ivoryos 1.3.2__tar.gz → 1.3.4__tar.gz

{ivoryos-1.3.2 → ivoryos-1.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ivoryos
-Version: 1.3.2
+Version: 1.3.4
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Author-email: Ivory Zhang <ivoryzhang@chem.ubc.ca>
 License: MIT
@@ -28,7 +28,8 @@ Dynamic: license-file
 [![YouTube](https://img.shields.io/badge/YouTube-tutorial-red?logo=youtube)](https://youtu.be/dFfJv9I2-1g)
 [![YouTube](https://img.shields.io/badge/YouTube-demo-red?logo=youtube)](https://youtu.be/flr5ydiE96s)
 [![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)
+
+[//]: # ([![Discord]&#40;https://img.shields.io/discord/1313641159356059770?label=Discord&logo=discord&color=5865F2&#41;]&#40;https://discord.gg/AX5P9EdGVX&#41;)
 
 ![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/ivoryos.png)
 # ivoryOS: interoperable Web UI for self-driving laboratories (SDLs)
@@ -101,11 +102,14 @@ pip install -e .
 ## Quick start
 In your SDL script, 
 ```python
+my_robot = Robot()
+
 import ivoryos
 
 ivoryos.run(__name__)
 ```
-Login: Create an account (local DB, bcrypt password)
+You can now access the web UI at http://127.0.0.1:8000,
+create an account, login, and start designing workflows!
 
 ----
 ## Features
@@ -127,6 +131,28 @@ Add single or multiple loggers:
 ivoryos.run(__name__, logger="logger name")
 ivoryos.run(__name__, logger=["logger 1", "logger 2"])
 ```
+### Human-in-the-loop
+Add single or multiple notification handlers for `pause` feature in flow control:
+```python
+
+def slack_bot(msg: str = "Hi"):
+    """
+    a function that can be used as a notification handler function("msg")
+    :param msg: message to send
+    """
+    from slack_sdk import WebClient
+
+    slack_token = "your slack token"
+    client = WebClient(token=slack_token)
+
+    my_user_id = "your user id"  # replace with your actual Slack user ID
+
+    client.chat_postMessage(channel=my_user_id, text=msg)
+
+import ivoryos
+ivoryos.run(__name__, notification_handler=slack_bot)
+```
+
 ### Directory Structure
 
 Created automatically on first run:
@@ -152,11 +178,10 @@ ivoryos.run(__name__)
 
 ## Roadmap
 
-- [x] Allow plugin pages ✅  
-- [x] pause, resume, abort current and pending workflows ✅
 - [ ] dropdown input 
 - [ ] snapshot version control
 - [ ] optimizer-agnostic
+- [ ] prefect compatibility
 - [ ] check batch-config file compatibility
 
 ---
@@ -198,4 +223,4 @@ For an additional perspective related to the development of the tool, please see
 ```
 ---
 ## Acknowledgements
-Authors acknowledge Telescope Innovations Corp., Hein Lab members for their valuable suggestions and contributions.
+Authors acknowledge Telescope Innovations Corp., UBC Hein Lab, and Acceleration Consortium members for their valuable suggestions and contributions.

{ivoryos-1.3.2 → ivoryos-1.3.4}/README.md

@@ -4,7 +4,8 @@
 [![YouTube](https://img.shields.io/badge/YouTube-tutorial-red?logo=youtube)](https://youtu.be/dFfJv9I2-1g)
 [![YouTube](https://img.shields.io/badge/YouTube-demo-red?logo=youtube)](https://youtu.be/flr5ydiE96s)
 [![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)
+
+[//]: # ([![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)
@@ -77,11 +78,14 @@ pip install -e .
 ## Quick start
 In your SDL script, 
 ```python
+my_robot = Robot()
+
 import ivoryos
 
 ivoryos.run(__name__)
 ```
-Login: Create an account (local DB, bcrypt password)
+You can now access the web UI at http://127.0.0.1:8000,
+create an account, login, and start designing workflows!
 
 ----
 ## Features
@@ -103,6 +107,28 @@ Add single or multiple loggers:
 ivoryos.run(__name__, logger="logger name")
 ivoryos.run(__name__, logger=["logger 1", "logger 2"])
 ```
+### Human-in-the-loop
+Add single or multiple notification handlers for `pause` feature in flow control:
+```python
+
+def slack_bot(msg: str = "Hi"):
+    """
+    a function that can be used as a notification handler function("msg")
+    :param msg: message to send
+    """
+    from slack_sdk import WebClient
+
+    slack_token = "your slack token"
+    client = WebClient(token=slack_token)
+
+    my_user_id = "your user id"  # replace with your actual Slack user ID
+
+    client.chat_postMessage(channel=my_user_id, text=msg)
+
+import ivoryos
+ivoryos.run(__name__, notification_handler=slack_bot)
+```
+
 ### Directory Structure
 
 Created automatically on first run:
@@ -128,11 +154,10 @@ ivoryos.run(__name__)
 
 ## Roadmap
 
-- [x] Allow plugin pages ✅  
-- [x] pause, resume, abort current and pending workflows ✅
 - [ ] dropdown input 
 - [ ] snapshot version control
 - [ ] optimizer-agnostic
+- [ ] prefect compatibility
 - [ ] check batch-config file compatibility
 
 ---
@@ -174,4 +199,4 @@ For an additional perspective related to the development of the tool, please see
 ```
 ---
 ## Acknowledgements
-Authors acknowledge Telescope Innovations Corp., Hein Lab members for their valuable suggestions and contributions.
+Authors acknowledge Telescope Innovations Corp., UBC Hein Lab, and Acceleration Consortium members for their valuable suggestions and contributions.

{ivoryos-1.3.2 → ivoryos-1.3.4}/ivoryos/app.py

@@ -41,7 +41,8 @@ def reset_old_schema(engine, db_dir):
     old_workflow_run = 'workflow_runs' in tables
     old_workflow_step = 'workflow_steps' in tables
 
-    if not has_workflow_phase:
+    # v1.3.4 only delete and backup when there is runs but no phases
+    if not has_workflow_phase and old_workflow_run:
         print("⚠️ Old workflow database detected! All previous workflows have been reset to support the new schema.")
         # Backup old DB
         db_path = os.path.join(db_dir, "ivoryos.db")

{ivoryos-1.3.2 → ivoryos-1.3.4}/ivoryos/server.py

@@ -49,6 +49,7 @@ def run(module=None, host="0.0.0.0", port=None, debug=None, llm_server=None, mod
         enable_design: bool = True,
         blueprint_plugins: Union[list, Blueprint] = [],
         exclude_names: list = [],
+        notification_handler=None,
         ):
     """
     Start ivoryOS app server.
@@ -65,6 +66,7 @@ def run(module=None, host="0.0.0.0", port=None, debug=None, llm_server=None, mod
     :param enable_design: enable design canvas, database and workflow execution
     :param blueprint_plugins: Union[list[Blueprint], Blueprint] custom Blueprint pages
     :param exclude_names: list[str] module names to exclude from parsing
+    :param notification_handler: notification handler function
     """
     app = create_app(config_class=config or get_config())  # Create app instance using factory function
 
@@ -113,11 +115,33 @@ def run(module=None, host="0.0.0.0", port=None, debug=None, llm_server=None, mod
                                        output_path=app.config["OUTPUT_FOLDER"] if module is not None else None)
     else:
         app.config["ENABLE_LLM"] = False
-    if logger and type(logger) is str:
-        utils.start_logger(socketio, log_filename=logger_path, logger_name=logger)
-    elif type(logger) is list:
-        for log in logger:
-            utils.start_logger(socketio, log_filename=logger_path, logger_name=log)
+
+
+    # --- Logger registration ---
+    if logger:
+        if isinstance(logger, str):
+            logger = [logger]  # convert single logger to list
+        elif not isinstance(logger, list):
+            raise TypeError("logger must be a string or a list of strings.")
+
+        for log_name in logger:
+            utils.start_logger(socketio, log_filename=logger_path, logger_name=log_name)
+
+    # --- Notification handler registration ---
+    if notification_handler:
+
+        # make it a list if a single function is passed
+        if callable(notification_handler):
+            notification_handler = [notification_handler]
+
+        if not isinstance(notification_handler, list):
+            raise ValueError("notification_handlers must be a callable or a list of callables.")
+
+        # validate all items are callable
+        for handler in notification_handler:
+            if not callable(handler):
+                raise TypeError(f"Handler {handler} is not callable.")
+            global_config.register_notification(handler)
 
     # TODO in case Python 3.12 or higher doesn't log URL
     # if sys.version_info >= (3, 12):
@@ -129,23 +153,6 @@ def run(module=None, host="0.0.0.0", port=None, debug=None, llm_server=None, mod
     # return app
 
 
-# def load_installed_plugins(app, socketio):
-#     """
-#     Dynamically load installed plugins and attach Flask-SocketIO.
-#     """
-#     plugin_names = []
-#     for entry_point in entry_points().get("ivoryos.plugins", []):
-#         plugin = entry_point.load()
-#
-#         # If the plugin has an `init_socketio()` function, pass socketio
-#         if hasattr(plugin, 'init_socketio'):
-#             plugin.init_socketio(socketio)
-#
-#         plugin_names.append(entry_point.name)
-#         app.register_blueprint(getattr(plugin, entry_point.name), url_prefix=f"{url_prefix}/{entry_point.name}")
-#
-#     return plugin_names
-
 
 def load_plugins(blueprints: Union[list, Blueprint], app, socketio):
     """

{ivoryos-1.3.2 → ivoryos-1.3.4}/ivoryos/utils/global_config.py

@@ -17,6 +17,8 @@ class GlobalConfig:
             cls._instance._runner_lock = threading.Lock()
             cls._instance._runner_status = None
             cls._instance._optimizers = {}
+            cls._instance._notification_handlers = []
+
         return cls._instance
 
     @property
@@ -28,6 +30,15 @@ class GlobalConfig:
         if self._deck is None:
             self._deck = value
 
+    def register_notification(self, handler):
+        if not callable(handler):
+            raise ValueError("Handler must be callable")
+        self._notification_handlers.append(handler)
+
+    @property
+    def notification_handlers(self):
+        return self._notification_handlers
+
     @property
     def building_blocks(self):
         return self._building_blocks

{ivoryos-1.3.2 → ivoryos-1.3.4}/ivoryos/utils/py_to_json.py

@@ -2,6 +2,20 @@ import ast
 import json
 import uuid
 
+
+from ivoryos.utils.global_config import GlobalConfig
+
+global_config = GlobalConfig()
+
+if global_config.building_blocks:
+    building_blocks = {
+        inner_key: f"{block_key}.{inner_key}"
+        for block_key, block_value in global_config.building_blocks.items()
+        for inner_key in block_value.keys()
+    }
+else:
+    building_blocks = {}
+
 def generate_uuid():
     return int(str(uuid.uuid4().int)[:15])
 
@@ -37,7 +51,7 @@ def convert_to_cards(source_code: str):
     def is_supported_assignment(node):
         return (
             isinstance(node.targets[0], ast.Name) and
-            isinstance(node.value, (ast.Constant, ast.Num, ast.Str, ast.NameConstant))
+            isinstance(node.value, ast.Constant)
         )
 
     class CardVisitor(ast.NodeVisitor):
@@ -143,11 +157,22 @@ def convert_to_cards(source_code: str):
                 f = f.value
             if isinstance(f, ast.Name):
                 func_parts.insert(0, f.id)
-            if not func_parts:
+
+            full_func_name = ".".join(func_parts)
+
+            # Check if this is a deck call or a building block
+            if full_func_name.startswith("deck.") or full_func_name.startswith("blocks."):
+                instrument = ".".join(func_parts[:-1])
+                action = func_parts[-1]
+            # not starting with deck or block, check if it's a decorated function
+            # ["general", "action"] or ["action"]
+            elif func_parts[-1] in building_blocks.keys():
+                instrument = building_blocks.get(func_parts[-1])
+                action = func_parts[-1]
+            else:
+                # ignore other calls
                 return
 
-            instrument = ".".join(func_parts[:-1])
-            action = func_parts[-1]
 
 
             # --- special case for time.sleep ---
@@ -181,7 +206,7 @@ def convert_to_cards(source_code: str):
             for kw in node.keywords:
                 if kw.arg is None and isinstance(kw.value, ast.Dict):
                     for k_node, v_node in zip(kw.value.keys, kw.value.values):
-                        key = k_node.s if isinstance(k_node, ast.Constant) else ast.unparse(k_node)
+                        key = k_node.value if isinstance(k_node, ast.Constant) else ast.unparse(k_node)
                         if isinstance(v_node, ast.Constant):
                             value = v_node.value
                         elif isinstance(v_node, ast.Name):
@@ -242,10 +267,14 @@ if __name__ == "__main__":
     # Step 4: Analyze the sample
     analysis_results = deck.sdl.analyze(param_1=1, param_2=2)
     
+    # test block 
+    result = blocks.general.test(**{'a': 1, 'b': 2})
+    
     # Brief pause for system stability
     time.sleep(1.0)
     
     # Return only analysis results
     return {'analysis_results': analysis_results}
     '''
-    print(json.dumps(convert_to_cards(test)))
+    from pprint import pprint
+    pprint(json.dumps(convert_to_cards(test)))

{ivoryos-1.3.2 → ivoryos-1.3.4}/ivoryos/utils/script_runner.py

@@ -19,6 +19,14 @@ 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:
@@ -161,7 +169,7 @@ class ScriptRunner:
                 start_time=datetime.now(),
             )
             db.session.add(step)
-            db.session.commit()
+            db.session.flush()
 
             logger.info(f"Executing: {line}")
             socketio.emit('execution', {'section': f"{section_name}-{index}"})
@@ -219,7 +227,7 @@ class ScriptRunner:
                               repeat_mode=repeat_mode
                               )
             db.session.add(run)
-            db.session.commit()
+            db.session.flush()
             run_id = run.id  # Save the ID
             try:
 
@@ -277,7 +285,7 @@ class ScriptRunner:
             start_time=datetime.now()
         )
         db.session.add(phase)
-        db.session.commit()
+        db.session.flush()
         phase_id = phase.id
 
         step_outputs = self.exec_steps(script, section_name, logger, socketio, phase_id=phase_id)
@@ -317,7 +325,7 @@ class ScriptRunner:
                     start_time=datetime.now()
                 )
                 db.session.add(phase)
-                db.session.commit()
+                db.session.flush()
 
                 phase_id = phase.id
                 output = self.exec_steps(script, "script", logger, socketio, phase_id, **kwargs)
@@ -371,7 +379,7 @@ class ScriptRunner:
                 start_time=datetime.now()
             )
             db.session.add(phase)
-            db.session.commit()
+            db.session.flush()
             phase_id = phase.id
 
             logger.info(f'Executing {run_name} experiment: {i_progress + 1}/{int(repeat_count)}')

{ivoryos-1.3.2 → ivoryos-1.3.4}/ivoryos/utils/task_runner.py

@@ -29,6 +29,7 @@ class TaskRunner:
         if not self.lock.acquire(blocking=False):
             current_status = global_config.runner_status
             current_status["status"] = "busy"
+            current_status["output"] = "busy"
             return current_status
 
 
@@ -71,7 +72,7 @@ class TaskRunner:
         with current_app.app_context():
             step = SingleStep(method_name=method_name, kwargs=kwargs, run_error=None, start_time=datetime.now())
             db.session.add(step)
-            db.session.commit()
+            db.session.flush()
             global_config.runner_status = {"id":step.id, "type": "task"}
             try:
                 output = function_executable(**kwargs)

{ivoryos-1.3.2 → ivoryos-1.3.4}/ivoryos/utils/utils.py

@@ -141,6 +141,7 @@ def _get_type_from_parameters(arg, parameters):
 def _convert_by_str(args, arg_types):
     """
     Converts a value to type through eval(f'{type}("{args}")')
+    v1.3.4 TODO try str lastly, otherwise it's always converted to str
     """
     if type(arg_types) is not list:
         arg_types = [arg_types]

ivoryos-1.3.4/ivoryos/version.py

@@ -0,0 +1 @@
+__version__ = "1.3.4"

{ivoryos-1.3.2 → ivoryos-1.3.4}/ivoryos.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ivoryos
-Version: 1.3.2
+Version: 1.3.4
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Author-email: Ivory Zhang <ivoryzhang@chem.ubc.ca>
 License: MIT
@@ -28,7 +28,8 @@ Dynamic: license-file
 [![YouTube](https://img.shields.io/badge/YouTube-tutorial-red?logo=youtube)](https://youtu.be/dFfJv9I2-1g)
 [![YouTube](https://img.shields.io/badge/YouTube-demo-red?logo=youtube)](https://youtu.be/flr5ydiE96s)
 [![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)
+
+[//]: # ([![Discord]&#40;https://img.shields.io/discord/1313641159356059770?label=Discord&logo=discord&color=5865F2&#41;]&#40;https://discord.gg/AX5P9EdGVX&#41;)
 
 ![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/ivoryos.png)
 # ivoryOS: interoperable Web UI for self-driving laboratories (SDLs)
@@ -101,11 +102,14 @@ pip install -e .
 ## Quick start
 In your SDL script, 
 ```python
+my_robot = Robot()
+
 import ivoryos
 
 ivoryos.run(__name__)
 ```
-Login: Create an account (local DB, bcrypt password)
+You can now access the web UI at http://127.0.0.1:8000,
+create an account, login, and start designing workflows!
 
 ----
 ## Features
@@ -127,6 +131,28 @@ Add single or multiple loggers:
 ivoryos.run(__name__, logger="logger name")
 ivoryos.run(__name__, logger=["logger 1", "logger 2"])
 ```
+### Human-in-the-loop
+Add single or multiple notification handlers for `pause` feature in flow control:
+```python
+
+def slack_bot(msg: str = "Hi"):
+    """
+    a function that can be used as a notification handler function("msg")
+    :param msg: message to send
+    """
+    from slack_sdk import WebClient
+
+    slack_token = "your slack token"
+    client = WebClient(token=slack_token)
+
+    my_user_id = "your user id"  # replace with your actual Slack user ID
+
+    client.chat_postMessage(channel=my_user_id, text=msg)
+
+import ivoryos
+ivoryos.run(__name__, notification_handler=slack_bot)
+```
+
 ### Directory Structure
 
 Created automatically on first run:
@@ -152,11 +178,10 @@ ivoryos.run(__name__)
 
 ## Roadmap
 
-- [x] Allow plugin pages ✅  
-- [x] pause, resume, abort current and pending workflows ✅
 - [ ] dropdown input 
 - [ ] snapshot version control
 - [ ] optimizer-agnostic
+- [ ] prefect compatibility
 - [ ] check batch-config file compatibility
 
 ---
@@ -198,4 +223,4 @@ For an additional perspective related to the development of the tool, please see
 ```
 ---
 ## Acknowledgements
-Authors acknowledge Telescope Innovations Corp., Hein Lab members for their valuable suggestions and contributions.
+Authors acknowledge Telescope Innovations Corp., UBC Hein Lab, and Acceleration Consortium members for their valuable suggestions and contributions.

ivoryos-1.3.2/ivoryos/version.py

@@ -1 +0,0 @@
-__version__ = "1.3.2"