mon Sep 17 00:00:00 2001
From: Lucas Givord <lucas.givord@kitware.com>
Date: Wed, 4 Jun 2025 09:47:31 +0200
Subject: [PATCH 02/17] feat(alert): add success alert type for the saving
 feature

---
 .../geos/trame/app/components/alertHandler.py | 24 ++++++++++++++++---
 geos-trame/src/geos/trame/app/core.py         |  2 +-
 geos-trame/src/geos/trame/app/deck/tree.py    | 13 ++++++----
 3 files changed, 31 insertions(+), 8 deletions(-)

diff --git a/geos-trame/src/geos/trame/app/components/alertHandler.py b/geos-trame/src/geos/trame/app/components/alertHandler.py
index 230b041fb..ea206d60b 100644
--- a/geos-trame/src/geos/trame/app/components/alertHandler.py
+++ b/geos-trame/src/geos/trame/app/components/alertHandler.py
@@ -5,6 +5,19 @@
 
 from trame.widgets import vuetify3
 
+from enum import Enum
+
+
+class AlertType( str, Enum ):
+    """Enum representing the type of VAlert.
+
+    For more information, see the uetify documentation:
+    https://vuetifyjs.com/en/api/VAlert/#props-type
+    """
+    SUCCESS = 'success'
+    WARNING = 'warning'
+    ERROR = 'error'
+
 
 class AlertHandler( vuetify3.VContainer ):
     """Vuetify component used to display an alert status.
@@ -26,8 +39,9 @@ def __init__( self ) -> None:
 
         self.state.alerts = []
 
-        self.ctrl.on_add_error.add_task( self.add_error )
-        self.ctrl.on_add_warning.add_task( self.add_warning )
+        self.server.controller.on_add_success.add_task( self.add_success )
+        self.server.controller.on_add_warning.add_task( self.add_warning )
+        self.server.controller.on_add_error.add_task( self.add_error )
 
         self.generate_alert_ui()
 
@@ -75,7 +89,7 @@ def add_alert( self, type: str, title: str, message: str ) -> None:
         self.state.dirty( "alerts" )
         self.state.flush()
 
-        if type == "warning":
+        if type == AlertType.WARNING:
             asyncio.get_event_loop().call_later( self.__lifetime_of_alert, self.on_close, alert_id )
 
     async def add_warning( self, title: str, message: str ) -> None:
@@ -86,6 +100,10 @@ async def add_error( self, title: str, message: str ) -> None:
         """Add an alert of type 'error'."""
         self.add_alert( "error", title, message )
 
+    async def add_success( self, title: str, message: str ) -> None:
+        """Add an alert of type 'success'."""
+        self.add_alert( AlertType.SUCCESS, title, message )
+
     def on_close( self, alert_id: int ) -> None:
         """Remove in the state the alert associated to the given id."""
         self.state.alerts = list( filter( lambda i: i[ "id" ] != alert_id, self.state.alerts ) )
diff --git a/geos-trame/src/geos/trame/app/core.py b/geos-trame/src/geos/trame/app/core.py
index 1f66b96ab..0a8f40973 100644
--- a/geos-trame/src/geos/trame/app/core.py
+++ b/geos-trame/src/geos/trame/app/core.py
@@ -61,7 +61,7 @@ def __init__( self, server: Server, file_name: str ) -> None:
         self.ctrl.simput_reload_data = self.simput_widget.reload_data
 
         # Tree
-        self.tree = DeckTree( self.state.sm_id )
+        self.tree = DeckTree( self.state.sm_id, self.ctrl )
 
         # Viewers
         self.region_viewer = RegionViewer()
diff --git a/geos-trame/src/geos/trame/app/deck/tree.py b/geos-trame/src/geos/trame/app/deck/tree.py
index 4979f3bec..b732ddea1 100644
--- a/geos-trame/src/geos/trame/app/deck/tree.py
+++ b/geos-trame/src/geos/trame/app/deck/tree.py
@@ -4,26 +4,28 @@
 import os
 from collections import defaultdict
 from typing import Any
-
 import dpath
 import funcy
 from pydantic import BaseModel
-from trame_simput import get_simput_manager
+
 from xsdata.formats.dataclass.parsers.config import ParserConfig
 from xsdata.formats.dataclass.serializers.config import SerializerConfig
 from xsdata.utils import text
 from xsdata_pydantic.bindings import DictDecoder, XmlContext, XmlSerializer
 
+from trame_server.controller import Controller
+from trame_simput import get_simput_manager
+
 from geos.trame.app.deck.file import DeckFile
 from geos.trame.app.geosTrameException import GeosTrameException
-from geos.trame.app.utils.file_utils import normalize_path, format_xml
 from geos.trame.schema_generated.schema_mod import Problem, Included, File, Functions
+from geos.trame.app.utils.file_utils import normalize_path, format_xml
 
 
 class DeckTree( object ):
     """A tree that represents a deck file along with all the available blocks and parameters."""
 
-    def __init__( self, sm_id: str | None = None, **kwargs: Any ) -> None:
+    def __init__( self, sm_id: str | None = None, ctrl: Controller = None, **kwargs: Any ) -> None:
         """Constructor."""
         super( DeckTree, self ).__init__( **kwargs )
 
@@ -33,6 +35,7 @@ def __init__( self, sm_id: str | None = None, **kwargs: Any ) -> None:
         self.root = None
         self.input_has_errors = False
         self._sm_id = sm_id
+        self._ctrl = ctrl
 
     def set_input_file( self, input_filename: str ) -> None:
         """Set a new input file.
@@ -172,6 +175,8 @@ def write_files( self ) -> None:
                 file.write( model_as_xml )
                 file.close()
 
+            self._ctrl.on_add_success( title="File saved", message=f"File {basename} has been saved." )
+
     @staticmethod
     def _append_include_file( model: Problem, included_file_path: str ) -> None:
         """Append an Included object which follows this structure according to the documentation.

From 6adbb9b138830e8022547b5f7a12a27527a26d4e Mon Sep 17 00:00:00 2001
From: Lucas Givord <lucas.givord@kitware.com>
Date: Tue, 8 Jul 2025 14:11:12 +0200
Subject: [PATCH 03/17] fix: well actor wasn't remove correctly

---
 .../src/geos/trame/app/ui/viewer/viewer.py    |  2 +
 .../geos/trame/app/ui/viewer/wellViewer.py    | 39 ++++++++++++++++---
 2 files changed, 36 insertions(+), 5 deletions(-)

diff --git a/geos-trame/src/geos/trame/app/ui/viewer/viewer.py b/geos-trame/src/geos/trame/app/ui/viewer/viewer.py
index e3c06d0a7..fea98c0b3 100644
--- a/geos-trame/src/geos/trame/app/ui/viewer/viewer.py
+++ b/geos-trame/src/geos/trame/app/ui/viewer/viewer.py
@@ -235,6 +235,7 @@ def _update_internalwell( self, path: str, show: bool ) -> None:
         """
         if not show:
             self.plotter.remove_actor( self.well_engine.get_actor( path ) )  # type: ignore
+            self.well_engine.remove_actor( path )
             return
 
         tube_actor = self.plotter.add_mesh( self.well_engine.get_tube( self.well_engine.get_last_mesh_idx() ) )
@@ -249,6 +250,7 @@ def _update_vtkwell( self, path: str, show: bool ) -> None:
         """
         if not show:
             self.plotter.remove_actor( self.well_engine.get_actor( path ) )  # type: ignore
+            self.well_engine.remove_actor( path )
             return
 
         tube_actor = self.plotter.add_mesh( self.well_engine.get_tube( self.well_engine.get_last_mesh_idx() ) )
diff --git a/geos-trame/src/geos/trame/app/ui/viewer/wellViewer.py b/geos-trame/src/geos/trame/app/ui/viewer/wellViewer.py
index 4196f7b87..237d50ca0 100644
--- a/geos-trame/src/geos/trame/app/ui/viewer/wellViewer.py
+++ b/geos-trame/src/geos/trame/app/ui/viewer/wellViewer.py
@@ -17,6 +17,12 @@ class Well:
     well_path: str
     polyline: pv.PolyData
     tube: pv.PolyData
+
+
+@dataclass
+class WellActor:
+    """A WellActor stores the VTK Actor representing a well."""
+    well_path: str
     actor: pv.Actor
 
 
@@ -28,6 +34,7 @@ def __init__( self, size: float, amplification: float ) -> None:
         A Well in GEOS could a InternalWell or a Vtkwell.
         """
         self._wells: list[ Well ] = []
+        self._wells_actors: list[ WellActor ] = []
 
         self.size: float = size
         self.amplification: float = amplification
@@ -51,7 +58,8 @@ def add_mesh( self, mesh: pv.PolyData, mesh_path: str ) -> int:
         radius = self.size * ( self.STARTING_VALUE / 100 )
         tube = mesh.tube( radius=radius, n_sides=50 )
 
-        self._wells.append( Well( mesh_path, mesh, tube, pv.Actor() ) )
+        self._wells.append( Well( mesh_path, mesh, tube ) )
+        self._wells_actors.append( WellActor( mesh_path, pv.Actor() ) )
 
         return len( self._wells ) - 1
 
@@ -78,21 +86,21 @@ def get_tube_size( self ) -> float:
 
     def append_actor( self, perforation_path: str, tube_actor: pv.Actor ) -> None:
         """Append a given actor, typically the Actor returned by the pv.Plotter() when a given mes is added."""
-        index = self._get_index_from_perforation( perforation_path )
+        index = self._get_actor_index_from_perforation( perforation_path )
         if index == -1:
             print( "Cannot found the well to remove from path: ", perforation_path )
             return
 
-        self._wells[ index ].actor = tube_actor
+        self._wells_actors[ index ].actor = tube_actor
 
     def get_actor( self, perforation_path: str ) -> pv.Actor | None:
         """Retrieve the polyline linked to a given perforation path."""
-        index = self._get_index_from_perforation( perforation_path )
+        index = self._get_actor_index_from_perforation( perforation_path )
         if index == -1:
             print( "Cannot found the well to remove from path: ", perforation_path )
             return None
 
-        return self._wells[ index ].actor
+        return self._wells_actors[ index ].actor
 
     def update( self, value: float ) -> None:
         """Update the radius of the tubes."""
@@ -108,6 +116,14 @@ def remove( self, perforation_path: str ) -> None:
 
         self._wells.remove( self._wells[ index ] )
 
+    def remove_actor( self, perforation_path: str ) -> None:
+        """Clear all data stored in this class."""
+        index = self._get_actor_index_from_perforation( perforation_path )
+        if index == -1:
+            print( "Cannot found the well to remove from path: ", perforation_path )
+
+        self._wells_actors.remove( self._wells_actors[ index ] )
+
     def _get_index_from_perforation( self, perforation_path: str ) -> int:
         """Retrieve the well associated to a given perforation, otherwise return -1."""
         index = -1
@@ -121,6 +137,19 @@ def _get_index_from_perforation( self, perforation_path: str ) -> int:
 
         return index
 
+    def _get_actor_index_from_perforation( self, perforation_path: str ) -> int:
+        """Retrieve the well actor associated to a given perforation, otherwise return -1."""
+        index = -1
+        if len( self._wells_actors ) == 0:
+            return index
+
+        for i in range( 0, len( self._wells_actors ) ):
+            if self._wells_actors[ i ].well_path in perforation_path:
+                index = i
+                break
+
+        return index
+
     def get_number_of_wells( self ) -> int:
         """Get the number of wells in the viewer."""
         return len( self._wells )

From 41d305472e11e143eeeca89f062a3baf9e2cf0bc Mon Sep 17 00:00:00 2001
From: Lucas Givord <lucas.givord@kitware.com>
Date: Tue, 22 Jul 2025 11:38:06 +0200
Subject: [PATCH 04/17] fix: update data added in the plotter

Previously user needs to trigger a render call to fix a bad scalar
array/lut when a new data was added in the pyvista.Plotter. We enforce it
when we trigger the 'update_viewer' method.
---
 geos-trame/src/geos/trame/app/ui/viewer/viewer.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/geos-trame/src/geos/trame/app/ui/viewer/viewer.py b/geos-trame/src/geos/trame/app/ui/viewer/viewer.py
index fea98c0b3..be6bdecbc 100644
--- a/geos-trame/src/geos/trame/app/ui/viewer/viewer.py
+++ b/geos-trame/src/geos/trame/app/ui/viewer/viewer.py
@@ -158,6 +158,9 @@ def update_viewer( self, active_block: BaseModel, path: str, show_obj: bool ) ->
             self.box_engine = BoxViewer( self.region_engine.input, box )
             self.box_engine.append_to_plotter( self.plotter )
 
+        # make sure that added data in the plot will be rendered with the correct scalar array/lut
+        self.plotter.update()
+
     def _on_clip_visibility_change( self, **kwargs: Any ) -> None:
         """Toggle cut plane visibility for all actors.
 

From 79b26e7c525953590715582fc689184e4eb21871 Mon Sep 17 00:00:00 2001
From: Lucas Givord <lucas.givord@kitware.com>
Date: Tue, 22 Jul 2025 15:52:23 +0200
Subject: [PATCH 05/17] viewer: remove Plotter dependency to the box engine

---
 .../src/geos/trame/app/ui/viewer/boxViewer.py | 39 +++++++------
 .../src/geos/trame/app/ui/viewer/viewer.py    | 55 ++++++++++++-------
 geos-trame/tests/test_box_intersection.py     |  2 +-
 3 files changed, 58 insertions(+), 38 deletions(-)

diff --git a/geos-trame/src/geos/trame/app/ui/viewer/boxViewer.py b/geos-trame/src/geos/trame/app/ui/viewer/boxViewer.py
index 05b59f106..71046b83d 100644
--- a/geos-trame/src/geos/trame/app/ui/viewer/boxViewer.py
+++ b/geos-trame/src/geos/trame/app/ui/viewer/boxViewer.py
@@ -22,32 +22,35 @@ def __init__( self, mesh: pv.UnstructuredGrid, box: Box ) -> None:
         self._box_polydata: pv.PolyData = None
         self._box_polydata_actor: pv.Actor = None
 
-        self._extracted_cell: pv.UnstructuredGrid = None
-        self._extracted_cell_actor: pv.Actor = None
+        self._extracted_cells: pv.UnstructuredGrid = None
+        self._extracted_cells_actor: pv.Actor = None
 
         self._compute_box_as_polydata()
         self._compute_intersected_cell()
 
-    def append_to_plotter( self, plotter: pv.Plotter ) -> None:
-        """Append the box and the intersected cell to the plotter.
+    def get_box_polydata( self ) -> pv.PolyData | None:
+        """Get the box polydata."""
+        return self._box_polydata
 
-        The box is represented as a polydata with a low opacity.
-        """
-        self._box_polydata_actor = plotter.add_mesh( self._box_polydata, opacity=0.2 )
+    def get_box_polydata_actor( self ) -> pv.Actor:
+        """Get the actor generated by a pv.Plotter for the box polydata."""
+        return self._box_polydata_actor
 
-        if self._extracted_cell is not None:
-            self._extracted_cell_actor = plotter.add_mesh( self._extracted_cell, show_edges=True )
+    def get_extracted_cells( self ) -> pv.UnstructuredGrid | None:
+        """Get the extracted cell polydata."""
+        return self._extracted_cells
 
-    def reset( self, plotter: pv.Plotter ) -> None:
-        """Reset the box viewer by removing the box and the intersected cell from the plotter."""
-        if self._box_polydata_actor is not None:
-            plotter.remove_actor( self._box_polydata_actor )
+    def get_extracted_cells_actor( self ) -> pv.Actor | None:
+        """Get the extracted cell polydata actor."""
+        return self._extracted_cells_actor
 
-        if self._extracted_cell_actor is not None:
-            plotter.remove_actor( self._extracted_cell_actor )
+    def set_box_polydata_actor( self, box_actor: pv.Actor ) -> None:
+        """Set the actor generated by a pv.Plotter for the box polydata."""
+        self._box_polydata_actor = box_actor
 
-        self._box_polydata = None
-        self._extracted_cell = None
+    def set_extracted_cells_actor( self, extracted_cell: pv.Actor ) -> None:
+        """Set the actor generated by a pv.Plotter for the extracted cell."""
+        self._extracted_cells_actor = extracted_cell
 
     def _compute_box_as_polydata( self ) -> None:
         """Create a polydata reresenting a BBox using pyvista and coordinates from the Geos Box."""
@@ -95,7 +98,7 @@ def _compute_intersected_cell( self ) -> None:
                 saved_ids.append( id )
 
         if len( saved_ids ) > 0:
-            self._extracted_cell = self._mesh.extract_cells( saved_ids )
+            self._extracted_cells = self._mesh.extract_cells( saved_ids )
 
     def _check_cell_inside_box( self, cell: pv.Cell, box_bounds: list[ float ] ) -> bool:
         """Check if the cell is inside the box bounds.
diff --git a/geos-trame/src/geos/trame/app/ui/viewer/viewer.py b/geos-trame/src/geos/trame/app/ui/viewer/viewer.py
index be6bdecbc..204dc4ac6 100644
--- a/geos-trame/src/geos/trame/app/ui/viewer/viewer.py
+++ b/geos-trame/src/geos/trame/app/ui/viewer/viewer.py
@@ -36,6 +36,7 @@ def __init__(
          - Vtkwell,
          - Perforation,
          - InternalWell
+         - Box
 
         Everything is handle in the method 'update_viewer()' which is trigger when the
         'state.object_state' changed (see DeckTree).
@@ -124,7 +125,7 @@ def rendering_menu_extra_items( self ) -> None:
     def update_viewer( self, active_block: BaseModel, path: str, show_obj: bool ) -> None:
         """Add from path the dataset given by the user.
 
-        Supported data type is: Vtkwell, Vtkmesh, InternalWell, Perforation.
+        Supported data type is: Vtkwell, Vtkmesh, InternalWell, Perforation, Box.
 
         object_state  : array used to store path to the data and if we want to show it or not.
         """
@@ -141,24 +142,10 @@ def update_viewer( self, active_block: BaseModel, path: str, show_obj: bool ) ->
             self._update_perforation( active_block, show_obj, path )
 
         if isinstance( active_block, Box ):
-            if self.region_engine.input.number_of_cells == 0 and show_obj:
-                self.ctrl.on_add_warning(
-                    "Can't display " + active_block.name,
-                    "Please display the mesh before creating a well",
-                )
-                return
+            self._update_box( active_block, show_obj )
 
-            if self.box_engine is not None:
-                self.box_engine.reset( self.plotter )
-
-            if not show_obj:
-                return
-
-            box: Box = active_block
-            self.box_engine = BoxViewer( self.region_engine.input, box )
-            self.box_engine.append_to_plotter( self.plotter )
-
-        # make sure that added data in the plot will be rendered with the correct scalar array/lut
+        # when data is added in the pv.Plotter, we need to refresh the scene to update
+        # the actor to avoid LUT issue.
         self.plotter.update()
 
     def _on_clip_visibility_change( self, **kwargs: Any ) -> None:
@@ -353,6 +340,36 @@ def _add_perforation( self, distance_from_head: float, path: str ) -> None:
         cell_id = self.region_engine.input.find_closest_cell( point_offsetted )
         cell = self.region_engine.input.extract_cells( [ cell_id ] )
         cell_actor = self.plotter.add_mesh( cell )
-        saved_perforation.add_extracted_cell( cell_actor )
+        saved_perforation.add_extracted_cells( cell_actor )
 
         self._perforations[ path ] = saved_perforation
+
+    def _update_box( self, active_block: Box, show_obj: bool ) -> None:
+        """Generate and display a Box and inner cell(s) from the mesh."""
+        if self.region_engine.input.number_of_cells == 0 and show_obj:
+            self.ctrl.on_add_warning(
+                "Can't display " + active_block.name,
+                "Please display the mesh before creating a well",
+            )
+            return
+
+        if self.box_engine is not None:
+            box_polydata_actor: pv.Actor = self.box_engine.get_box_polydata_actor()
+            extracted_cell_actor: pv.Actor = self.box_engine.get_extracted_cells_actor()
+            self.plotter.remove_actor( box_polydata_actor )
+            self.plotter.remove_actor( extracted_cell_actor )
+
+        if not show_obj:
+            return
+
+        box: Box = active_block
+        self.box_engine = BoxViewer( self.region_engine.input, box )
+
+        box_polydata: pv.PolyData = self.box_engine.get_box_polydata()
+        extracted_cell: pv.UnstructuredGrid = self.box_engine.get_extracted_cells()
+
+        if box_polydata is not None and extracted_cell is not None:
+            _box_polydata_actor = self.plotter.add_mesh( box_polydata, opacity=0.2 )
+            _extracted_cells_actor = self.plotter.add_mesh( extracted_cell, show_edges=True )
+            self.box_engine.set_box_polydata_actor( _box_polydata_actor )
+            self.box_engine.set_extracted_cells_actor( _extracted_cells_actor )
diff --git a/geos-trame/tests/test_box_intersection.py b/geos-trame/tests/test_box_intersection.py
index 22b39f00c..06db5df41 100644
--- a/geos-trame/tests/test_box_intersection.py
+++ b/geos-trame/tests/test_box_intersection.py
@@ -27,7 +27,7 @@ def test_box_intersection( trame_server_layout: tuple[ Server, VAppLayout ] ) ->
     app.deckInspector.state.flush()
 
     box = app.deckViewer.box_engine._box
-    cells = app.deckViewer.box_engine._extracted_cell
+    cells = app.deckViewer.box_engine._extracted_cells
 
     assert box is not None
     assert box.x_min == '{ 3509, 4117, -596 }'

From 1d8c975e1b1b73891ca32cfda0357d6996d9dd8d Mon Sep 17 00:00:00 2001
From: Paloma Martinez <104762252+paloma-martinez@users.noreply.github.com>
Date: Thu, 30 Oct 2025 17:44:35 +0100
Subject: [PATCH 06/17] Fix typo

---
 geos-trame/src/geos/trame/app/ui/viewer/viewer.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/geos-trame/src/geos/trame/app/ui/viewer/viewer.py b/geos-trame/src/geos/trame/app/ui/viewer/viewer.py
index 204dc4ac6..2536c8d7e 100644
--- a/geos-trame/src/geos/trame/app/ui/viewer/viewer.py
+++ b/geos-trame/src/geos/trame/app/ui/viewer/viewer.py
@@ -340,7 +340,7 @@ def _add_perforation( self, distance_from_head: float, path: str ) -> None:
         cell_id = self.region_engine.input.find_closest_cell( point_offsetted )
         cell = self.region_engine.input.extract_cells( [ cell_id ] )
         cell_actor = self.plotter.add_mesh( cell )
-        saved_perforation.add_extracted_cells( cell_actor )
+        saved_perforation.add_extracted_cell( cell_actor )
 
         self._perforations[ path ] = saved_perforation
 

From 8896a8807831d32fcf82f42c17341d3ece8ad471 Mon Sep 17 00:00:00 2001
From: Jacques Franc <49998870+jafranc@users.noreply.github.com>
Date: Fri, 31 Oct 2025 16:48:04 +0100
Subject: [PATCH 07/17] Update python-package.yml

---
 .github/workflows/python-package.yml | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 8ae0563e8..f46dc1e0e 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -71,6 +71,12 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
+    
+    - name: Install OSMesa
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libosmesa6-dev libgl1-mesa-glx libglu1-mesa xvfb
+
     - name: Install package
       # working-directory: ./${{ matrix.package-name }}
       run: |
@@ -94,8 +100,10 @@ jobs:
       run: |
         yapf -r --diff ./${{ matrix.package-name }} --style .style.yapf
     - name: Test with pytest
+      env:
+          PYVISTA_OFF_SCREEN: true
       #working-directory: ./${{ matrix.package-name }}
       run:
       # python -m pytest ./${{ matrix.package-name }} --doctest-modules --junitxml=junit/test-results.xml --cov-report=xml --cov-report=html |
       # wrap pytest to avoid error when no tests in the package
-        sh -c 'python -m pytest ./${{ matrix.package-name }}; ret=$?; [ $ret = 5 ] && exit 0 || exit $ret'
\ No newline at end of file
+        sh -c 'python -m pytest ./${{ matrix.package-name }}; ret=$?; [ $ret = 5 ] && exit 0 || exit $ret'

From 560518da5b22a9b871a18dbb21b28253e2c44e5c Mon Sep 17 00:00:00 2001
From: Jacques Franc <49998870+jafranc@users.noreply.github.com>
Date: Fri, 31 Oct 2025 17:03:39 +0100
Subject: [PATCH 08/17] Update python-package.yml

---
 .github/workflows/python-package.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 2cb9428bd..3869e370b 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -96,7 +96,7 @@ jobs:
     - name: Install OSMesa
       run: |
         sudo apt-get update
-        sudo apt-get install -y libosmesa6-dev libgl1-mesa-glx libglu1-mesa xvfb
+        sudo apt-get install -y libosmesa6
 
     - name: Install package
       # working-directory: ./${{ matrix.package-name }}

From a2a7a638a2ab6303f05dcb38c919052e38009480 Mon Sep 17 00:00:00 2001
From: Jacques Franc <49998870+jafranc@users.noreply.github.com>
Date: Fri, 31 Oct 2025 17:14:46 +0100
Subject: [PATCH 09/17] Update python-package.yml

---
 .github/workflows/python-package.yml | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 3869e370b..5835c55c8 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -93,10 +93,16 @@ jobs:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
     
-    - name: Install OSMesa
+    - 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 \
+            libgl1-mesa-dev \
+            libx11-dev \
+            libxext-dev
 
     - name: Install package
       # working-directory: ./${{ matrix.package-name }}

From ab01e6ae098ea406d2763013f348e73cd0f47c98 Mon Sep 17 00:00:00 2001
From: Jacques Franc <49998870+jafranc@users.noreply.github.com>
Date: Sun, 2 Nov 2025 18:49:34 +0000
Subject: [PATCH 10/17] fix pyvista init in test

---
 .github/workflows/python-package.yml          | 22 +++++++++----------
 .../src/geos/trame/app/ui/viewer/viewer.py    |  1 +
 2 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 5835c55c8..fc7be3ecd 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -93,16 +93,16 @@ jobs:
         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 \
-            libegl1-mesa-dev \
-            libgles2-mesa-dev \
-            libgl1-mesa-dev \
-            libx11-dev \
-            libxext-dev
+    # - name: Install OSMesa and GL
+    #   run: |
+    #     sudo apt-get update
+    #     sudo apt-get install -y libosmesa6      
+    #     sudo apt-get install -y \
+    #         libegl1-mesa-dev \
+    #         libgles2-mesa-dev \
+    #         libgl1-mesa-dev \
+    #         libx11-dev \
+    #         libxext-dev
 
     - name: Install package
       # working-directory: ./${{ matrix.package-name }}
@@ -126,8 +126,6 @@ jobs:
       run: |
         yapf -r --diff ./${{ matrix.package-name }} --style .style.yapf
     - name: Test with pytest
-      env:
-          PYVISTA_OFF_SCREEN: true
       #working-directory: ./${{ matrix.package-name }}
       run:
       # python -m pytest ./${{ matrix.package-name }} --doctest-modules --junitxml=junit/test-results.xml --cov-report=xml --cov-report=html |
diff --git a/geos-trame/src/geos/trame/app/ui/viewer/viewer.py b/geos-trame/src/geos/trame/app/ui/viewer/viewer.py
index 2536c8d7e..252e793e2 100644
--- a/geos-trame/src/geos/trame/app/ui/viewer/viewer.py
+++ b/geos-trame/src/geos/trame/app/ui/viewer/viewer.py
@@ -50,6 +50,7 @@ def __init__(
         self._cell_data_array_names: list[ str ] = []
         self._source = source
         self._pl = pv.Plotter()
+        self._pl.iren.initialize()
         self._mesh_actor: vtkActor | None = None
 
         self.CUT_PLANE = "on_cut_plane_visibility_change"

From 348f10064a7dcd08ff3bd012c4f908bf0ccce1d7 Mon Sep 17 00:00:00 2001
From: Jacques Franc <49998870+jafranc@users.noreply.github.com>
Date: Mon, 3 Nov 2025 08:59:53 +0100
Subject: [PATCH 11/17] debug CI

---
 .github/workflows/python-package.yml | 52 ++++++++++++++++------------
 1 file changed, 30 insertions(+), 22 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index fc7be3ecd..94db536fc 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -57,20 +57,20 @@ jobs:
       fail-fast: false
       max-parallel: 3
       matrix:
-        python-version: ["3.10","3.11","3.12"]
+        python-version: ["3.12"]
         package-name: 
-          - geos-ats
-          - geos-utils
-          - geos-geomechanics
-          - geos-mesh
-          - geos-posp
-          - geos-processing
-          - geos-timehistory
+          # - geos-ats
+          # - geos-utils
+          # - geos-geomechanics
+          # - geos-mesh
+          # - geos-posp
+          # - geos-processing
+          # - geos-timehistory
           - geos-trame
-          - geos-xml-tools
-          - geos-xml-viewer
-          - hdf5-wrapper
-          - pygeos-tools
+          # - geos-xml-tools
+          # - geos-xml-viewer
+          # - hdf5-wrapper
+          # - pygeos-tools
         include:
           - package-name: geos-geomechanics
             dependencies: "geos-utils"
@@ -93,16 +93,24 @@ jobs:
         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 \
-    #         libegl1-mesa-dev \
-    #         libgles2-mesa-dev \
-    #         libgl1-mesa-dev \
-    #         libx11-dev \
-    #         libxext-dev
+    - name: Install OSMesa and GL
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libosmesa6      
+        sudo apt-get install -y \
+            libegl1-mesa-dev \
+            libgles2-mesa-dev \
+            libgl1-mesa-dev \
+            libx11-dev \
+            libxext-dev
+
+    - name: ssh
+      uses: lhotari/action-upterm@v1
+      with:
+# limits ssh access and adds the ssh public key for the user which triggered the workflow
+        limit-access-to-actor: true
+# limits ssh access and adds the ssh public keys of the listed GitHub users
+        limit-access-to-users: GitHubLogin
 
     - name: Install package
       # working-directory: ./${{ matrix.package-name }}

From 5e7334344a7e805ca95970f16a765569ebcb1d2a Mon Sep 17 00:00:00 2001
From: Jacques Franc <49998870+jafranc@users.noreply.github.com>
Date: Mon, 3 Nov 2025 09:19:23 +0100
Subject: [PATCH 12/17] debug CI

---
 .github/workflows/python-package.yml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 94db536fc..cd8fbae3f 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -104,14 +104,6 @@ jobs:
             libx11-dev \
             libxext-dev
 
-    - name: ssh
-      uses: lhotari/action-upterm@v1
-      with:
-# limits ssh access and adds the ssh public key for the user which triggered the workflow
-        limit-access-to-actor: true
-# limits ssh access and adds the ssh public keys of the listed GitHub users
-        limit-access-to-users: GitHubLogin
-
     - name: Install package
       # working-directory: ./${{ matrix.package-name }}
       run: |
@@ -140,6 +132,14 @@ jobs:
       # wrap pytest to avoid error when no tests in the package
         sh -c 'python -m pytest ./${{ matrix.package-name }}; ret=$?; [ $ret = 5 ] && exit 0 || exit $ret'
 
+    - name: ssh
+      uses: lhotari/action-upterm@v1
+      with:
+# limits ssh access and adds the ssh public key for the user which triggered the workflow
+        limit-access-to-actor: true
+# limits ssh access and adds the ssh public keys of the listed GitHub users
+        limit-access-to-users: GitHubLogin
+
   # check if GEOS has label for testing GEOS integration
   check_integration_label:
     runs-on: ubuntu-latest

From 0fed0625504f68112605321d0d7189bb01b24a0f Mon Sep 17 00:00:00 2001
From: Jacques Franc <49998870+jafranc@users.noreply.github.com>
Date: Mon, 3 Nov 2025 09:29:56 +0100
Subject: [PATCH 13/17] debug CI

---
 .github/workflows/python-package.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index cd8fbae3f..0ffe5e660 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -130,7 +130,8 @@ jobs:
       run:
       # python -m pytest ./${{ matrix.package-name }} --doctest-modules --junitxml=junit/test-results.xml --cov-report=xml --cov-report=html |
       # wrap pytest to avoid error when no tests in the package
-        sh -c 'python -m pytest ./${{ matrix.package-name }}; ret=$?; [ $ret = 5 ] && exit 0 || exit $ret'
+      # sh -c 'python -m pytest ./${{ matrix.package-name }}; ret=$?; [ $ret = 5 ] && exit 0 || exit $ret
+        sh -c 'python -m pytest ./${{ matrix.package-name }};'
 
     - name: ssh
       uses: lhotari/action-upterm@v1

From 7efbf7f3c4da63b241a73b2ddda63f284cb9eca7 Mon Sep 17 00:00:00 2001
From: Jacques Franc <49998870+jafranc@users.noreply.github.com>
Date: Mon, 3 Nov 2025 09:52:07 +0100
Subject: [PATCH 14/17] debug CI

---
 .github/workflows/python-package.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 0ffe5e660..57eed6775 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -137,9 +137,9 @@ jobs:
       uses: lhotari/action-upterm@v1
       with:
 # limits ssh access and adds the ssh public key for the user which triggered the workflow
-        limit-access-to-actor: true
+        limit-access-to-actor: false
 # limits ssh access and adds the ssh public keys of the listed GitHub users
-        limit-access-to-users: GitHubLogin
+        # limit-access-to-users: GitHubLogin
 
   # check if GEOS has label for testing GEOS integration
   check_integration_label:

From fb38c366d638de862ba48169af3db64676069c9b Mon Sep 17 00:00:00 2001
From: Jacques Franc <49998870+jafranc@users.noreply.github.com>
Date: Mon, 3 Nov 2025 10:06:24 +0100
Subject: [PATCH 15/17] debug CI

---
 .github/workflows/python-package.yml | 11 +----------
 1 file changed, 1 insertion(+), 10 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 57eed6775..bcc237b60 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -130,16 +130,7 @@ jobs:
       run:
       # python -m pytest ./${{ matrix.package-name }} --doctest-modules --junitxml=junit/test-results.xml --cov-report=xml --cov-report=html |
       # wrap pytest to avoid error when no tests in the package
-      # sh -c 'python -m pytest ./${{ matrix.package-name }}; ret=$?; [ $ret = 5 ] && exit 0 || exit $ret
-        sh -c 'python -m pytest ./${{ matrix.package-name }};'
-
-    - name: ssh
-      uses: lhotari/action-upterm@v1
-      with:
-# limits ssh access and adds the ssh public key for the user which triggered the workflow
-        limit-access-to-actor: false
-# limits ssh access and adds the ssh public keys of the listed GitHub users
-        # limit-access-to-users: GitHubLogin
+        sh -c 'python -m pytest ./${{ matrix.package-name }}; ret=$?; [ $ret = 5 ] && exit 0 || exit $ret'
 
   # check if GEOS has label for testing GEOS integration
   check_integration_label:

From d45b0b919d13dcc052cb30aab437bcde65c30f5c Mon Sep 17 00:00:00 2001
From: Jacques Franc <49998870+jafranc@users.noreply.github.com>
Date: Mon, 3 Nov 2025 10:16:30 +0100
Subject: [PATCH 16/17] clean up CI and restore all tests

---
 .github/workflows/python-package.yml | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index bcc237b60..377f67e8a 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -59,18 +59,18 @@ jobs:
       matrix:
         python-version: ["3.12"]
         package-name: 
-          # - geos-ats
-          # - geos-utils
-          # - geos-geomechanics
-          # - geos-mesh
-          # - geos-posp
-          # - geos-processing
-          # - geos-timehistory
+          - geos-ats
+          - geos-utils
+          - geos-geomechanics
+          - geos-mesh
+          - geos-posp
+          - geos-processing
+          - geos-timehistory
           - geos-trame
-          # - geos-xml-tools
-          # - geos-xml-viewer
-          # - hdf5-wrapper
-          # - pygeos-tools
+          - geos-xml-tools
+          - geos-xml-viewer
+          - hdf5-wrapper
+          - pygeos-tools
         include:
           - package-name: geos-geomechanics
             dependencies: "geos-utils"

From da1cf5b90907530b2a98c4b4497ef1c3acdcf591 Mon Sep 17 00:00:00 2001
From: Jacques Franc <49998870+jafranc@users.noreply.github.com>
Date: Mon, 3 Nov 2025 10:47:04 +0100
Subject: [PATCH 17/17] restore all python version

looks like workflow edition trigger all test-integration. But could be justified
---
 .github/workflows/python-package.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 377f67e8a..10d5e5130 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -57,7 +57,7 @@ jobs:
       fail-fast: false
       max-parallel: 3
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.10","3.11","3.12"]
         package-name: 
           - geos-ats
           - geos-utils