Add new stone format, Plugins, and Custom classes

README.md

@@ -84,7 +84,7 @@ simulation:
   time_step: 0.001
   max_time: 10.0
 
-components:
+nodes:
   - id: reactor1
     IdealGasReactor:
       temperature: 1000      # K

boulder/app.py

@@ -3,7 +3,11 @@
 import dash
 import dash_bootstrap_components as dbc
 
-from . import callbacks
+# Import cantera_converter early to ensure plugins are loaded at app startup
+from . import (
+    callbacks,
+    cantera_converter,  # noqa: F401
+)
 from .config import (
     get_config_from_path_with_comments,
     get_initial_config,
@@ -12,6 +16,11 @@
 from .layout import get_layout
 from .styles import CYTOSCAPE_STYLESHEET
 
+# Create a single, shared converter instance for the app
+# This ensures that the same set of discovered plugins is used everywhere.
+CONVERTER = cantera_converter.CanteraConverter()
+
+
 # Initialize the Dash app with Bootstrap
 app = dash.Dash(
     __name__,

boulder/callbacks/graph_callbacks.py

@@ -77,11 +77,11 @@ def add_reactor(trigger_data: dict, config: dict) -> Any:
             "type": trigger_data["type"],
             "properties": trigger_data["properties"],
         }
-        if any(comp["id"] == new_reactor["id"] for comp in config["components"]):
+        if any(node["id"] == new_reactor["id"] for node in config["nodes"]):
             return dash.no_update
 
-        new_components = [*config.get("components", []), new_reactor]
-        new_config = {**config, "components": new_components}
+        new_nodes = [*config.get("nodes", []), new_reactor]
+        new_config = {**config, "nodes": new_nodes}
         return new_config
 
     # STEP 1: Trigger MFC addition and close modal immediately

boulder/callbacks/modal_callbacks.py

@@ -50,9 +50,9 @@ def update_mfc_options(config: dict) -> tuple[list[dict], list[dict]]:
             "Reservoir",
         ]
         options = [
-            {"label": comp["id"], "value": comp["id"]}
-            for comp in config.get("components", [])
-            if comp.get("type") in valid_types
+            {"label": node["id"], "value": node["id"]}
+            for node in config.get("nodes", [])
+            if node.get("type") in valid_types
         ]
         return options, options
 
@@ -225,7 +225,7 @@ def generate_reactor_id(is_open: bool, config: dict) -> Union[str, Any]:
         if not is_open:
             return dash.no_update
 
-        existing_ids = [comp.get("id", "") for comp in config.get("components", [])]
+        existing_ids = [node.get("id", "") for node in config.get("nodes", [])]
 
         i = 1
         while f"reactor_{i}" in existing_ids:
@@ -273,9 +273,9 @@ def set_default_mfc_values(is_open: bool, config: dict) -> tuple:
             return dash.no_update, dash.no_update, dash.no_update
 
         reactor_ids = [
-            comp.get("id")
-            for comp in config.get("components", [])
-            if comp.get("type")
+            node.get("id")
+            for node in config.get("nodes", [])
+            if node.get("type")
             in ["IdealGasReactor", "ConstVolReactor", "ConstPReactor", "Reservoir"]
         ]
 

boulder/callbacks/properties_callbacks.py

@@ -26,9 +26,9 @@ def show_properties_editable(last_selected, edit_mode, config):
         if last_selected and last_selected.get("type") == "node":
             node_id = last_selected["data"]["id"]
             # Find the latest node data from config
-            for comp in config["components"]:
-                if comp["id"] == node_id:
-                    node_data = [comp]
+            for node in config["nodes"]:
+                if node["id"] == node_id:
+                    node_data = [node]
                     break
         elif last_selected and last_selected.get("type") == "edge":
             edge_id = last_selected["data"]["id"]
@@ -267,11 +267,11 @@ def save_properties(n_clicks, node_data, edge_data, config, values, ids):
         if node_data:
             data = node_data[0]
             comp_id = data["id"]
-            new_components = []
-            for comp in config["components"]:
-                if comp["id"] == comp_id:
+            new_nodes = []
+            for node in config["nodes"]:
+                if node["id"] == comp_id:
                     # Ensure properties dict exists
-                    props = dict(comp.get("properties", {}))
+                    props = dict(node.get("properties", {}))
                     for v, i in zip(values, ids):
                         key = i["prop"]
                         # Convert to float if key is temperature or pressure
@@ -282,10 +282,10 @@ def save_properties(n_clicks, node_data, edge_data, config, values, ids):
                                 props[key] = v
                         else:
                             props[key] = v
-                    new_components.append({**comp, "properties": props})
+                    new_nodes.append({**node, "properties": props})
                 else:
-                    new_components.append(comp)
-            return {**config, "components": new_components}
+                    new_nodes.append(node)
+            return {**config, "nodes": new_nodes}
         elif edge_data:
             data = edge_data[0]
             conn_id = data["id"]

boulder/callbacks/simulation_callbacks.py

@@ -65,6 +65,7 @@ def handle_mechanism_upload(
             Output("simulation-error-display", "style"),
             Output("simulation-results-card", "style"),
             Output("simulation-data", "data"),
+            Output("simulation-running", "data", allow_duplicate=True),
         ],
         [
             Input("run-simulation", "n_clicks"),
@@ -87,8 +88,14 @@ def run_simulation(
         mechanism_select: str,
         custom_mechanism: str,
         uploaded_filename: str,
-    ) -> Tuple[Any, Any, Any, str, Any, Dict[str, str], Dict[str, str], Dict[str, Any]]:
-        from ..cantera_converter import CanteraConverter, DualCanteraConverter
+    ) -> Tuple[
+        Any, Any, Any, str, Any, Dict[str, str], Dict[str, str], Dict[str, Any], bool
+    ]:
+        from ..cantera_converter import (
+            CanteraConverter,
+            DualCanteraConverter,
+            get_plugins,
+        )
         from ..config import USE_DUAL_CONVERTER
         from ..utils import apply_theme_to_figure
 
@@ -102,6 +109,7 @@ def run_simulation(
                 {"display": "none"},
                 {"display": "none"},
                 {},
+                False,
             )
 
         # Determine the mechanism to use
@@ -123,13 +131,16 @@ def run_simulation(
 
         try:
             if USE_DUAL_CONVERTER:
-                dual_converter = DualCanteraConverter(mechanism=mechanism)
+                dual_converter = DualCanteraConverter(
+                    mechanism=mechanism, plugins=get_plugins()
+                )
                 network, results, code_str = dual_converter.build_network_and_code(
                     config
                 )
             else:
-                single_converter = CanteraConverter(mechanism=mechanism)
-                network, results = single_converter.build_network(config)
+                # Build using a fresh converter with discovered plugins
+                converter = CanteraConverter(mechanism=mechanism, plugins=get_plugins())
+                network, results = converter.build_network(config)
                 code_str = ""
 
             # Build initial plots from the first available reactor (no strict need)
@@ -187,11 +198,14 @@ def run_simulation(
                 {"display": "none"},
                 {"display": "block"},
                 simulation_data,
+                False,
             )
 
         except Exception as e:
             message = f"Error during simulation: {str(e)}"
             print(f"ERROR: {message}")
+            # IMPORTANT: update simulation-data with a non-empty payload so the
+            # overlay-clearing callback (listening to simulation-data) fires.
             return (
                 go.Figure(),
                 go.Figure(),
@@ -200,8 +214,15 @@ def run_simulation(
                 message,
                 {"display": "block", "color": "red"},
                 {"display": "none"},
-                {},
+                {"error": message},
+                False,
             )
+        finally:
+            # Safety net: if any future refactor throws before returns,
+            # the overlay will still be cleared by downstream callback since we
+            # always return a value in both success and error paths above.
+            # No-op here intentionally.
+            ...
 
     # Overlay style now handled client-side for zero-lag responsiveness