feat: apply jafranc review comments on PR#251 (euler surface)

.github/workflows/python-package.yml

@@ -158,7 +158,7 @@ jobs:
 
   check_force_integration_label:
     runs-on: ubuntu-latest
-    needs: [build]
+    # needs: [build]
     outputs:
       has_geos_integration_force_label: ${{ steps.set-label.outputs.has_label }}
     steps:

.github/workflows/test_geos_integration.yml

@@ -25,7 +25,7 @@ jobs:
 
     container:
       # using this image to get access to python 3.10+
-      image: geosx/ubuntu22.04-gcc12:${{ needs.setup.outputs.tag }}
+      image: geosx/ubuntu24.04-gcc13:${{ needs.setup.outputs.tag }}
 
     steps:
     - name: Checkout geosPythonPackages
@@ -44,22 +44,25 @@ jobs:
     - name: Install Build Dependencies
       run: |
         apt-get update
-        apt-get install -y make python3-numpy python3-dev python3-venv python3-pip
+        apt-get install -y make python3-numpy python3-dev python3-venv python3-setuptools
 
         # Ensure pip installs scripts to /usr/local/bin 
         export PATH="/usr/local/bin:$PATH"
         echo "PATH=/usr/local/bin:$PATH" >> $GITHUB_ENV
 
+        # For Ubuntu 24.04 with Python 3.12+, setuptools is required (distutils was removed)
+        # Upgrade setuptools to latest versions
+        python3 -m pip install --break-system-packages --upgrade setuptools
+
         # Set environment variables to handle setuptools/distutils issues
-        echo "SETUPTOOLS_USE_DISTUTILS=stdlib" >> $GITHUB_ENV
         echo "PIP_DISABLE_PIP_VERSION_CHECK=1" >> $GITHUB_ENV
         echo "PYTHONDONTWRITEBYTECODE=1" >> $GITHUB_ENV
-
+        
     - name: Setup test environment
       run: |
         echo "Setting up test environment..."
         GEOS_ROOT="$(pwd)/GEOS"
-        SETUP_PYTHON_ENVIRONMENT_SCRIPT="$GEOS_ROOT/scripts/setupPythonEnvironment.bash"
+        SETUP_PYTHON_ENVIRONMENT_SCRIPT="${GEOS_ROOT}/scripts/setupPythonEnvironment.bash"
 
         if [ -n "${{ github.head_ref }}" ]; then
           CURRENT_GEOSPYTHONPACKAGES_BRANCH_NAME="${{ github.head_ref }}"
@@ -100,7 +103,7 @@ jobs:
           -DENABLE_YAPF=OFF \
           -DGEOS_ENABLE_TESTS=OFF \
           -DGEOS_ENABLE_CONTACT=OFF \
-          -DGEOS_ENABLE_FLUIDFLOW=ON \
+          -DGEOS_ENABLE_FLUIDFLOW=OFF \
           -DGEOS_ENABLE_INDUCEDSEISMICITY=OFF \
           -DGEOS_ENABLE_MULTIPHYSICS=OFF \
           -DGEOS_ENABLE_SIMPLEPDE=OFF \
@@ -119,6 +122,11 @@ jobs:
       run: |
         echo "=== Test 1: Direct setupPythonEnvironment.bash execution ==="
         mkdir -p bin_direct
+
+        # # encapsulate env
+        python3 -m venv geos-venv
+        . geos-venv/bin/activate
+        python -m pip install --upgrade pip setuptools wheel
 
         # The setup script searches specific paths but pip installs to /usr/local/bin
         # We need to patch the setup script to also search /usr/local/bin
@@ -130,8 +138,22 @@ jobs:
 
         # Add /usr/local/bin to the MOD_SEARCH_PATH array right after the python bin directory
         # We insert /usr/local/bin as the second entry
-        sed -i '/^declare -a MOD_SEARCH_PATH=.*PYTHON_TARGET)"/a\                            "/usr/local/bin"' "$TEMP_SETUP_SCRIPT"
-
+        # sed -i '/^declare -a MOD_SEARCH_PATH=.*PYTHON_TARGET)"/a\                            "/usr/local/bin"' "$TEMP_SETUP_SCRIPT"
+        # Only add --break-system-packages for Python >= 3.12
+        # PYTHON_VERSION=$($(which python3) -c 'import sys; print(f"{sys.version_info.major}.{sys.version_info.minor}")')
+        # if [[ "$PYTHON_VERSION" == "3.12" || "$PYTHON_VERSION" > "3.12" ]]; then
+        # sed -i 's/${PIP_CMD} install/${PIP_CMD} install --break-system-packages/g' "$TEMP_SETUP_SCRIPT"
+        # sed -i 's/$PYTHON_TARGET -m pip install --upgrade pip setuptools wheel/$PYTHON_TARGET -m pip install --upgrade setuptools/' "$TEMP_SETUP_SCRIPT"
+        # fi
+        cat "$TEMP_SETUP_SCRIPT"
+        export PIP_NO_BUILD_ISOLATION=1
+        bash "$TEMP_SETUP_SCRIPT" \
+          -p $(which python) \
+          -b "$(pwd)/bin_direct" \
+          --python-pkg-branch "$CURRENT_GEOSPYTHONPACKAGES_BRANCH_NAME" \
+          --verbose
+        cat "$TEMP_SETUP_SCRIPT"
+        export PIP_NO_BUILD_ISOLATION=1
         bash "$TEMP_SETUP_SCRIPT" \
           -p $(which python3) \
           -b "$(pwd)/bin_direct" \
@@ -210,6 +232,8 @@ jobs:
           echo "Creating symlink from PyGEOSX virtual environment..."
           ln -s "$(pwd)/lib/PYGEOSX/bin/test_geosx_xml_tools" python/geosx/bin/test_geosx_xml_tools
         else
+          # If the real test script is not found, create a placeholder so the test step can proceed.
+          # This ensures the workflow does not fail due to a missing test script, but signals that a real test should be provided.
           echo "Creating placeholder test script..."
           echo '#!/usr/bin/env python3' > python/geosx/bin/test_geosx_xml_tools
           echo 'import sys' >> python/geosx/bin/test_geosx_xml_tools
@@ -252,6 +276,16 @@ jobs:
         # Ensure geosx_python_tools is built (provides format_xml)
         echo "Building geosx_python_tools dependency..."
         make geosx_python_tools -j8
+
+        # The geosx_format_all_xml_files target has a bug - it depends on 'geosx_xml_tools' which doesn't exist
+        # It should depend on 'geosx_python_tools'. Since we can't modify the CMakeLists.txt,
+        # we'll run the formatting command directly instead
+        # To solve the bug in cmake, we would have to change:
+        # add_custom_target( geosx_format_all_xml_files
+        #           COMMAND bash ${CMAKE_SOURCE_DIR}/../scripts/formatXMLFiles.bash -g ${CMAKE_BINARY_DIR}/bin/format_xml ${CMAKE_SOURCE_DIR} ${CMAKE_SOURCE_DIR}/../examples
+        #           WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+        #           DEPENDS geosx_python_tools  # ← Change this!
+        #         )
 
         echo "Running XML formatting directly (bypassing broken make target)..."
         if [ -f "bin/format_xml" ] && [ -f "$GEOS_ROOT/scripts/formatXMLFiles.bash" ]; then
@@ -274,7 +308,16 @@ jobs:
         run: |
           if [[ "${{ needs.test_geos_integration.result }}" == "success" ]]; then
             echo "All integration tests passed successfully!" >> $GITHUB_STEP_SUMMARY
-          else
+          elif [[ "${{ needs.test_geos_integration.result }}" == "failure" ]]; then
             echo "Integration tests failed. Please review the logs." >> $GITHUB_STEP_SUMMARY
             exit 1
-          fi
+          elif [[ "${{ needs.test_geos_integration.result }}" == "cancelled" ]]; then
+            echo "Integration tests were cancelled." >> $GITHUB_STEP_SUMMARY
+            exit 0
+          elif [[ "${{ needs.test_geos_integration.result }}" == "skipped" ]]; then
+            echo "Integration tests were skipped." >> $GITHUB_STEP_SUMMARY
+            exit 0
+          else
+            echo "Integration tests ended with unknown status: ${{ needs.test_geos_integration.result }}" >> $GITHUB_STEP_SUMMARY
+            exit 1
+          fi

.github/workflows/typing-check.yml

@@ -30,7 +30,7 @@ jobs:
       # working-directory: ./${{ matrix.package-name }}
       run: |
         python -m pip install --upgrade pip
-        python -m pip install mypy ruff types-PyYAML types-pytz
+        python -m pip install mypy ruff types-PyYAML types-paramiko types-pytz
 
     - name: Typing check with mypy
       #  working-directory: ./${{ matrix.package-name }}

.gitignore

@@ -37,6 +37,9 @@ MANIFEST
 *.manifest
 *.spec
 
+#env (do not port user-specs)
+.env
+
 # Installer logs
 pip-log.txt
 pip-delete-this-directory.txt
@@ -165,4 +168,4 @@ cython_debug/
 #.idea/
 
 # VSCode
-.vscode
+.vscode

geos-trame/README.rst

@@ -21,7 +21,21 @@ Build and install the Vue components
     cd vue-components
     npm i
     npm run build
-    cd -
+    cd ..
+
+then configure the .env
+
+    sh configure.sh
+
+this will generate a `dotenv` environement file defining useful path to trame,
+
+.. code-block:: console
+
+    cat .env
+        TEMPLATE_DIR=/path/to/geosPythonPackages/geos-trame/src/geos/trame/io/jinja_t
+        ASSETS_DIR=/path/to/geosPythonPackages/geos-trame/src/geos/trame/assets
+
+those will have lower precedence than local environement variables if defined
 
 Install the application
 

geos-trame/configure.sh

@@ -0,0 +1,4 @@
+#!/bin/sh
+
+echo "TEMPLATE_DIR=${PWD}/src/geos/trame/app/io/jinja_t/" >> ${PWD}/src/geos/trame/assets/.env
+echo "ASSETS_DIR=${PWD}/src/geos/trame/assets/" >> ${PWD}/src/geos/trame/assets/.env

geos-trame/pyproject.toml

@@ -31,18 +31,19 @@ keywords = [
 
 dependencies = [
     "setuptools",
-    "typing-extensions==4.12.2",
     "trame==3.6.5",
-    "trame-vuetify==2.7.1",
+    "trame-vuetify==3.1.0",
     "trame-code==1.0.1",
     "trame-server==3.2.3",
-    "trame-client==3.5.0",
+    "trame-client==3.11.2",
     "trame-simput==2.4.3",
-    "trame-vtk>=2.8.14",
+    "trame-vtk==2.10.0",
     "matplotlib==3.9.4",
     "trame-matplotlib==2.0.3",
     "trame-components==2.4.2",
+    "python-dotenv>=1.2.1",
     "mpld3<0.5.11",
+    "paramiko==4.0.0",
     "xsdata[cli]>=25.4",
     "xsdata-pydantic[lxml]==24.5",
     "pyvista==0.45.2",
@@ -51,7 +52,7 @@ dependencies = [
     "funcy==2.0",
     "pytz==2025.2",
     "typing_inspect==0.9.0",
-    "typing_extensions>=4.12",
+    "typing_extensions>=4.15.0",
     "PyYAML",
 ]
 
@@ -73,7 +74,8 @@ test = [
     "pixelmatch==0.3.0",
     "Pillow==11.0.0",
     "pytest-mypy==0.10.3",
-    "pytest-xprocess==1.0.2"
+    "pytest-xprocess==1.0.2",
+    "playwright==1.59.0"
 ]
 
 [project.readme]
@@ -94,7 +96,7 @@ include-package-data = true
 # include = ['geos-trame*']
 
 [tool.setuptools.package-data]
-"*" = ["*.js", "*.css"]
+"*" = ["*.js", "*.css","assets/*","*.jinja","*.json",".env"]
 
 [tool.pytest.ini_options]
 addopts = [

geos-trame/src/geos/trame/app/core.py

@@ -1,7 +1,8 @@
 # SPDX-License-Identifier: Apache-2.0
 # SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
 # SPDX-FileContributor: Lionel Untereiner, Jacques Franc
-
+# ignore context collapsing as it is clearer this way
+# ruff: noqa: SIM117
 from trame.ui.vuetify3 import VAppLayout
 from trame.decorators import TrameApp
 from trame.widgets import html, simput
@@ -24,6 +25,9 @@
 from geos.trame.app.ui.viewer.viewer import DeckViewer
 from geos.trame.app.components.alertHandler import AlertHandler
 
+from geos.trame.app.io.simulation import Simulation
+from geos.trame.app.ui.simulation_view import define_simulation_view
+
 import sys
 
 
@@ -38,10 +42,12 @@ def __init__( self, server: Server, file_name: str ) -> None:
         self.deckEditor: DeckEditor | None = None
         self.timelineEditor: TimelineEditor | None = None
         self.deckInspector: DeckInspector | None = None
+        self.simulationLauncher: Simulation | None = None
         self.server = server
         server.enable_module( module )
 
         self.state.input_file = file_name
+        self.state.user_id = None
 
         # TODO handle hot_reload
 
@@ -67,6 +73,9 @@ def __init__( self, server: Server, file_name: str ) -> None:
         self.region_viewer = RegionViewer()
         self.well_viewer = WellViewer( 5, 5 )
 
+        ######## Simulation runner
+        self.simulation = Simulation( server=server )
+
         # Data loader
         self.data_loader = DataLoader( self.tree, self.region_viewer, self.well_viewer, trame_server=server )
 
@@ -177,24 +186,6 @@ def build_ui( self ) -> None:
                     ):
                         vuetify.VIcon( "mdi-content-save-outline" )
 
-                    with html.Div(
-                            style=
-                            "height: 100%; width: 300px; display: flex; align-items: center; justify-content: space-between;",
-                            v_if=( "tab_idx == 1", ),
-                    ):
-                        vuetify.VBtn(
-                            "Run",
-                            style="z-index: 1;",
-                        )
-                        vuetify.VBtn(
-                            "Kill",
-                            style="z-index: 1;",
-                        )
-                        vuetify.VBtn(
-                            "Clear",
-                            style="z-index: 1;",
-                        )
-
             # input file editor
             with vuetify.VCol( v_show=( "tab_idx == 0", ), classes="flex-grow-1 pa-0 ma-0" ):
                 if self.tree.input_file is not None:
@@ -208,3 +199,16 @@ def build_ui( self ) -> None:
                         "The file " + self.state.input_file + " cannot be parsed.",
                         file=sys.stderr,
                     )
+
+            with vuetify.VCol( v_show=( "tab_idx == 1" ), classes="flex-grow-1 pa-0 ma-0" ):
+                if self.simulation is not None:
+                    define_simulation_view( self.server )
+                else:
+                    self.ctrl.on_add_error(
+                        "Error",
+                        "The execution context " + self.state.exec_context + " is not consistent.",
+                    )
+                    print(
+                        "The execution context " + self.state.exec_context + " is not consistent.",
+                        file=sys.stderr,
+                    )