Fix threads in offline deployment

src/common/common.py

@@ -32,29 +32,6 @@
 OS_PLATFORM = sys.platform
 
 
-def get_max_threads() -> int:
-    """
-    Get max threads for current deployment mode.
-
-    In local mode, checks for UI override in session state.
-    In online mode, uses the configured value directly.
-
-    Returns:
-        int: Maximum number of threads to use for parallel processing.
-    """
-    settings = st.session_state.get("settings", {})
-    max_threads_config = settings.get("max_threads", {"local": 4, "online": 2})
-
-    if settings.get("online_deployment", False):
-        return max_threads_config.get("online", 2)
-    else:
-        # Local mode: check for UI override, fallback to config default
-        return st.session_state.get(
-            "max_threads_override",
-            max_threads_config.get("local", 4)
-        )
-
-
 def is_safe_workspace_name(name: str) -> bool:
     """
     Check if a workspace name is safe (no path traversal characters).

src/workflow/CommandExecutor.py

@@ -9,6 +9,7 @@
 import sys
 import importlib.util
 import json
+import streamlit as st
 
 class CommandExecutor:
     """
@@ -25,6 +26,28 @@ def __init__(self, workflow_dir: Path, logger: Logger, parameter_manager: Parame
         self.logger = logger
         self.parameter_manager = parameter_manager
 
+    def _get_max_threads(self) -> int:
+        """
+        Get max threads for current deployment mode.
+
+        In local mode, reads from parameter manager (persisted params.json).
+        In online mode, uses the configured value directly from settings.
+
+        Returns:
+            int: Maximum number of threads to use for parallel processing (minimum 1).
+        """
+        settings = st.session_state.get("settings", {})
+        max_threads_config = settings.get("max_threads", {"local": 4, "online": 2})
+
+        if settings.get("online_deployment", False):
+            value = max_threads_config.get("online", 2)
+        else:
+            default = max_threads_config.get("local", 4)
+            params = self.parameter_manager.get_parameters_from_json()
+            value = params.get("max_threads", default)
+
+        return max(1, int(value))
+
     def run_multiple_commands(
         self, commands: list[str]
     ) -> bool:
@@ -43,10 +66,8 @@ def run_multiple_commands(
         Returns:
             bool: True if all commands succeeded, False if any failed.
         """
-        from src.common.common import get_max_threads
-
         # Get thread settings and calculate distribution
-        max_threads = get_max_threads()
+        max_threads = self._get_max_threads()
         num_commands = len(commands)
         parallel_commands = min(num_commands, max_threads)
 
@@ -234,8 +255,7 @@ def run_topp(self, tool: str, input_output: dict, custom_params: dict = {}) -> b
             n_processes = max(io_lengths)
 
         # Calculate threads per command based on max_threads setting
-        from src.common.common import get_max_threads
-        max_threads = get_max_threads()
+        max_threads = self._get_max_threads()
         parallel_commands = min(n_processes, max_threads)
         threads_per_command = max(1, max_threads // parallel_commands)
 

src/workflow/StreamlitUI.py

@@ -1112,11 +1112,12 @@ def parameter_section(self, custom_parameter_function) -> None:
         if not st.session_state.settings.get("online_deployment", False):
             max_threads_config = st.session_state.settings.get("max_threads", {})
             default_threads = max_threads_config.get("local", 4)
-            st.number_input(
-                "Threads",
+            self.input_widget(
+                key="max_threads",
+                default=default_threads,
+                name="Threads",
+                widget_type="number",
                 min_value=1,
-                value=default_threads,
-                key="max_threads_override",
                 help="Maximum threads for parallel processing. Threads are distributed between parallel commands and per-tool thread allocation."
             )