ivoryos 1.2.5__py3-none-any.whl → 1.4.4__py3-none-any.whl

ivoryos/utils/script_runner.py

@@ -1,22 +1,42 @@
 import ast
+import asyncio
 import os
-import csv
 import threading
 import time
 from datetime import datetime
+from typing import List, Dict, Any
+
+import pandas as pd
 
 from ivoryos.utils import utils, bo_campaign
-from ivoryos.utils.db_models import Script, WorkflowRun, WorkflowStep, db, SingleStep
+from ivoryos.utils.db_models import Script, WorkflowRun, WorkflowStep, db, WorkflowPhase
 from ivoryos.utils.global_config import GlobalConfig
+from ivoryos.utils.decorators import BUILDING_BLOCKS
+from ivoryos.utils.nest_script import validate_and_nest_control_flow
 
 global_config = GlobalConfig()
 global deck
 deck = None
 # global deck, registered_workflows
 # deck, registered_workflows = None, None
+class HumanInterventionRequired(Exception):
+    pass
+
+def pause(reason="Human intervention required"):
+    handlers = global_config.notification_handlers
+    if handlers:
+        for handler in handlers:
+            try:
+                handler(reason)
+            except Exception as e:
+                print(f"[notify] handler {handler} failed: {e}")
+    # raise error to pause workflow in gui
+    raise HumanInterventionRequired(reason)
 
 class ScriptRunner:
     def __init__(self, globals_dict=None):
+        self.logger = None
+        self.socketio = None
         self.retry = False
         if globals_dict is None:
             globals_dict = globals()
@@ -59,13 +79,23 @@ class ScriptRunner:
         """Force stop everything, including ongoing tasks."""
         self.stop_current_event.set()
         self.abort_pending()
+        if not self.pause_event.is_set():
+            self.pause_event.set()
+        if self.lock.locked():
+            self.lock.release()
 
 
-    def run_script(self, script, repeat_count=1, run_name=None, logger=None, socketio=None, config=None, bo_args=None,
-                   output_path="", compiled=False, current_app=None, history=None, optimizer=None):
+    def run_script(self, script, repeat_count=1, run_name=None, logger=None, socketio=None, config=None,
+                   output_path="", compiled=False, current_app=None, history=None, optimizer=None, batch_mode=None,
+                   batch_size=1, objectives=None, parameters=None, constraints=None, steps=None, optimizer_cls=None):
+
+
+        self.socketio = socketio
+        self.logger = logger
         global deck
         if deck is None:
             deck = global_config.deck
+
         # print("history", history)
         if self.current_app is None:
             self.current_app = current_app
@@ -73,21 +103,23 @@ class ScriptRunner:
 
         # Try to acquire lock without blocking
         if not self.lock.acquire(blocking=False):
-            if logger:
-                logger.info("System is busy. Please wait for it to finish or stop it before starting a new one.")
+            if self.logger:
+                self.logger.info("System is busy. Please wait for it to finish or stop it before starting a new one.")
             return None
 
         self.reset_stop_event()
 
         thread = threading.Thread(
             target=self._run_with_stop_check,
-            args=(script, repeat_count, run_name, logger, socketio, config, bo_args, output_path, current_app, compiled,
-                  history, optimizer)
+            args=(script, repeat_count, run_name, config, output_path, current_app, compiled,
+                  history, optimizer, batch_mode, batch_size, objectives, parameters, constraints, steps, optimizer_cls),
         )
         thread.start()
         return thread
 
-    def exec_steps(self, script, section_name, logger, socketio, run_id, i_progress, **kwargs):
+
+
+    async def exec_steps(self, script, section_name, phase_id, kwargs_list=None, batch_size=1):
         """
         Executes a function defined in a string line by line
         :param func_str: The function as a string
@@ -95,6 +127,8 @@ class ScriptRunner:
         :return: The final result of the function execution
         """
         _func_str = script.python_script or script.compile()
+        _, return_list = script.config_return()
+
         step_list: list = script.convert_to_lines(_func_str).get(section_name, [])
         global deck
         # global deck, registered_workflows
@@ -110,262 +144,302 @@ class ScriptRunner:
         # Parse function body from string
         temp_connections = global_config.defined_variables
         # Prepare execution environment
-        exec_globals = {"deck": deck, "time":time}  # Add required global objects
+        exec_globals = {"deck": deck, "time":time, "pause": pause}  # Add required global objects
         # exec_globals = {"deck": deck, "time": time, "registered_workflows":registered_workflows}  # Add required global objects
         exec_globals.update(temp_connections)
+
         exec_locals = {}  # Local execution scope
 
         # Define function arguments manually in exec_locals
-        exec_locals.update(kwargs)
+        # exec_locals.update(kwargs)
         index = 0
+        if kwargs_list:
+            results = kwargs_list.copy()
+        else:
+            results = [{} for _ in range(batch_size)]
+        nest_script = validate_and_nest_control_flow(script.script_dict.get(section_name, []))
 
-        # Execute each line dynamically
-        while index < len(step_list):
-            if self.stop_current_event.is_set():
-                logger.info(f'Stopping execution during {section_name}')
-                step = WorkflowStep(
-                    workflow_id=run_id,
-                    phase=section_name,
-                    repeat_index=i_progress,
-                    step_index=index,
-                    method_name="stop",
-                    start_time=datetime.now(),
-                    end_time=datetime.now(),
-                    run_error=False,
-                )
-                db.session.add(step)
-                break
-            line = step_list[index]
-            method_name = line.strip().split("(")[0] if "(" in line else line.strip()
-            start_time = datetime.now()
-            step = WorkflowStep(
-                workflow_id=run_id,
-                phase=section_name,
-                repeat_index=i_progress,
-                step_index=index,
-                method_name=method_name,
-                start_time=start_time,
-            )
-            db.session.add(step)
-            db.session.commit()
-            logger.info(f"Executing: {line}")
-            socketio.emit('execution', {'section': f"{section_name}-{index}"})
-            # self._emit_progress(socketio, 100)
-            # if line.startswith("registered_workflows"):
-            #     line = line.replace("registered_workflows.", "")
-            try:
-                if line.startswith("time.sleep("): # add safe sleep for time.sleep lines
-                    duration_str = line[len("time.sleep("):-1]
-                    duration = float(duration_str)
-                    self.safe_sleep(duration)
-                else:
-                    exec(line, exec_globals, exec_locals)
-                step.run_error = False
-            except Exception as e:
-                logger.error(f"Error during script execution: {e}")
-                socketio.emit('error', {'message': str(e)})
-
-                step.run_error = True
-                self.toggle_pause()
-            step.end_time = datetime.now()
-            # db.session.add(step)
-            db.session.commit()
+        await self._execute_steps_batched(nest_script, results, phase_id=phase_id, section_name=section_name)
 
-            self.pause_event.wait()
+        return results  # Return the 'results' variable
 
-            # todo update script during the run
-            # _func_str = script.compile()
-            # step_list: list = script.convert_to_lines(_func_str).get(section_name, [])
-            if not step.run_error:
-                index += 1
-            elif not self.retry:
-                index += 1
-        return exec_locals  # Return the 'results' variable
-
-    def _run_with_stop_check(self, script: Script, repeat_count: int, run_name: str, logger, socketio, config, bo_args,
-                             output_path, current_app, compiled, history=None, optimizer=None):
+    def _run_with_stop_check(self, script: Script, repeat_count: int, run_name: str, config,
+                             output_path, current_app, compiled, history=None, optimizer=None, batch_mode=None,
+                             batch_size=None, objectives=None, parameters=None, constraints=None, steps=None, optimizer_cls=None):
         time.sleep(1)
         # _func_str = script.compile()
         # step_list_dict: dict = script.convert_to_lines(_func_str)
-        self._emit_progress(socketio, 1)
+        self._emit_progress(1)
         filename = None
         error_flag = False
         # create a new run entry in the database
-        try:
-            with current_app.app_context():
-                run = WorkflowRun(name=script.name or "untitled", platform=script.deck or "deck",start_time=datetime.now())
-                db.session.add(run)
-                db.session.commit()
-                run_id = run.id  # Save the ID
-                global_config.runner_status = {"id":run_id, "type": "workflow"}
+        repeat_mode = "batch" if config else "optimizer" if optimizer else "repeat"
+        if optimizer_cls is not None:
+            # try:
+            if self.logger:
+                self.logger.info(f"Initializing optimizer {optimizer_cls.__name__}")
+            optimizer = optimizer_cls(experiment_name=run_name, parameter_space=parameters, objective_config=objectives,
+                                  parameter_constraints=constraints,
+                                  optimizer_config=steps, datapath=output_path)
+            current_app.config["LAST_OPTIMIZER"] = optimizer
+            # except Exception as e:
+            #     if self.logger:
+            #         self.logger.error(f"Error during optimizer initialization: {e.__str__()}")
+
+        with current_app.app_context():
+            run = WorkflowRun(name=script.name or "untitled", platform=script.deck or "deck", start_time=datetime.now(),
+                              repeat_mode=repeat_mode
+                              )
+            db.session.add(run)
+            db.session.flush()
+            run_id = run.id  # Save the ID
+            db.session.commit()
 
+            try:
+            # if True:
+                global_config.runner_status = {"id":run_id, "type": "workflow"}
                 # Run "prep" section once
-                self._run_actions(script, section_name="prep", logger=logger, socketio=socketio, run_id=run_id)
+                asyncio.run(self._run_actions(script, section_name="prep", run_id=run_id))
                 output_list = []
                 _, arg_type = script.config("script")
                 _, return_list = script.config_return()
                 # Run "script" section multiple times
                 if repeat_count:
-                    self._run_repeat_section(repeat_count, arg_type, bo_args, output_list, script,
-                                             run_name, return_list, compiled, logger, socketio,
-                                             history, output_path, run_id=run_id, optimizer=optimizer)
+                    asyncio.run(
+                        self._run_repeat_section(repeat_count, arg_type, output_list, script,
+                                             run_name, return_list, compiled,
+                                             history, output_path, run_id=run_id, optimizer=optimizer,
+                                             batch_mode=batch_mode, batch_size=batch_size, objectives=objectives)
+                    )
                 elif config:
-                    self._run_config_section(config, arg_type, output_list, script, run_name, logger,
-                                             socketio, run_id=run_id, compiled=compiled)
+                    asyncio.run(
+                        self._run_config_section(
+                            config, arg_type, output_list, script, run_name,
+                            run_id=run_id, compiled=compiled, batch_mode=batch_mode, batch_size=batch_size
+                        )
+                    )
+
                 # Run "cleanup" section once
-                self._run_actions(script, section_name="cleanup", logger=logger, socketio=socketio,run_id=run_id)
+                asyncio.run(self._run_actions(script, section_name="cleanup", run_id=run_id))
                 # Reset the running flag when done
-
                 # Save results if necessary
+                if not script.python_script and return_list:
+                    # print(output_list)
 
-                if not script.python_script and output_list:
-                    filename = self._save_results(run_name, arg_type, return_list, output_list, logger, output_path)
-                self._emit_progress(socketio, 100)
+                    filename = self._save_results(run_name, arg_type, return_list, output_list, output_path)
 
-        except Exception as e:
-            logger.error(f"Error during script execution: {e.__str__()}")
-            error_flag = True
-        finally:
-            self.lock.release()
-            with current_app.app_context():
-                run = db.session.get(WorkflowRun, run_id)
+
+            except Exception as e:
+                if self.logger:
+                    self.logger.error(f"Error during script execution: {e.__str__()}")
+                error_flag = True
+            finally:
+                self._emit_progress(100)
+                if self.lock.locked():
+                    self.lock.release()
+
+
+        with current_app.app_context():
+            run = db.session.get(WorkflowRun, run_id)
+            if run is None:
+                if self.logger:
+                    self.logger.info("Error: Run not found in database.")
+            else:
                 run.end_time = datetime.now()
-                run.output_file = filename
+                run.data_path = filename
                 run.run_error = error_flag
                 db.session.commit()
 
 
-    def _run_actions(self, script, section_name="", logger=None, socketio=None, run_id=None):
+    async def _run_actions(self, script, section_name="", run_id=None):
         _func_str = script.python_script or script.compile()
         step_list: list = script.convert_to_lines(_func_str).get(section_name, [])
-        logger.info(f'Executing {section_name} steps') if step_list else logger.info(f'No {section_name} steps')
+        if not step_list:
+            if self.logger:
+                self.logger.info(f'No {section_name} steps')
+            return None
+        if self.logger:
+            self.logger.info(f'Executing {section_name} steps')
         if self.stop_pending_event.is_set():
-            logger.info(f"Stopping execution during {section_name} section.")
-            return
-        if step_list:
-            self.exec_steps(script, section_name, logger, socketio, run_id=run_id, i_progress=0)
+            if self.logger:
+                self.logger.info(f"Stopping execution during {section_name} section.")
+            return None
 
-    def _run_config_section(self, config, arg_type, output_list, script, run_name, logger, socketio, run_id, compiled=True):
+        phase = WorkflowPhase(
+            run_id=run_id,
+            name=section_name,
+            repeat_index=0,
+            start_time=datetime.now()
+        )
+        db.session.add(phase)
+        db.session.flush()
+        phase_id = phase.id
+
+        step_outputs = await self.exec_steps(script, section_name, phase_id=phase_id)
+        # Save phase-level output
+        phase.outputs = step_outputs
+        phase.end_time = datetime.now()
+        db.session.commit()
+        return step_outputs
+
+    async def _run_config_section(self, config, arg_type, output_list, script, run_name, run_id,
+                                  compiled=True, batch_mode=False, batch_size=1):
         if not compiled:
             for i in config:
                 try:
                     i = utils.convert_config_type(i, arg_type)
                     compiled = True
                 except Exception as e:
-                    logger.info(e)
+                    if self.logger:
+                        self.logger.error(e)
                     compiled = False
                     break
         if compiled:
-            for i, kwargs in enumerate(config):
-                kwargs = dict(kwargs)
+            batch_size = int(batch_size)
+            nested_list = [config[i:i + batch_size] for i in range(0, len(config), batch_size)]
+
+            for i, kwargs_list in enumerate(nested_list):
+                # kwargs = dict(kwargs)
                 if self.stop_pending_event.is_set():
-                    logger.info(f'Stopping execution during {run_name}: {i + 1}/{len(config)}')
+                    if self.logger:
+                        self.logger.info(f'Stopping execution during {run_name}: {i + 1}/{len(config)}')
                     break
-                logger.info(f'Executing {i + 1} of {len(config)} with kwargs = {kwargs}')
-                progress = ((i + 1) * 100 / len(config)) - 0.1
-                self._emit_progress(socketio, progress)
-                # fname = f"{run_name}_script"
-                # function = self.globals_dict[fname]
-                output = self.exec_steps(script, "script", logger, socketio, run_id, i, **kwargs)
+                if self.logger:
+                    self.logger.info(f'Executing {i + 1} of {len(nested_list)} with kwargs = {kwargs_list}')
+                progress = ((i + 1) * 100 / len(nested_list)) - 0.1
+                self._emit_progress(progress)
+
+                phase = WorkflowPhase(
+                    run_id=run_id,
+                    name="main",
+                    repeat_index=i,
+                    parameters=kwargs_list,
+                    start_time=datetime.now()
+                )
+                db.session.add(phase)
+                db.session.flush()
+
+                phase_id = phase.id
+                output = await self.exec_steps(script, "script", phase_id, kwargs_list=kwargs_list, )
+                # print(output)
                 if output:
                     # kwargs.update(output)
-                    output_list.append(output)
-
-    def _run_repeat_section(self, repeat_count, arg_types, bo_args, output_list, script, run_name, return_list, compiled,
-                            logger, socketio, history, output_path, run_id, optimizer=None):
-        if bo_args:
-            logger.info('Initializing optimizer...')
-            if compiled:
-                ax_client = bo_campaign.ax_init_opc(bo_args)
-            else:
-                if history:
-                    import pandas as pd
-                    file_path = os.path.join(output_path, history)
-                    previous_runs = pd.read_csv(file_path).to_dict(orient='records')
-                    ax_client = bo_campaign.ax_init_form(bo_args, arg_types, len(previous_runs))
-                    for row in previous_runs:
-                        parameter = {key: value for key, value in row.items() if key in arg_types.keys()}
-                        raw_data = {key: value for key, value in row.items() if key in return_list}
-                        _, trial_index = ax_client.attach_trial(parameter)
-                        ax_client.complete_trial(trial_index=trial_index, raw_data=raw_data)
-                        output_list.append(row)
-                else:
-                    ax_client = bo_campaign.ax_init_form(bo_args, arg_types)
-        elif optimizer and history:
-            import pandas as pd
+                    for output_dict in output:
+                        output_list.append(output_dict)
+                    phase.outputs = output
+                phase.end_time = datetime.now()
+                db.session.commit()
+        return output_list
+
+    async def _run_repeat_section(self, repeat_count, arg_types, output_list, script, run_name, return_list, compiled,
+                            history, output_path, run_id, optimizer=None, batch_mode=None,
+                            batch_size=None, objectives=None):
+
+        if optimizer and history:
             file_path = os.path.join(output_path, history)
 
             previous_runs = pd.read_csv(file_path)
+
+            expected_cols = list(arg_types.keys()) + list(return_list)
+
+            actual_cols = previous_runs.columns.tolist()
+
+            # NOT okay if it misses columns
+            if set(expected_cols) - set(actual_cols):
+                if self.logger:
+                    self.logger.warning(f"Missing columns from history .csv file. Expecting {expected_cols} but got {actual_cols}")
+                raise ValueError("Missing columns from history .csv file.")
+
+            # okay if there is extra columns
+            if set(actual_cols) - set(expected_cols):
+                if self.logger:
+                    self.logger.warning(f"Extra columns from history .csv file. Expecting {expected_cols} but got {actual_cols}")
+
             optimizer.append_existing_data(previous_runs)
-            for row in previous_runs:
+
+            for row in previous_runs.to_dict(orient='records'):
                 output_list.append(row)
 
 
 
         for i_progress in range(int(repeat_count)):
             if self.stop_pending_event.is_set():
-                logger.info(f'Stopping execution during {run_name}: {i_progress + 1}/{int(repeat_count)}')
+                if self.logger:
+                    self.logger.info(f'Stopping execution during {run_name}: {i_progress + 1}/{int(repeat_count)}')
                 break
-            logger.info(f'Executing {run_name} experiment: {i_progress + 1}/{int(repeat_count)}')
+
+            phase = WorkflowPhase(
+                run_id=run_id,
+                name="main",
+                repeat_index=i_progress,
+                start_time=datetime.now()
+            )
+            db.session.add(phase)
+            db.session.flush()
+            phase_id = phase.id
+            if self.logger:
+                self.logger.info(f'Executing {run_name} experiment: {i_progress + 1}/{int(repeat_count)}')
             progress = (i_progress + 1) * 100 / int(repeat_count) - 0.1
-            self._emit_progress(socketio, progress)
-            if bo_args:
-                try:
-                    parameters, trial_index = ax_client.get_next_trial()
-                    logger.info(f'Output value: {parameters}')
-                    # fname = f"{run_name}_script"
-                    # function = self.globals_dict[fname]
-                    output = self.exec_steps(script, "script", logger, socketio, run_id, i_progress, **parameters)
-
-                    _output = {key: value for key, value in output.items() if key in return_list}
-                    ax_client.complete_trial(trial_index=trial_index, raw_data=_output)
-                    output.update(parameters)
-                except Exception as e:
-                    logger.info(f'Optimization error: {e}')
-                    break
-            elif optimizer:
+            self._emit_progress(progress)
+
+            # Optimizer for UI
+            if optimizer:
                 try:
-                    parameters = optimizer.suggest(1)
-                    logger.info(f'Output value: {parameters}')
-                    output = self.exec_steps(script, "script", logger, socketio, run_id, i_progress, **parameters)
+                    parameters = optimizer.suggest(n=batch_size)
+                    if self.logger:
+                        self.logger.info(f'Parameters: {parameters}')
+                    phase.parameters = parameters
+
+                    output = await self.exec_steps(script, "script",  phase_id, kwargs_list=parameters)
                     if output:
                         optimizer.observe(output)
-                        output.update(parameters)
+                        
+                    else:
+                        if self.logger:
+                            self.logger.info('No output from script')
+
+
                 except Exception as e:
-                    logger.info(f'Optimization error: {e}')
+                    if self.logger:
+                        self.logger.info(f'Optimization error: {e}')
                     break
             else:
-                # fname = f"{run_name}_script"
-                # function = self.globals_dict[fname]
-                output = self.exec_steps(script, "script", logger, socketio, run_id, i_progress)
+
+                output = await self.exec_steps(script, "script", phase_id, batch_size=batch_size)
 
             if output:
-                output_list.append(output)
-                logger.info(f'Output value: {output}')
+                # print("output: ", output)
+                output_list.extend(output)
+                if self.logger:
+                    self.logger.info(f'Output value: {output}')
+                phase.outputs = output
+
+            phase.end_time = datetime.now()
+            db.session.commit()
+
+            if optimizer and self._check_early_stop(output, objectives):
+                if self.logger:
+                    self.logger.info('Early stopping')
+                break
+                
 
-        if bo_args:
-            ax_client.save_to_json_file(os.path.join(output_path, f"{run_name}_ax_client.json"))
-        logger.info(
-            f'Optimization complete. Results saved to {os.path.join(output_path, f"{run_name}_ax_client.json")}'
-        )
         return output_list
 
-    @staticmethod
-    def _save_results(run_name, arg_type, return_list, output_list, logger, output_path):
-        args = list(arg_type.keys()) if arg_type else []
-        args.extend(return_list)
+    def _save_results(self, run_name, arg_type, return_list, output_list, output_path):
+        output_columns = list(arg_type.keys()) + list(return_list)
+
         filename = run_name + "_" + datetime.now().strftime("%Y-%m-%d %H-%M") + ".csv"
         file_path = os.path.join(output_path, filename)
-        with open(file_path, "w", newline='') as file:
-            writer = csv.DictWriter(file, fieldnames=args)
-            writer.writeheader()
-            writer.writerows(output_list)
-        logger.info(f'Results saved to {file_path}')
+        df = pd.DataFrame(output_list)
+        df = df.loc[:, [c for c in output_columns if c in df.columns]]
+
+        df. to_csv(file_path, index=False)
+        if self.logger:
+            self.logger.info(f'Results saved to {file_path}')
         return filename
 
-    @staticmethod
-    def _emit_progress(socketio, progress):
-        socketio.emit('progress', {'progress': progress})
+    def _emit_progress(self, progress):
+        self.socketio.emit('progress', {'progress': progress})
 
     def safe_sleep(self, duration: float):
         interval = 1  # check every 1 second
@@ -383,4 +457,314 @@ class ScriptRunner:
                 "paused": self.paused,
                 "stop_pending": self.stop_pending_event.is_set(),
                 "stop_current": self.stop_current_event.is_set(),
-            }
+            }
+
+
+    async def _execute_steps_batched(self, steps: List[Dict], contexts: List[Dict[str, Any]], phase_id, section_name):
+        """
+        Execute a list of steps for multiple samples, batching where appropriate.
+        """
+        for step in steps:
+            action = step["action"]
+            instrument = step["instrument"]
+            action_id = step["id"]
+            if action == "if":
+                await self._execute_if_batched(step, contexts, phase_id=phase_id, step_index=action_id,
+                                               section_name=section_name)
+            elif action == "repeat":
+                await self._execute_repeat_batched(step, contexts, phase_id=phase_id, step_index=action_id,
+                                                   section_name=section_name)
+            elif action == "while":
+                await self._execute_while_batched(step, contexts, phase_id=phase_id, step_index=action_id,
+                                                  section_name=section_name)
+            elif instrument == "variable":
+                await self._execute_variable_batched(step, contexts, phase_id=phase_id, step_index=action_id,
+                                                     section_name=section_name)
+                # print("Variable executed", "current context", contexts)
+            else:
+                # Regular action - check if batch
+                if step.get("batch_action", False):
+                    # Execute once for all samples
+                    await self._execute_action_once(step, contexts[0], phase_id=phase_id, step_index=action_id,
+                                                        section_name=section_name)
+
+                else:
+                    # Execute for each sample
+                    for context in contexts:
+                        await self._execute_action(step, context, phase_id=phase_id, step_index=action_id,
+                                                   section_name=section_name)
+                        self.pause_event.wait()
+
+
+
+    async def _execute_if_batched(self, step: Dict, contexts: List[Dict[str, Any]], phase_id, step_index, section_name):
+        """Execute if/else block for multiple samples."""
+        # Evaluate condition for each sample
+        for context in contexts:
+            condition = self._evaluate_condition(step["args"]["statement"], context)
+
+            if condition:
+                await self._execute_steps_batched(step["if_block"], [context], phase_id=phase_id, section_name=section_name)
+            else:
+                await self._execute_steps_batched(step["else_block"], [context], phase_id=phase_id, section_name=section_name)
+
+
+    async def _execute_repeat_batched(self, step: Dict, contexts: List[Dict[str, Any]], phase_id, step_index, section_name):
+        """Execute repeat block for multiple samples."""
+        times = step["args"].get("statement", 1)
+
+        for i in range(times):
+            # Add repeat index to all contexts
+            # for context in contexts:
+            #     context["repeat_index"] = i
+
+            await self._execute_steps_batched(step["repeat_block"], contexts, phase_id=phase_id, section_name=section_name)
+
+
+    async def _execute_while_batched(self, step: Dict, contexts: List[Dict[str, Any]], phase_id, step_index, section_name):
+        """Execute while block for multiple samples."""
+        max_iterations = step["args"].get("max_iterations", 1000)
+        active_contexts = contexts.copy()
+        iteration = 0
+
+        while iteration < max_iterations and active_contexts:
+            # Filter contexts that still meet the condition
+            still_active = []
+
+            for context in active_contexts:
+                condition = self._evaluate_condition(step["args"]["statement"], context)
+
+                if condition:
+                    context["while_index"] = iteration
+                    still_active.append(context)
+
+            if not still_active:
+                break
+
+            # Execute for contexts that are still active
+            await self._execute_steps_batched(step["while_block"], still_active, phase_id=phase_id, section_name=section_name)
+            active_contexts = still_active
+            iteration += 1
+
+        if iteration >= max_iterations:
+            raise RuntimeError(f"While loop exceeded max iterations ({max_iterations})")
+
+    async def _execute_action(self, step: Dict, context: Dict[str, Any], phase_id=1, step_index=1, section_name=None):
+        """Execute a single action with parameter substitution."""
+        # Substitute parameters in args
+        if self.stop_current_event.is_set():
+            return context
+        substituted_args = self._substitute_params(step["args"], context)
+
+        # Get the component and method
+        instrument = step.get("instrument", "")
+        action = step["action"]
+        if instrument and "." in instrument:
+            instrument_type, instrument = instrument.split(".")
+        else:
+            instrument_type = ""
+        # Execute the action
+        step_db = WorkflowStep(
+            phase_id=phase_id,
+            step_index=step_index,
+            method_name=action,
+            start_time=datetime.now(),
+        )
+        db.session.add(step_db)
+        db.session.flush()
+        try:
+
+            # print(f"step {section_name}-{step_index}")
+            self.socketio.emit('execution', {'section': f"{section_name}-{step_index-1}"})
+            if action == "wait":
+                duration = float(substituted_args["statement"])
+                self.safe_sleep(duration)
+
+            elif action == "pause":
+                msg = substituted_args.get("statement", "")
+                pause(msg)
+
+            elif instrument_type == "deck" and hasattr(deck, instrument):
+                component = getattr(deck, instrument)
+                if hasattr(component, action):
+                    method = getattr(component, action)
+
+                    # Execute and handle return value
+                    if step.get("coroutine", False):
+                        result = await method(**substituted_args)
+                    else:
+                        result = method(**substituted_args)
+
+                    # Store return value if specified
+                    return_var = step.get("return", "")
+                    if return_var:
+                        context[return_var] = result
+
+            elif instrument_type == "blocks" and instrument in BUILDING_BLOCKS.keys():
+                # Inject all block categories
+                method_collection = BUILDING_BLOCKS[instrument]
+                if action in method_collection.keys():
+                    method = method_collection[action]["func"]
+
+                    # Execute and handle return value
+                    # print(step.get("coroutine", False))
+                    if step.get("coroutine", False):
+                        result = await method(**substituted_args)
+                    else:
+                        result = method(**substituted_args)
+
+                    # Store return value if specified
+                    return_var = step.get("return", "")
+                    if return_var:
+                        context[return_var] = result
+        except HumanInterventionRequired as e:
+            self.logger.warning(f"Human intervention required: {e}")
+            self.socketio.emit('human_intervention', {'message': str(e)})
+            # Instead of auto-resume, explicitly stay paused until user action
+            # step.run_error = False
+            self.toggle_pause()
+
+        except Exception as e:
+            self.logger.error(f"Error during script execution: {e}")
+            self.socketio.emit('error', {'message': str(e)})
+
+            step_db.run_error = True
+            self.toggle_pause()
+        finally:
+            step_db.end_time = datetime.now()
+            step_db.output = context
+            db.session.commit()
+
+            self.pause_event.wait()
+
+        return context
+
+    async def _execute_action_once(self, step: Dict, context: Dict[str, Any], phase_id, step_index, section_name):
+        """Execute a batch action once (not per sample)."""
+        # print(f"Executing batch action: {step['action']}")
+        return await self._execute_action(step, context, phase_id=phase_id, step_index=step_index, section_name=section_name)
+
+    @staticmethod
+    def _substitute_params(args: Dict[str, Any], context: Dict[str, Any]) -> Dict[str, Any]:
+        """Substitute parameter placeholders like #param_1 with actual values."""
+        substituted = {}
+
+        for key, value in args.items():
+            if isinstance(value, str) and value.startswith("#"):
+                param_name = value[1:]  # Remove '#'
+                substituted[key] = context.get(param_name)
+            else:
+                substituted[key] = value
+
+        return substituted
+
+    @staticmethod
+    def _evaluate_condition(condition_str: str, context: Dict[str, Any]) -> bool:
+        """
+        Safely evaluate a condition string with context variables.
+        """
+        # Create evaluation context with all variables
+        eval_context = {}
+
+        # Substitute variables in the condition string
+        substituted = condition_str
+        for key, value in context.items():
+            # Replace #variable with actual variable name for eval
+            substituted = substituted.replace(f"#{key}", key)
+            # Add variable to eval context
+            eval_context[key] = value
+
+        try:
+            # Safe evaluation with variables in scope
+            result = eval(substituted, {"__builtins__": {}}, eval_context)
+            return bool(result)
+        except Exception as e:
+            raise ValueError(f"Error evaluating condition '{condition_str}': {e}")
+
+    def _check_early_stop(self, output, objectives):
+        for row in output:
+            all_met = True
+            for obj in objectives:
+                name = obj['name']
+                minimize = obj.get('minimize', True)
+                threshold = obj.get('early_stop', None)
+
+                if threshold is None:
+                    all_met = False
+                    break# Skip if no early stop defined
+
+                value = row[name]
+                if minimize and value > threshold:
+                    all_met = False
+                    break
+                elif not minimize and value < threshold:
+                    all_met = False
+                    break
+
+            if all_met:
+                return True  # At least one row meets all early stop thresholds
+
+        return False  # No row met all thresholds
+
+    async def _execute_variable_batched(self, step: Dict, contexts: List[Dict[str, Any]], phase_id, step_index,
+                                        section_name):
+        """Execute variable assignment for multiple samples."""
+        var_name = step["action"]  # "vial" in your example
+        var_value = step["args"]["statement"]
+        arg_type = step["arg_types"]["statement"]
+
+        for context in contexts:
+            # Substitute any variable references in the value
+            if isinstance(var_value, str):
+                substituted_value = var_value
+
+                # Replace all variable references (with or without #) with their values
+                for key, val in context.items():
+                    # Handle both #variable and variable (without #)
+                    substituted_value = substituted_value.replace(f"#{key}", str(val))
+                    # For expressions like "vial+10", replace variable name directly
+                    # Use word boundaries to avoid partial matches
+                    import re
+                    substituted_value = re.sub(r'\b' + re.escape(key) + r'\b', str(val), substituted_value)
+
+                # Handle based on type
+                if arg_type == "float":
+                    try:
+                        # Evaluate as expression (e.g., "10.0+10" becomes 20.0)
+                        result = eval(substituted_value, {"__builtins__": {}}, {})
+                        context[var_name] = float(result)
+                    except:
+                        # If eval fails, try direct conversion
+                        context[var_name] = float(substituted_value)
+
+                elif arg_type == "int":
+                    try:
+                        result = eval(substituted_value, {"__builtins__": {}}, {})
+                        context[var_name] = int(result)
+                    except:
+                        context[var_name] = int(substituted_value)
+
+                elif arg_type == "bool":
+                    try:
+                        # Evaluate boolean expressions
+                        result = eval(substituted_value, {"__builtins__": {}}, {})
+                        context[var_name] = bool(result)
+                    except:
+                        context[var_name] = substituted_value.lower() in ['true', '1', 'yes']
+
+                else:  # "str"
+                    # For strings, check if it looks like an expression
+                    if any(char in substituted_value for char in ['+', '-', '*', '/', '>', '<', '=', '(', ')']):
+                        try:
+                            # Try to evaluate as expression
+                            result = eval(substituted_value, {"__builtins__": {}}, context)
+                            context[var_name] = result
+                        except:
+                            # If eval fails, store as string
+                            context[var_name] = substituted_value
+                    else:
+                        context[var_name] = substituted_value
+            else:
+                # Direct numeric or boolean value
+                context[var_name] = var_value
+