ivoryos 0.1.21__py3-none-any.whl → 0.1.23__py3-none-any.whl

ivoryos/utils/form.py

@@ -1,6 +1,8 @@
+from enum import Enum
+
 from wtforms.fields.choices import SelectField
 from wtforms.fields.core import Field
-from wtforms.validators import InputRequired
+from wtforms.validators import InputRequired, ValidationError
 from wtforms.widgets.core import TextInput
 
 from flask_wtf import FlaskForm
@@ -187,6 +189,30 @@ class VariableOrBoolField(BooleanField):
         return "y"
 
 
+class FlexibleEnumField(StringField):
+    def __init__(self, label=None, validators=None, choices=None, script=None, **kwargs):
+        super().__init__(label, validators, **kwargs)
+        self.script = script
+        self.enum_class = choices
+        self.choices = [e.name for e in self.enum_class]
+        # self.value_list = [e.name for e in self.enum_class]
+
+
+    def process_formdata(self, valuelist):
+        if valuelist:
+            key = valuelist[0]
+            if key in self.choices:
+                # Convert the string key to Enum instance
+                self.data = self.enum_class[key].value
+            elif self.data.startswith("#"):
+                if not self.script.editing_type == "script":
+                    raise ValueError(self.gettext("Variable is not supported in prep/cleanup"))
+                self.data = self.data
+            else:
+                raise ValidationError(
+                    f"Invalid choice: '{key}'. Must match one of {list(self.enum_class.__members__.keys())}")
+
+
 def format_name(name):
     """Converts 'example_name' to 'Example Name'."""
     name = name.split(".")[-1]
@@ -218,20 +244,39 @@ def create_form_for_method(method, autofill, script=None, design=True):
         if param.name == 'self':
             continue
         formatted_param_name = format_name(param.name)
+
+        default_value = None
+        if autofill:
+            default_value = f'#{param.name}'
+        else:
+            if param.default is not param.empty:
+                if isinstance(param.default, Enum):
+                    default_value = param.default.name
+                else:
+                    default_value = param.default
+
         field_kwargs = {
             "label": formatted_param_name,
-            "default": f'#{param.name}' if autofill else (param.default if param.default is not param.empty else None),
+            "default": default_value,
             "validators": [InputRequired()] if param.default is param.empty else None,
             **({"script": script} if (autofill or design) else {})
         }
-        field_class, placeholder_text = annotation_mapping.get(
-            param.annotation,
-            (VariableOrStringField if design else StringField, f'Enter {param.annotation} value')
-        )
+        if isinstance(param.annotation, type) and issubclass(param.annotation, Enum):
+            # enum_class = [(e.name, e.value) for e in param.annotation]
+            field_class = FlexibleEnumField
+            placeholder_text = f"Choose or type a value for {param.annotation.__name__} (start with # for custom)"
+            extra_kwargs = {"choices": param.annotation}
+        else:
+            field_class, placeholder_text = annotation_mapping.get(
+                param.annotation,
+                (VariableOrStringField if design else StringField, f'Enter {param.annotation} value')
+            )
+            extra_kwargs = {}
+
         render_kwargs = {"placeholder": placeholder_text}
 
         # Create the field with additional rendering kwargs for placeholder text
-        field = field_class(**field_kwargs, render_kw=render_kwargs)
+        field = field_class(**field_kwargs, render_kw=render_kwargs, **extra_kwargs)
         setattr(DynamicForm, param.name, field)
 
     # setattr(DynamicForm, f'add', fname)

ivoryos/utils/llm_agent.py

@@ -162,7 +162,7 @@ can you also help find the default value you can't find the info from my request
 
 if __name__ == "__main__":
     from pprint import pprint
-    from example.sdl_example.abstract_sdl import deck
+    from example.abstract_sdl_example.abstract_sdl import deck
 
     from utils import parse_functions
 

ivoryos/utils/script_runner.py

@@ -6,15 +6,18 @@ import time
 from datetime import datetime
 
 from ivoryos.utils import utils
-from ivoryos.utils.db_models import Script
+from ivoryos.utils.db_models import Script, WorkflowRun, WorkflowStep, db
 from ivoryos.utils.global_config import GlobalConfig
 
 global_config = GlobalConfig()
 global deck
 deck = None
+# global deck, registered_workflows
+# deck, registered_workflows = None, None
 
 class ScriptRunner:
     def __init__(self, globals_dict=None):
+        self.retry = False
         if globals_dict is None:
             globals_dict = globals()
         self.globals_dict = globals_dict
@@ -57,7 +60,8 @@ class ScriptRunner:
         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=""):
+                   output_path="", current_app=None):
+ # Get run.id
         global deck
         if deck is None:
             deck = global_config.deck
@@ -71,14 +75,13 @@ class ScriptRunner:
         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))
+                                  args=(script, repeat_count, run_name, logger, socketio, config, bo_args, output_path, current_app))
         thread.start()
         return thread
 
-    def exex_steps(self, script, section_name, logger, socketio, **kwargs):
+    def exec_steps(self, script, section_name, logger, socketio, run_id, i_progress, **kwargs):
         """
-        Executes a function defined in a string line by line.
-
+        Executes a function defined in a string line by line
         :param func_str: The function as a string
         :param kwargs: Arguments to pass to the function
         :return: The final result of the function execution
@@ -86,8 +89,15 @@ class ScriptRunner:
         _func_str = script.compile()
         step_list: list = script.convert_to_lines(_func_str).get(section_name, [])
         global deck
+        # global deck, registered_workflows
         if deck is None:
             deck = global_config.deck
+        # if registered_workflows is None:
+        #     registered_workflows = global_config.registered_workflows
+
+        # for i, line in enumerate(step_list):
+        #     if line.startswith("registered_workflows"):
+        #
         # func_str = script.compile()
         # Parse function body from string
         temp_connections = global_config.defined_variables
@@ -105,27 +115,65 @@ class ScriptRunner:
         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]
-            logger.info(f"Executing: {line}")  # Debugging output
+            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,
+            )
+            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:
-                exec(line, exec_globals, exec_locals)
+                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': e.__str__()})
+                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()
+
             self.pause_event.wait()
 
             # todo update script during the run
             # _func_str = script.compile()
             # step_list: list = script.convert_to_lines(_func_str).get(section_name, [])
-            index += 1
+            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):
+                             output_path, current_app):
         time.sleep(1)
         # _func_str = script.compile()
         # step_list_dict: dict = script.convert_to_lines(_func_str)
@@ -133,39 +181,49 @@ class ScriptRunner:
 
         # Run "prep" section once
         script_dict = script.script_dict
-        self._run_actions(script, section_name="prep", logger=logger, socketio=socketio)
-        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, logger, socketio)
-        elif config:
-            self._run_config_section(config, arg_type, output_list, script, run_name, logger,
-                                     socketio)
-
-        # Run "cleanup" section once
-        self._run_actions(script, section_name="cleanup", logger=logger, socketio=socketio)
-        # Reset the running flag when done
-        with self.lock:
-            self.is_running = False
-        # Save results if necessary
-        if output_list:
-            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 = WorkflowRun(name=script.name or "untitled", platform=script.deck,start_time=datetime.now())
+            db.session.add(run)
+            db.session.flush()
 
-    def _run_actions(self, script, section_name="", logger=None, socketio=None):
+            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()
+
+            # 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)
+            elif config:
+                self._run_config_section(config, arg_type, output_list, script, run_name, logger,
+                                         socketio, run_id=run.id)
+
+            # Run "cleanup" section once
+            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
+            # Save results if necessary
+            filename = None
+            if output_list:
+                filename = self._save_results(run_name, arg_type, return_list, output_list, logger, output_path)
+            self._emit_progress(socketio, 100)
+            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()
         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.exex_steps(script, section_name, logger, socketio)
+        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):
+    def _run_config_section(self, config, arg_type, output_list, script, run_name, logger, socketio, run_id):
         compiled = True
         for i in config:
             try:
@@ -185,22 +243,22 @@ class ScriptRunner:
                 self._emit_progress(socketio, progress)
                 # fname = f"{run_name}_script"
                 # function = self.globals_dict[fname]
-                output = self.exex_steps(script, "script", logger, socketio, **kwargs)
+                output = self.exec_steps(script, "script", logger, socketio, run_id, i, **kwargs)
                 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,
-                            logger, socketio):
+                            logger, socketio, run_id):
         if bo_args:
             logger.info('Initializing optimizer...')
             ax_client = utils.ax_initiation(bo_args, arg_types)
-        for i in range(int(repeat_count)):
+        for i_progress in range(int(repeat_count)):
             if self.stop_pending_event.is_set():
-                logger.info(f'Stopping execution during {run_name}: {i + 1}/{int(repeat_count)}')
+                logger.info(f'Stopping execution during {run_name}: {i_progress + 1}/{int(repeat_count)}')
                 break
-            logger.info(f'Executing {run_name} experiment: {i + 1}/{int(repeat_count)}')
-            progress = (i + 1) * 100 / int(repeat_count) - 0.1
+            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:
@@ -208,7 +266,7 @@ class ScriptRunner:
                     logger.info(f'Output value: {parameters}')
                     # fname = f"{run_name}_script"
                     # function = self.globals_dict[fname]
-                    output = self.exex_steps(script, "script", logger, socketio, **parameters)
+                    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)
@@ -219,7 +277,7 @@ class ScriptRunner:
             else:
                 # fname = f"{run_name}_script"
                 # function = self.globals_dict[fname]
-                output = self.exex_steps(script, "script", logger, socketio)
+                output = self.exec_steps(script, "script", logger, socketio, run_id, i_progress)
 
             if output:
                 output_list.append(output)
@@ -237,7 +295,16 @@ class ScriptRunner:
             writer.writeheader()
             writer.writerows(output_list)
         logger.info(f'Results saved to {file_path}')
+        return filename
 
     @staticmethod
     def _emit_progress(socketio, progress):
         socketio.emit('progress', {'progress': progress})
+
+    def safe_sleep(self, duration: float):
+        interval = 1  # check every 1 second
+        end_time = time.time() + duration
+        while time.time() < end_time:
+            if self.stop_current_event.is_set():
+                return  # Exit early if stop is requested
+            time.sleep(min(interval, end_time - time.time()))

ivoryos/utils/utils.py

@@ -407,3 +407,26 @@ def check_config_duplicate(config):
     """
     hashable_data = [tuple(sorted(d.items())) for d in config]
     return any(count > 1 for count in Counter(hashable_data).values())
+
+
+def get_method_from_workflow(function_string, func_name="workflow"):
+    """Creates a function from a string and assigns it a new name."""
+
+    namespace = {}
+    exec(function_string, globals(), namespace)  # Execute the string in a safe namespace
+    # func_name = next(iter(namespace))
+    # Get the function name dynamically
+    return namespace[func_name]
+
+
+# def load_workflows(script):
+#
+#     class RegisteredWorkflows:
+#         pass
+#     deck_name = script.deck
+#     workflows = Script.query.filter(Script.deck == deck_name, Script.name != script.name, Script.registered==True).all()
+#     for workflow in workflows:
+#         compiled_strs = workflow.compile().get('script', "")
+#         method = get_method_from_workflow(compiled_strs, func_name=workflow.name)
+#         setattr(RegisteredWorkflows, workflow.name, staticmethod(method))
+#     global_config.registered_workflows = RegisteredWorkflows()

ivoryos/version.py

@@ -1 +1 @@
-__version__ = "0.1.21"
+__version__ = "0.1.23"

{ivoryos-0.1.21.dist-info → ivoryos-0.1.23.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ivoryos
-Version: 0.1.21
+Version: 0.1.23
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Home-page: https://gitlab.com/heingroup/ivoryos
 Author: Ivory Zhang
@@ -36,7 +36,7 @@ Requires-Dist: python-dotenv
 - [Instructions for use](#instructions-for-use)
 - [Demo](#demo)
 - [Roadmap](#roadmap)
-- [License](#license)
+
 
 ## Description
 Granting SDLs flexibility and modularity makes it almost impossible to design a UI, yet it's a necessity for allowing more people to interact with it (democratisation). 
@@ -93,6 +93,10 @@ Create an account and login (local database)
   - **Database**: manage workflows in _Library_ tab.
 - **Info page**: additional info in _About_ tab.
 
+[//]: # (![Discord](https://img.shields.io/discord/1313641159356059770))
+
+[//]: # (![PyPI - Downloads](https://img.shields.io/pypi/dm/ivoryos))
+
 
 ### Additional settings
 #### AI assistant
@@ -133,7 +137,7 @@ After one successful connection, a blueprint will be automatically saved and mad
 ivoryos.run()
 ```
 ## Demo
-In the [abstract_sdl.py](https://gitlab.com/heingroup/ivoryos/-/blob/main/example/sdl_example/abstract_sdl.py), where instances of `AbstractSDL` is created as `sdl`,
+In the [abstract_sdl.py](https://gitlab.com/heingroup/ivoryos/-/blob/main/example/abstract_sdl_example/abstract_sdl.py), where instances of `AbstractSDL` is created as `sdl`,
 addresses will be available on terminal.
 ```Python
 ivoryos.run(__name__)

{ivoryos-0.1.21.dist-info → ivoryos-0.1.23.dist-info}/RECORD

@@ -1,46 +1,50 @@
-ivoryos/__init__.py,sha256=bx8EuJ5ObYwuwlW3KnWQwXG-AdWWyi-F0kaOLe7WeUo,5978
+ivoryos/__init__.py,sha256=pvQVtXOuDSaOwxMkcfgE00kEVXMFUsOsvjv49-Hy0Z4,6877
 ivoryos/config.py,sha256=3FPBYTIBhQTKDvsEoR8ZeTmg65D-CSFEdGmOuIL4pSI,1311
-ivoryos/version.py,sha256=qEmNtjnOwhDYQ0cHPPtUkUaghzD2xl0thJEznl4giYw,23
+ivoryos/version.py,sha256=0byemO6n6WCv41u9vBG2AIsOkVbxLvok7puvwy8EhfU,23
 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/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=MmrcKrkjSKS589XhDdvPc7kWO0ApCNVZCtrgfzTAAN8,14163
+ivoryos/routes/control/control.py,sha256=bxNYR-VAFA7tSswDt5k130AnIx1f64_R9N2B9kMridI,14160
 ivoryos/routes/control/templates/control/controllers.html,sha256=iIp0h6WA68gQj9OsoiB7dU1BqH8CGomTueR73F4C8eY,4274
-ivoryos/routes/control/templates/control/controllers_home.html,sha256=xFnBXTWMlyi2naMSsCEqFlX-Z1HJJDDtzITPvq-3nng,2733
+ivoryos/routes/control/templates/control/controllers_home.html,sha256=VQ77HRvBlyBrQ3al5fcKF5Y6_vKtU8WeAhilqQQltAo,2997
 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=h4b5r1K5W3psqze0v2QF_jX0ADppy8XdFBQLJb41LOU,5808
-ivoryos/routes/database/templates/database/experiment_database.html,sha256=GeZjx220PdAt_dVN6kigsaNzvaruPlrSSii1cka56NE,3530
+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/templates/database/step_card.html,sha256=F4JRfacrEQfk2rrEbcI_i7G84nzKKDmCrMSmStLb4W4,290
+ivoryos/routes/database/templates/database/workflow_run_database.html,sha256=MczK9my9u0SyQsMFLbc6CXeZqKaBo5vk1SpwjkcZdqk,3571
 ivoryos/routes/design/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ivoryos/routes/design/design.py,sha256=rIy6LCMw6ck4bxuPqoxIV6F1vZxY8aZ3Au5pm74dfr8,23934
-ivoryos/routes/design/templates/design/experiment_builder.html,sha256=2cT25URI6NoRDKuU6xl8Vsv4pqyQhhx-Fu8JOfPIP8k,27110
-ivoryos/routes/design/templates/design/experiment_run.html,sha256=t4Pq6uIltm3sq5cDb4zQa9i98iOQFNumkSa24vzCZrY,26001
+ivoryos/routes/design/design.py,sha256=gO8FKuSdGD6EiN3cbspk7jv6y2Ar25A-ZdrCyUTInpE,25221
+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/main/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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