feat: add logic to check user modification in trame-geos (#96)

* feat: add properties checker

* test: add properties checker test

* feat: use simput to check values

* refactor: type checking and split files

* feat: properties checked using geometry data

* refactor: remove src nesting + mypy checks working

* chore: add geos-trame to type checked packages

* chore: remove black/isort and add ruff

* refactor: ruff checks

* docs: remove duplicate CONTRIBUTING and update README

* feat: load data upon check fields

* refactor: add src folder and split geos_trame into geos/trame

* chore: update path

* Add type hints for YAML

---------

Co-authored-by: Jean Fechter <jean.fechter@kitware.com>

Author: lucas-givord

.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-timehistory", "geos-utils", "geos-xml-tools", "hdf5-wrapper"]
+        package-name: ["geos-geomechanics", "geos-posp", "geos-timehistory", "geos-utils", "geos-trame", "geos-xml-tools", "hdf5-wrapper"]
 
     steps:
     - uses: actions/checkout@v4
@@ -30,7 +30,7 @@ jobs:
       # working-directory: ./${{ matrix.package-name }}
       run: |
         python -m pip install --upgrade pip
-        python -m pip install mypy ruff
+        python -m pip install mypy ruff types-PyYAML
 
     - name: Typing check with mypy
       #  working-directory: ./${{ matrix.package-name }}

geos-trame/.pre-commit-config.yaml

@@ -1,17 +1,23 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 22.3.0
-    hooks:
-      - id: black
-        exclude: ^.*\b(schema_generated)\b.*$
-        entry: black --check --force-exclude
-
   - repo: https://github.com/codespell-project/codespell
     rev: v2.1.0
     hooks:
       - id: codespell
 
-  - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.11.12
+    hooks:
+      - id: ruff
+        args: ["--config", "./.ruff.toml"]
+
+  - repo: https://github.com/google/yapf
+    rev: v0.43.0
+    hooks:
+      - id: yapf
+        args: ["-ir", "--style", "./.style.yapf"]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.16.0
     hooks:
-      - id: flake8
+      - id: mypy
+        additional_dependencies: [types-PyYAML]

geos-trame/CONTRIBUTING.rst

@@ -47,14 +47,23 @@ To be able to run the test suite, make sure to install the additionals dependenc
 
 Then you can run the test with `pytest .`
 
+Optional
+--------
+
+To use pre-commit hooks (ruff, mypy, yapf,...), make sure to install the dev dependencies:
+
+.. code-block:: console
+
+    pip install -e '.[dev]'
+
 Regarding GEOS
 --------------
 
 This application takes an XML file from the GEOS project to load dynamically all of its components.
 To be able to do that, we need first to generate the corresponding python class based on a
 xsd schema provided by GEOS.
 
-`For more details <src/geos_trame/schema_generated/README.md>`_
+`For more details <src/geos/trame/schema_generated/README.md>`_
 
 Features
 --------

geos-trame/README.rst

@@ -47,6 +47,7 @@ dependencies = [
     "funcy==2.0",
     "typing_inspect==0.9.0",
     "typing_extensions>=4.12",
+    "PyYAML",
 ]
 
 [project.optional-dependencies]
@@ -56,14 +57,16 @@ build = [
 dev = [
     "pylint",
     "mypy",
-    "black",
-    "isort"
+    "types-PyYAML",
+    "ruff",
+    "pre-commit"
 ]
 test = [
     "pytest==8.3.3",
     "pytest-seleniumbase==4.31.6",
     "pixelmatch==0.3.0",
     "Pillow==11.0.0",
+    "pytest-mypy==0.10.3",
     "pytest-xprocess==1.0.2"
 ]
 
@@ -72,10 +75,10 @@ file = "README.md"
 content-type = "text/markdown"
 
 [project.scripts]
-geos-trame = "geos_trame.app.__main__:main"
+geos-trame = "geos.trame.app.main:main"
 
 [project.entry-points.jupyter_serverproxy_servers]
-geos-trame = "geos_trame.app.jupyter:jupyter_proxy_info"
+geos-trame = "geos.trame.app.jupyter:jupyter_proxy_info"
 
 [tool.setuptools]
 license-files = ["LICENSE"]
@@ -116,18 +119,3 @@ disable = [
     "R0913", # (too-many-arguments)
     "W0105", # (pointless-string-statement)
 ]
-
-[tool.black]
-line-length = 88
-target-version = ['py310']
-include = '\.pyi?$'
-extend-exclude = '''
-src/geos_trame/schema_generated/*.py
-'''
-
-[tool.isort]
-profile = "black"
-src_paths = ["src", "tests"]
-blackArgs = ["--preview"]
-py_version = 310
-

geos-trame/pyproject.toml

@@ -7,14 +7,14 @@
 
 
 class AlertHandler( vuetify3.VContainer ):
-    """
-    Vuetify component used to display an alert status.
+    """Vuetify component used to display an alert status.
 
     This alert will be displayed in the bottom right corner of the screen.
     It will be displayed until closed by the user or after 10 seconds if it is a success or warning.
     """
 
-    def __init__( self ):
+    def __init__( self ) -> None:
+        """Constructor."""
         super().__init__(
             fluid=True,
             classes="pa-0 ma-0",
@@ -31,31 +31,32 @@ def __init__( self ):
 
         self.generate_alert_ui()
 
-    def generate_alert_ui( self ):
-        """
-        Generate the alert UI.
+    def generate_alert_ui( self ) -> None:
+        """Generate the alert UI.
 
         The alert will be displayed in the bottom right corner of the screen.
 
         Use an abritary z-index value to put the alert on top of the other components.
         """
-        with self:
-            with vuetify3.VCol( style="width: 40%; position: fixed; right: 50px; bottom: 50px; z-index: 100;", ):
-                vuetify3.VAlert(
-                    style="max-height: 20vh; overflow-y: auto",
-                    classes="ma-2",
-                    v_for=( "(status, index) in alerts", ),
-                    key="status",
-                    type=( "status.type", "info" ),
-                    text=( "status.message", "" ),
-                    title=( "status.title", "" ),
-                    closable=True,
-                    click_close=( self.on_close, f"[status.id]" ),
-                )
-
-    def add_alert( self, type: str, title: str, message: str ):
-        """
-        Add a status to the stack with a unique id.
+        with (
+                self,
+                vuetify3.VCol( style="width: 40%; position: fixed; right: 50px; bottom: 50px; z-index: 100;", ),
+        ):
+            vuetify3.VAlert(
+                style="max-height: 20vh; overflow-y: auto",
+                classes="ma-2",
+                v_for=( "(status, index) in alerts", ),
+                key="status",
+                type=( "status.type", "info" ),
+                text=( "status.message", "" ),
+                title=( "status.title", "" ),
+                closable=True,
+                click_close=( self.on_close, "[status.id]" ),
+            )
+
+    def add_alert( self, type: str, title: str, message: str ) -> None:
+        """Add a status to the stack with a unique id.
+
         If there are more than 5 alerts displayed, remove the oldest.
         A warning will be automatically closed after 10 seconds.
         """
@@ -77,21 +78,15 @@ def add_alert( self, type: str, title: str, message: str ):
         if type == "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 ):
-        """
-        Add an alert of type "warning"
-        """
+    async def add_warning( self, title: str, message: str ) -> None:
+        """Add an alert of type 'warning'."""
         self.add_alert( "warning", title, message )
 
-    async def add_error( self, title: str, message: str ):
-        """
-        Add an alert of type "error"
-        """
+    async def add_error( self, title: str, message: str ) -> None:
+        """Add an alert of type 'error'."""
         self.add_alert( "error", title, message )
 
-    def on_close( self, alert_id ):
-        """
-        Remove in the state the alert associated to the given id.
-        """
+    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 ) )
         self.state.flush()

geos-trame/src/geos_trame/__init__.py geos-trame/src/geos/trame/__init__.pygeos-trame/src/geos_trame/__init__.py renamed to geos-trame/src/geos/trame/__init__.py

@@ -0,0 +1,90 @@
+# SPDX-License-Identifier: Apache-2.0
+# SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
+# SPDX-FileContributor: Kitware
+from typing import Any
+
+from trame_client.widgets.core import AbstractElement
+from trame_simput import get_simput_manager
+
+from geos.trame.app.data_types.field_status import FieldStatus
+from geos.trame.app.data_types.renderable import Renderable
+from geos.trame.app.deck.tree import DeckTree
+from geos.trame.app.ui.viewer.regionViewer import RegionViewer
+from geos.trame.app.utils.geos_utils import group_name_ref_array_to_list
+
+# Doc reference: https://geosx-geosx.readthedocs-hosted.com/en/latest/docs/sphinx/datastructure/CompleteXMLSchema.html
+attributes_to_check = [ ( "region_attribute", str ), ( "fields_to_import", list ), ( "surfacicFieldsToImport", list ) ]
+
+
+class PropertiesChecker( AbstractElement ):
+    """Validity checker of properties within a deck tree."""
+
+    def __init__( self, tree: DeckTree, region_viewer: RegionViewer, **kwargs: Any ) -> None:
+        """Constructor."""
+        super().__init__( "div", **kwargs )
+
+        self.tree = tree
+        self.region_viewer = region_viewer
+        self.simput_manager = get_simput_manager( id=self.state.sm_id )
+
+    def check_fields( self ) -> None:
+        """Check all the fields in the deck_tree.
+
+        Get the names of all the cell data arrays from the input of the region viewer, then check that
+        all the attributes in `attributes_to_check` have a value corresponding to one of the array names.
+        """
+        array_names = self._get_array_names()
+        for field in self.state.deck_tree:
+            self._check_field( field, array_names )
+        self.state.dirty( "deck_tree" )
+        self.state.flush()
+
+    def _check_field( self, field: dict, array_names: list[ str ] ) -> None:
+        """Check that all the attributes in `attributes_to_check` have a value corresponding to one of the array names.
+
+        Set the `valid` property to the result of this check, and if necessary, indicate which properties are invalid.
+        """
+        if len( array_names ) == 0 and Renderable.VTKMESH.value in field[ "id" ]:
+            self.ctrl.load_vtkmesh_from_id( field[ "id" ] )
+            array_names = self._get_array_names()
+            field[ "drawn" ] = True
+        field[ "valid" ] = FieldStatus.VALID.value
+        field[ "invalid_properties" ] = []
+
+        proxy = self.simput_manager.proxymanager.get( field[ "id" ] )
+        if proxy is not None:
+            for attr, expected_type in attributes_to_check:
+                if attr in proxy.definition:
+                    if ( expected_type is str and proxy[ attr ]  # value is not empty (valid)
+                         and proxy[ attr ] not in array_names  # value is not in the expected names
+                        ):
+                        field[ "invalid_properties" ].append( attr )
+                    elif expected_type is list:
+                        arrays: list[ str ] | None = group_name_ref_array_to_list( proxy[ attr ] )
+                        if arrays is None:
+                            field[ "invalid_properties" ].append( attr )
+                            continue
+                        for array_name in arrays:
+                            if array_name not in array_names:
+                                field[ "invalid_properties" ].append( attr )
+                                break
+
+        if len( field[ "invalid_properties" ] ) != 0:
+            field[ "valid" ] = FieldStatus.INVALID.value
+        else:
+            field.pop( "invalid_properties", None )
+
+        if field[ "children" ] is not None:
+            # Parents are only valid if all children are valid
+            field[ "invalid_children" ] = []
+            for child in field[ "children" ]:
+                self._check_field( child, array_names )
+                if child[ "valid" ] == FieldStatus.INVALID.value:
+                    field[ "valid" ] = FieldStatus.INVALID.value
+                    field[ "invalid_children" ].append( child[ "title" ] )
+            if len( field[ "invalid_children" ] ) == 0:
+                field.pop( "invalid_children", None )
+
+    def _get_array_names( self ) -> list[ str ]:
+        cellData = self.region_viewer.input.GetCellData()
+        return [ cellData.GetArrayName( i ) for i in range( cellData.GetNumberOfArrays() ) ]