ivoryos 1.0.0__py3-none-any.whl → 1.0.3__py3-none-any.whl

ivoryos/utils/script_runner.py

@@ -5,8 +5,8 @@ import threading
 import time
 from datetime import datetime
 
-from ivoryos.utils import utils
-from ivoryos.utils.db_models import Script, WorkflowRun, WorkflowStep, db
+from ivoryos.utils import utils, bo_campaign
+from ivoryos.utils.db_models import Script, WorkflowRun, WorkflowStep, db, SingleStep
 from ivoryos.utils.global_config import GlobalConfig
 
 global_config = GlobalConfig()
@@ -26,8 +26,9 @@ class ScriptRunner:
         self.stop_pending_event = threading.Event()
         self.stop_current_event = threading.Event()
         self.is_running = False
-        self.lock = threading.Lock()
+        self.lock = global_config.runner_lock
         self.paused = False
+        self.current_app = None
 
     def toggle_pause(self):
         """Toggles between pausing and resuming the script"""
@@ -59,23 +60,29 @@ class ScriptRunner:
         self.stop_current_event.set()
         self.abort_pending()
 
+
     def run_script(self, script, repeat_count=1, run_name=None, logger=None, socketio=None, config=None, bo_args=None,
-                   output_path="", current_app=None):
- # Get run.id
+                   output_path="", compiled=False, current_app=None):
         global deck
         if deck is None:
             deck = global_config.deck
-        time.sleep(1)
-        with self.lock:
-            if self.is_running:
+
+        if self.current_app is None:
+            self.current_app = current_app
+        # time.sleep(1)  # Optional: may help ensure deck readiness
+
+        # 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.")
-                return None
-            self.is_running = True
+            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))
+        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)
+        )
         thread.start()
         return thread
 
@@ -86,7 +93,7 @@ class ScriptRunner:
         :param kwargs: Arguments to pass to the function
         :return: The final result of the function execution
         """
-        _func_str = script.compile()
+        _func_str = script.python_script or script.compile()
         step_list: list = script.convert_to_lines(_func_str).get(section_name, [])
         global deck
         # global deck, registered_workflows
@@ -138,6 +145,8 @@ class ScriptRunner:
                 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)
@@ -158,7 +167,7 @@ class ScriptRunner:
                 step.run_error = True
                 self.toggle_pause()
             step.end_time = datetime.now()
-            db.session.add(step)
+            # db.session.add(step)
             db.session.commit()
 
             self.pause_event.wait()
@@ -173,7 +182,7 @@ class ScriptRunner:
         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):
+                             output_path, current_app, compiled):
         time.sleep(1)
         # _func_str = script.compile()
         # step_list_dict: dict = script.convert_to_lines(_func_str)
@@ -183,11 +192,12 @@ class ScriptRunner:
         script_dict = script.script_dict
         with current_app.app_context():
 
-            run = WorkflowRun(name=script.name or "untitled", platform=script.deck,start_time=datetime.now())
+            run = WorkflowRun(name=script.name or "untitled", platform=script.deck or "deck",start_time=datetime.now())
             db.session.add(run)
-            db.session.flush()
-
-            self._run_actions(script, section_name="prep", logger=logger, socketio=socketio, run_id=run.id)
+            db.session.commit()
+            run_id = run.id  # Save the ID
+            global_config.runner_status = {"id":run_id, "type": "workflow"}
+            self._run_actions(script, section_name="prep", logger=logger, socketio=socketio, run_id=run_id)
             output_list = []
             _, arg_type = script.config("script")
             _, return_list = script.config_return()
@@ -195,43 +205,46 @@ class ScriptRunner:
             # 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, logger, socketio, run_id=run.id)
+                                         run_name, return_list, compiled, logger, socketio, run_id=run_id)
             elif config:
                 self._run_config_section(config, arg_type, output_list, script, run_name, logger,
-                                         socketio, run_id=run.id)
+                                         socketio, run_id=run_id, compiled=compiled)
 
             # Run "cleanup" section once
-            self._run_actions(script, section_name="cleanup", logger=logger, socketio=socketio,run_id=run.id)
+            self._run_actions(script, section_name="cleanup", logger=logger, socketio=socketio,run_id=run_id)
             # Reset the running flag when done
-            with self.lock:
-                self.is_running = False
+            self.lock.release()
             # Save results if necessary
             filename = None
-            if 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)
+        with current_app.app_context():
+            run = db.session.get(WorkflowRun, run_id)  # SQLAlchemy 1.4+ recommended method
             run.end_time = datetime.now()
             run.data_path = filename
             db.session.commit()
 
     def _run_actions(self, script, section_name="", logger=None, socketio=None, run_id=None):
-        _func_str = script.compile()
+        _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 self.stop_pending_event.is_set():
             logger.info(f"Stopping execution during {section_name} section.")
             return
-        self.exec_steps(script, section_name, logger, socketio, run_id=run_id, i_progress=0)
+        if step_list:
+            self.exec_steps(script, section_name, logger, socketio, run_id=run_id, i_progress=0)
 
-    def _run_config_section(self, config, arg_type, output_list, script, run_name, logger, socketio, run_id):
-        compiled = True
-        for i in config:
-            try:
-                i = utils.convert_config_type(i, arg_type)
-            except Exception as e:
-                logger.info(e)
-                compiled = False
-                break
+    def _run_config_section(self, config, arg_type, output_list, script, run_name, logger, socketio, run_id, compiled=True):
+        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)
+                    compiled = False
+                    break
         if compiled:
             for i, kwargs in enumerate(config):
                 kwargs = dict(kwargs)
@@ -248,11 +261,14 @@ class ScriptRunner:
                     # 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,
+    def _run_repeat_section(self, repeat_count, arg_types, bo_args, output_list, script, run_name, return_list, compiled,
                             logger, socketio, run_id):
         if bo_args:
             logger.info('Initializing optimizer...')
-            ax_client = utils.ax_initiation(bo_args, arg_types)
+            if compiled:
+                ax_client = bo_campaign.ax_init_opc(bo_args)
+            else:
+                ax_client = bo_campaign.ax_init_form(bo_args, arg_types)
         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)}')
@@ -311,9 +327,9 @@ class ScriptRunner:
 
     def get_status(self):
         """Returns current status of the script runner."""
-        with self.lock:
+        with self.current_app.app_context():
             return {
-                "is_running": self.is_running,
+                "is_running": self.lock.locked(),
                 "paused": self.paused,
                 "stop_pending": self.stop_pending_event.is_set(),
                 "stop_current": self.stop_current_event.is_set(),

ivoryos/utils/task_runner.py

@@ -0,0 +1,81 @@
+import threading
+import time
+from datetime import datetime
+
+from ivoryos.utils.db_models import db, SingleStep
+from ivoryos.utils.global_config import GlobalConfig
+
+global_config = GlobalConfig()
+global deck
+deck = None
+
+
+class TaskRunner:
+    def __init__(self, globals_dict=None):
+        self.retry = False
+        if globals_dict is None:
+            globals_dict = globals()
+        self.globals_dict = globals_dict
+        self.lock = global_config.runner_lock
+
+
+    def run_single_step(self, component, method, kwargs, wait=True, current_app=None):
+        global deck
+        if deck is None:
+            deck = global_config.deck
+
+        # Try to acquire lock without blocking
+        if not self.lock.acquire(blocking=False):
+            current_status = global_config.runner_status
+            current_status["status"] = "busy"
+            return current_status
+
+
+        if wait:
+            output = self._run_single_step(component, method, kwargs, current_app)
+        else:
+            print("running with thread")
+            thread = threading.Thread(
+                target=self._run_single_step, args=(component, method, kwargs, current_app)
+            )
+            thread.start()
+            time.sleep(0.1)
+            output = {"status": "task started", "task_id": global_config.runner_status.get("id")}
+
+        return output
+
+    def _get_executable(self, component, deck, method):
+        if component.startswith("deck."):
+            component = component.split(".")[1]
+            instrument = getattr(deck, component)
+        else:
+            temp_connections = global_config.defined_variables
+            instrument = temp_connections.get(component)
+        function_executable = getattr(instrument, method)
+        return function_executable
+
+    def _run_single_step(self, component, method, kwargs, current_app=None):
+        try:
+            function_executable = self._get_executable(component, deck, method)
+            method_name = f"{function_executable.__self__.__class__.__name__}.{function_executable.__name__}"
+        except Exception as e:
+            self.lock.release()
+            return {"status": "error", "msg": e.__str__()}
+
+        # with self.lock:
+        with current_app.app_context():
+            step = SingleStep(method_name=method_name, kwargs=kwargs, run_error=False, start_time=datetime.now())
+            db.session.add(step)
+            db.session.commit()
+            global_config.runner_status = {"id":step.id, "type": "task"}
+            try:
+                output = function_executable(**kwargs)
+                step.output = output
+                step.end_time = datetime.now()
+            except Exception as e:
+                step.run_error = e.__str__()
+                step.end_time = datetime.now()
+            finally:
+                db.session.commit()
+                self.lock.release()
+            return output

ivoryos/utils/utils.py

@@ -240,74 +240,6 @@ def start_logger(socketio: SocketIO, logger_name: str, log_filename: str = None)
     return logger
 
 
-def ax_wrapper(data: dict, arg_types: list):
-    """
-    Ax platform wrapper function for creating optimization campaign parameters and objective from the web form input
-    :param data: e.g.,
-    {
-        "param_1_type": "range", "param_1_value": [1,2],
-        "param_2_type": "range", "param_2_value": [1,2],
-        "obj_1_min": True,
-        "obj_2_min": True
-    }
-    :return: the optimization campaign parameters
-    parameter=[
-        {"name": "param_1", "type": "range", "bounds": [1,2]},
-        {"name": "param_1", "type": "range", "bounds": [1,2]}
-    ]
-    objectives=[
-        {"name": "obj_1", "min": True, "threshold": None},
-        {"name": "obj_2", "min": True, "threshold": None},
-    ]
-    """
-    from ax.service.utils.instantiation import ObjectiveProperties
-    parameter = []
-    objectives = {}
-    # Iterate through the webui_data dictionary
-    for key, value in data.items():
-        # Check if the key corresponds to a parameter type
-        if "_type" in key:
-            param_name = key.split("_type")[0]
-            param_type = value
-            param_value = data[f"{param_name}_value"].split(",")
-            try:
-                values = [float(v) for v in param_value]
-            except Exception:
-                values = param_value
-            if param_type == "range":
-                param = {"name": param_name, "type": param_type, "bounds": values}
-            if param_type == "choice":
-                param = {"name": param_name, "type": param_type, "values": values}
-            if param_type == "fixed":
-                param = {"name": param_name, "type": param_type, "value": values[0]}
-            _type = arg_types[param_name] if arg_types[param_name] in ["str", "bool", "int"] else "float"
-            param.update({"value_type": _type})
-            parameter.append(param)
-        elif key.endswith("_min"):
-            if not value == 'none':
-                obj_name = key.split("_min")[0]
-                is_min = True if value == "minimize" else False
-
-                threshold = None if f"{obj_name}_threshold" not in data else data[f"{obj_name}_threshold"]
-                properties = ObjectiveProperties(minimize=is_min)
-                objectives[obj_name] = properties
-
-    return parameter, objectives
-
-
-def ax_initiation(data, arg_types):
-    """
-    create Ax campaign from the web form input
-    :param data:
-    """
-    install_and_import("ax", "ax-platform")
-    parameter, objectives = ax_wrapper(data, arg_types)
-    from ax.service.ax_client import AxClient
-    ax_client = AxClient()
-    ax_client.create_experiment(parameter, objectives=objectives)
-    return ax_client
-
-
 def get_arg_type(args, parameters):
     """get argument type from signature"""
     arg_types = {}

ivoryos/version.py

@@ -1 +1 @@
-__version__ = "1.0.0"
+__version__ = "1.0.3"

{ivoryos-1.0.0.dist-info → ivoryos-1.0.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ivoryos
-Version: 1.0.0
+Version: 1.0.3
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Home-page: https://gitlab.com/heingroup/ivoryos
 Author: Ivory Zhang
@@ -22,8 +22,8 @@ Requires-Dist: python-dotenv
 [![PyPI version](https://img.shields.io/pypi/v/ivoryos)](https://pypi.org/project/ivoryos/)
 ![License](https://img.shields.io/pypi/l/ivoryos)
 [![YouTube](https://img.shields.io/badge/YouTube-video-red?logo=youtube)](https://youtu.be/dFfJv9I2-1g)
-[![Published](https://img.shields.io/badge/Nature_Communications-paper-blue)](https://www.nature.com/articles/s41467-025-60514-w)
-
+[![Published](https://img.shields.io/badge/Nature_Comm.-paper-blue)](https://www.nature.com/articles/s41467-025-60514-w)
+[![Discord](https://img.shields.io/discord/1313641159356059770?label=Discord&logo=discord&color=5865F2)](https://discord.gg/AX5P9EdGVX)
 
 ![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/ivoryos.png)
 # ivoryOS: interoperable Web UI for self-driving laboratories (SDLs)

{ivoryos-1.0.0.dist-info → ivoryos-1.0.3.dist-info}/RECORD

@@ -1,26 +1,26 @@
 ivoryos/__init__.py,sha256=1v6LwuIao8WbmSskifzdfde7E_gH3PWCYaNpLaRtYZk,7341
 ivoryos/config.py,sha256=3FPBYTIBhQTKDvsEoR8ZeTmg65D-CSFEdGmOuIL4pSI,1311
-ivoryos/version.py,sha256=J-j-u0itpEFT6irdmWmixQqYMadNl1X91TxUmoiLHMI,22
+ivoryos/version.py,sha256=2plzdEEb24FLjE2I2XyBBcJEPYWHccNL4SgtLC_6erg,22
 ivoryos/routes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ivoryos/routes/auth/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ivoryos/routes/auth/auth.py,sha256=7CdXjGAr1B_xsmwweakTWOoROgsOJf0MNTzlMP_5Nus,3240
+ivoryos/routes/auth/auth.py,sha256=rvqMf4oeYXIjcsNWPbHoxK4QJRbM4YSMCl3IDRMnYtM,3255
 ivoryos/routes/auth/templates/auth/login.html,sha256=WSRrKbdM_oobqSXFRTo-j9UlOgp6sYzS9tm7TqqPULI,1207
 ivoryos/routes/auth/templates/auth/signup.html,sha256=b5LTXtpfTSkSS7X8u1ldwQbbgEFTk6UNMAediA5BwBY,1465
 ivoryos/routes/control/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ivoryos/routes/control/control.py,sha256=bxNYR-VAFA7tSswDt5k130AnIx1f64_R9N2B9kMridI,14160
+ivoryos/routes/control/control.py,sha256=AaXqXqaIIed9xBVQsk52CNnNDTSofje5qQAfDGWd1Q0,16404
 ivoryos/routes/control/templates/control/controllers.html,sha256=iIp0h6WA68gQj9OsoiB7dU1BqH8CGomTueR73F4C8eY,4274
-ivoryos/routes/control/templates/control/controllers_home.html,sha256=VQ77HRvBlyBrQ3al5fcKF5Y6_vKtU8WeAhilqQQltAo,2997
+ivoryos/routes/control/templates/control/controllers_home.html,sha256=qAM4iZBEuXvSgGUWWVVIe2E9MPJOeG7U214hYM84jIE,2976
 ivoryos/routes/control/templates/control/controllers_new.html,sha256=uOQo9kYmwX2jk3KZDkMUF_ylfNUIs_oIWb_kk_MMVDM,4921
 ivoryos/routes/database/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ivoryos/routes/database/database.py,sha256=uchoLXRx8ShJZIu20NZya6FJ4LMg2b9yvn6hjEq3dlU,7687
-ivoryos/routes/database/templates/database/experiment_database.html,sha256=edlCcKfrS91gGG1dPFQjC9xD7F7nWNNqS3S6Oa7apzs,3460
-ivoryos/routes/database/templates/database/experiment_step_view.html,sha256=u8_XYhiZ98PzglMzFEkuM1Tk9hVWf79xXIrpHVDxKa0,3618
+ivoryos/routes/database/database.py,sha256=kP5dEb5TvX3GlePk2sxlpwer8AsTM36kdeCkzAiFkR8,9837
+ivoryos/routes/database/templates/database/scripts_database.html,sha256=tEpKOj1UGz7mcDq11guwP48XJxwawjxjPvxRhKiIG2I,3640
 ivoryos/routes/database/templates/database/step_card.html,sha256=F4JRfacrEQfk2rrEbcI_i7G84nzKKDmCrMSmStLb4W4,290
-ivoryos/routes/database/templates/database/workflow_run_database.html,sha256=MczK9my9u0SyQsMFLbc6CXeZqKaBo5vk1SpwjkcZdqk,3571
+ivoryos/routes/database/templates/database/workflow_database.html,sha256=fsJHrYeEHGBKRn1pIxWITE6e93tdZsXH3zRs9Ob5FX0,4467
+ivoryos/routes/database/templates/database/workflow_view.html,sha256=u8_XYhiZ98PzglMzFEkuM1Tk9hVWf79xXIrpHVDxKa0,3618
 ivoryos/routes/design/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ivoryos/routes/design/design.py,sha256=ViVCys-yPv_W4B2JrLT9A4jf8_2N_QDHgbEVUwGFre4,25334
+ivoryos/routes/design/design.py,sha256=Ju9Hz0khhAk6HmnZd3Er3PglFkvZBNPAJ-fPJMfrrIM,29328
 ivoryos/routes/design/templates/design/experiment_builder.html,sha256=rEdcHj5onJG_4MejdFBPnJVzsvCMp1KDteqNkpx24kQ,29430
-ivoryos/routes/design/templates/design/experiment_run.html,sha256=Q7cYYTgvZ8SBzqkDEhAwR634-LLcYq4Gof4bpH_adt0,30397
+ivoryos/routes/design/templates/design/experiment_run.html,sha256=7VP0Vo98phcYnFennd5vqaMK1M1QBwDmM-b9aZb8jOw,26282
 ivoryos/routes/main/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ivoryos/routes/main/main.py,sha256=yuVJzXAob1kc1dfflkTBIZQ0tdf6kChfuq-uQlN1e9Q,957
 ivoryos/routes/main/templates/main/help.html,sha256=IOktMEsOPk0SCiMBXZ4mpffClERAyX8W82fel71M3M0,9370
@@ -31,20 +31,22 @@ ivoryos/static/style.css,sha256=zQVx35A5g6JMJ-K84-6fSKtzXGjp_p5ZVG6KLHPM2IE,4021
 ivoryos/static/gui_annotation/Slide1.png,sha256=Lm4gdOkUF5HIUFaB94tl6koQVkzpitKj43GXV_XYMMc,121727
 ivoryos/static/gui_annotation/Slide2.PNG,sha256=z3wQ9oVgg4JTWVLQGKK_KhtepRHUYP1e05XUWGT2A0I,118761
 ivoryos/static/js/overlay.js,sha256=dPxop19es0E0ZUSY3d_4exIk7CJuQEnlW5uTt5fZfzI,483
-ivoryos/static/js/socket_handler.js,sha256=YGwWlT8TqNBvvIzs2G9g1g7nM2-vUPZjCwmQt4Yv0Uw,5078
+ivoryos/static/js/socket_handler.js,sha256=2Iyv_3METjhSlSavs_L9FE3PKY4xDEpfzJpd2FywY9o,5300
 ivoryos/static/js/sortable_card.js,sha256=ifmlGe3yy0U_KzMphV4ClRhK2DLOvkELYMlq1vECuac,807
 ivoryos/static/js/sortable_design.js,sha256=wwpKfIzZGDxfX3moNz0cvPvm9YyHmopZK3wmkUdnBiw,4333
 ivoryos/templates/base.html,sha256=sDdwqOIUP2Get-py4E59PkieoGWLFpX6wAJe93s4aRo,8518
 ivoryos/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ivoryos/utils/client_proxy.py,sha256=AzcSQGMqeCqVULP1a7vEKNe135NZYryVX63ke0wgK04,2099
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 ivoryos/utils/form.py,sha256=b3JKxRc1jN45-bXyfzSJT1lcssUuxT86FhRmNUDv5-U,20973
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 ivoryos/utils/llm_agent.py,sha256=-lVCkjPlpLues9sNTmaT7bT4sdhWvV2DiojNwzB2Lcw,6422
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