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

ivoryos/utils/task_runner.py

@@ -1,7 +1,10 @@
+import inspect
+import asyncio
 import threading
 import time
 from datetime import datetime
 
+from ivoryos.utils.decorators import BUILDING_BLOCKS
 from ivoryos.utils.db_models import db, SingleStep
 from ivoryos.utils.global_config import GlobalConfig
 
@@ -18,8 +21,7 @@ class TaskRunner:
         self.globals_dict = globals_dict
         self.lock = global_config.runner_lock
 
-
-    def run_single_step(self, component, method, kwargs, wait=True, current_app=None):
+    async def run_single_step(self, component, method, kwargs, wait=True, current_app=None):
         global deck
         if deck is None:
             deck = global_config.deck
@@ -28,18 +30,18 @@ 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
 
-
         if wait:
-            output = self._run_single_step(component, method, kwargs, current_app)
+            output = await 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)
+            # Create background task properly
+            async def background_runner():
+                await self._run_single_step(component, method, kwargs, current_app)
+
+            asyncio.create_task(background_runner())
+            await asyncio.sleep(0.1)  # Change time.sleep to await asyncio.sleep
             output = {"status": "task started", "task_id": global_config.runner_status.get("id")}
 
         return output
@@ -48,37 +50,82 @@ class TaskRunner:
         if component.startswith("deck."):
             component = component.split(".")[1]
             instrument = getattr(deck, component)
+            function_executable = getattr(instrument, method)
+        elif component.startswith("blocks."):
+            component = component.split(".")[1]
+            function_executable = BUILDING_BLOCKS[component][method]["func"]
         else:
             temp_connections = global_config.defined_variables
             instrument = temp_connections.get(component)
-        function_executable = getattr(instrument, method)
+            function_executable = getattr(instrument, method)
         return function_executable
 
-    def _run_single_step(self, component, method, kwargs, current_app=None):
+    async 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__}"
+            method_name = f"{component}.{method}"
         except Exception as e:
             self.lock.release()
-            return {"status": "error", "msg": e.__str__()}
+            return {"status": "error", "msg": str(e)}
 
-        # with self.lock:
+        # Flask context is NOT async → just use normal "with"
         with current_app.app_context():
-            step = SingleStep(method_name=method_name, kwargs=kwargs, run_error=False, start_time=datetime.now())
+            step = SingleStep(
+                method_name=method_name,
+                kwargs=kwargs,
+                run_error=None,
+                start_time=datetime.now()
+            )
             db.session.add(step)
-            db.session.commit()
-            global_config.runner_status = {"id":step.id, "type": "task"}
+            db.session.flush()
+            global_config.runner_status = {"id": step.id, "type": "task"}
+
             try:
-                output = function_executable(**kwargs)
+                kwargs = self._convert_kwargs_type(kwargs, function_executable)
+
+                if inspect.iscoroutinefunction(function_executable):
+                    output = await function_executable(**kwargs)
+                else:
+                    output = function_executable(**kwargs)
+
                 step.output = output
                 step.end_time = datetime.now()
                 success = True
             except Exception as e:
-                step.run_error = e.__str__()
+                step.run_error = str(e)
                 step.end_time = datetime.now()
                 success = False
-                output = e.__str__()
+                output = str(e)
             finally:
                 db.session.commit()
                 self.lock.release()
-            return dict(success=success, output=output)
+
+            return dict(success=success, output=output)
+
+    @staticmethod
+    def _convert_kwargs_type(kwargs, function_executable):
+        def convert_guess(str_value):
+            str_value = str_value.strip()
+            if str_value.isdigit() or (str_value.startswith('-') and str_value[1:].isdigit()):
+                return int(str_value)
+            try:
+                return float(str_value)
+            except ValueError:
+                return str_value
+
+        sig = inspect.signature(function_executable)
+        converted = {}
+
+        for name, value in kwargs.items():
+            if name in sig.parameters:
+                param = sig.parameters[name]
+                if param.annotation != inspect.Parameter.empty:
+                    # convert using type hint
+                    try:
+                        converted[name] = param.annotation(value)
+                    except Exception:
+                        converted[name] = value
+                else:
+                    # no type hint → guess
+                    converted[name] = convert_guess(value)
+        return converted

ivoryos/utils/utils.py

@@ -1,6 +1,7 @@
 import ast
 import importlib
 import inspect
+import json
 import logging
 import os
 import pickle
@@ -15,7 +16,7 @@ from flask_login import current_user
 from flask_socketio import SocketIO
 
 from ivoryos.utils.db_models import Script
-
+from ivoryos.utils.decorators import BUILDING_BLOCKS
 
 def get_script_file():
     """Get script from Flask session and returns the script"""
@@ -105,7 +106,8 @@ def _inspect_class(class_object=None, debug=False):
             try:
                 annotation = inspect.signature(method)
                 docstring = inspect.getdoc(method)
-                functions[function] = dict(signature=annotation, docstring=docstring)
+                coroutine = inspect.iscoroutinefunction(method)
+                functions[function] = dict(signature=annotation, docstring=docstring, coroutine=coroutine,)
 
             except Exception:
                 pass
@@ -141,6 +143,7 @@ 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]
@@ -151,6 +154,7 @@ def _convert_by_str(args, arg_types):
                 return args
             except Exception:
                 raise TypeError(f"Input type error: cannot convert '{args}' to {arg_type}.")
+    return args
 
 
 def _convert_by_class(args, arg_types):
@@ -348,8 +352,8 @@ def create_deck_snapshot(deck, save: bool = False, output_path: str = '', exclud
             for name, class_type in items.items():
                 print(f"  {name}: {class_type}")
 
-        print_section("✅ INCLUDED", deck_summary["included"])
-        print_section("❌ FAILED", deck_summary["failed"])
+        print_section("✅ INCLUDED MODULES", deck_summary["included"])
+        print_section("❌ FAILED MODULES", deck_summary["failed"])
         print("\n")
 
     print_deck_snapshot(deck_summary)
@@ -364,6 +368,28 @@ def create_deck_snapshot(deck, save: bool = False, output_path: str = '', exclud
     return deck_snapshot
 
 
+def create_block_snapshot(save: bool = False, output_path: str = ''):
+    block_snapshot = {}
+    included = {}
+    failed = {}
+    for category, data in BUILDING_BLOCKS.items():
+        key = f"blocks.{category}"
+        block_snapshot[key] = {}
+
+        for func_name, meta in data.items():
+            func = meta["func"]
+            block_snapshot[key][func_name] = {
+                "signature": meta["signature"],
+                "docstring": meta["docstring"],
+                "coroutine": meta["coroutine"],
+                "path": f"{func.__module__}.{func.__qualname__}"
+            }
+    if block_snapshot:
+        print(f"\n=== ✅ BUILDING_BLOCKS ({len(block_snapshot)}) ===")
+        for category, blocks in block_snapshot.items():
+            print(f"  {category}: ", ",".join(blocks.keys()))
+    return block_snapshot
+
 def load_deck(pkl_name: str):
     """
     Loads a pickled deck snapshot from disk on offline mode
@@ -420,4 +446,21 @@ def get_local_ip():
         ip = '127.0.0.1'
     finally:
         s.close()
-    return ip
+    return ip
+
+
+def safe_dump(obj):
+    try:
+        json.dumps(obj)
+        return obj
+    except (TypeError, OverflowError):
+        return repr(obj)  # store readable representation
+
+
+def create_module_snapshot(module):
+    classes = inspect.getmembers(module, inspect.isclass)
+    api_variables = {}
+    for i in classes:
+        # globals()[i[0]] = i[1]
+        api_variables[i[0]] = i[1]
+    return api_variables

ivoryos/version.py

@@ -1 +1 @@
-__version__ = "1.2.5"
+__version__ = "1.4.4"

{ivoryos-1.2.5.dist-info → ivoryos-1.4.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ivoryos
-Version: 1.2.5
+Version: 1.4.4
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Author-email: Ivory Zhang <ivoryzhang@chem.ubc.ca>
 License: MIT
@@ -9,6 +9,7 @@ Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: bcrypt
+Requires-Dist: Flask[async]
 Requires-Dist: Flask-Login
 Requires-Dist: Flask-Session
 Requires-Dist: Flask-SocketIO
@@ -16,10 +17,24 @@ Requires-Dist: Flask-SQLAlchemy
 Requires-Dist: Flask-WTF
 Requires-Dist: SQLAlchemy-Utils
 Requires-Dist: python-dotenv
+Requires-Dist: pandas
 Requires-Dist: astor; python_version < "3.9"
-Provides-Extra: optimizer
-Requires-Dist: ax-platform; extra == "optimizer"
-Requires-Dist: baybe; extra == "optimizer"
+Provides-Extra: optimizer-ax
+Requires-Dist: ax-platform; extra == "optimizer-ax"
+Provides-Extra: optimizer-baybe
+Requires-Dist: baybe; extra == "optimizer-baybe"
+Provides-Extra: optimizer-nimo
+Requires-Dist: nimo; extra == "optimizer-nimo"
+Provides-Extra: optimizers
+Requires-Dist: ax-platform>=1.1.2; extra == "optimizers"
+Requires-Dist: baybe>=0.14.0; extra == "optimizers"
+Requires-Dist: nimo; extra == "optimizers"
+Provides-Extra: doc
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: sphinx-rtd-theme; extra == "doc"
+Requires-Dist: sphinxcontrib-httpdomain; extra == "doc"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
 Dynamic: license-file
 
 [![Documentation Status](https://readthedocs.org/projects/ivoryos/badge/?version=latest)](https://ivoryos.readthedocs.io/en/latest/?badge=latest)
@@ -28,33 +43,36 @@ 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)
 
-![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/ivoryos.png)
-# ivoryOS: interoperable Web UI for self-driving laboratories (SDLs)
-A **plug-and-play** web interface for flexible SDLs 
+[//]: # ([![Discord]&#40;https://img.shields.io/discord/1313641159356059770?label=Discord&logo=discord&color=5865F2&#41;]&#40;https://discord.gg/AX5P9EdGVX&#41;)
+
+![ivoryos_logo.png](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/ivoryos_logo.png)
+
+# [IvoryOS](https://ivoryos.ai): interoperable orchestrator for self-driving laboratories (SDLs) 
+
+A **plug-and-play** web interface for flexible, modular SDLs —
+you focus on developing protocols, IvoryOS handles the rest.
+
+![code_launch_design.png](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/code_launch_design.png)
 
 ---
 
 ## Table of Contents
-- [Description](#description)
+- [What IvoryOS does](#what-ivoryos-does)
 - [System requirements](#system-requirements)
 - [Installation](#installation)
-- [Quick Start](#quick-start)
 - [Features](#features)
 - [Demo](#demo)
 - [Roadmap](#roadmap)
+- [Contributing](#contributing)
 - [Acknowledgements](#acknowledgements)
 
 ---
-## Description
-Building UIs for SDLs is challenging because flexibility and modularity make them unpredictable — yet accessibility is essential for **democratisation** of AI-driven scientific discovery.
-
-**IvoryOS** bridges the gap by:
-- Dynamically inspecting initialized Python modules (hardware APIs, high-level functions, or workflows)
-- Automatically displaying functions and parameters in a web UI
-- Allowing users to **design**, **manage**, and **execute** experimental workflows with minimal changes to existing scripts
-- Providing natural language support for workflow design and execution, check [IvoryOS MCP](https://gitlab.com/heingroup/ivoryos-suite/ivoryos-mcp) for more details.
+## What IvoryOS Does
+- Turns Python modules into UIs by dynamically inspecting your hardware APIs, functions, and workflows.
+- Standardizes optimization inputs/outputs, making any optimizer plug-and-play.
+- Provides a visual workflow builder for designing and running experiments.
+- Adds natural-language control for creating and executing workflows, see [IvoryOS MCP](https://gitlab.com/heingroup/ivoryos-suite/ivoryos-mcp) for more details.
 
 ----
 ## System Requirements
@@ -76,10 +94,13 @@ Building UIs for SDLs is challenging because flexibility and modularity make the
 - SQLAlchemy-Utils~=0.41  
 - Flask-WTF~=1.2  
 - python-dotenv==1.0.1  
+- pandas
 
 **Optional:**
-- ax-platform (≥1.0, Python≥3.10)
-- baybe
+- ax-platform==1.1.2
+- baybe==0.14.0
+- nimo
+- slack-sdk
 </details>
 
 ---
@@ -90,22 +111,31 @@ From PyPI:
 ```bash
 pip install ivoryos
 ```
-From source:
-```bash
-git clone https://gitlab.com/heingroup/ivoryos.git
-cd ivoryos
-pip install -e .
-```
+
+[//]: # (From source:)
+
+[//]: # (```bash)
+
+[//]: # (git clone https://gitlab.com/heingroup/ivoryos.git)
+
+[//]: # (cd ivoryos)
+
+[//]: # (pip install -e .)
+
+[//]: # (```)
 
 
 ## Quick start
-In your SDL script, 
+In your script, where you initialize or import your robot:
 ```python
+my_robot = Robot()
+
 import ivoryos
 
 ivoryos.run(__name__)
 ```
-Login: Create an account (local DB, bcrypt password)
+Then run the script and visit `http://localhost:8000` in your browser.
+Use `admin` for both username and password, and start building workflows!
 
 ----
 ## Features
@@ -127,42 +157,72 @@ Add single or multiple loggers:
 ivoryos.run(__name__, logger="logger name")
 ivoryos.run(__name__, logger=["logger 1", "logger 2"])
 ```
+### Human-in-the-loop
+Use `pause` in flow control to pause the workflow and send a notification with custom message handler(s). 
+When run into `pause`, it will pause, send a message, and wait for human's response. Example of a Slack bot:
+```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:
+Created automatically in the same working directory on the first run:
+<details>
+<summary>click to see the data folder structure</summary>
+
 - **`ivoryos_data/`**: 
-  - **`ivoryos_data/config_csv/`**: Batch configuration `csv`
-  - **`ivoryos_data/pseudo_deck/`**: Offline deck `.pkl`
-  - **`ivoryos_data/results/`**: Execution results
-  - **`ivoryos_data/scripts/`**: Compiled workflows Python scripts
-- **`default.log`**: Application logs
-- **`ivoryos.db`**: Local database
+  - **`config_csv/`**: Batch configuration `csv`
+  - **`pseudo_deck/`**: Offline deck `.pkl`
+  - **`results/`**: Execution results
+  - **`scripts/`**: Compiled workflows Python scripts
+  - **`default.log`**: Application logs
+  - **`ivoryos.db`**: Local database
+</details>
+
 ---
-## Demo
-In the [abstract_sdl.py](https://gitlab.com/heingroup/ivoryos/-/blob/main/example/abstract_sdl_example/abstract_sdl.py)
-```Python
-ivoryos.run(__name__)
-```
 
- * Running on all addresses (0.0.0.0)
- * Running on http://127.0.0.1:8000
- * Running on http://0.0.0.0:8000
+## Demo
+Online demo at [demo.ivoryos.ai](https://demo.ivoryos.ai). 
+Local version in [abstract_sdl.py](https://gitlab.com/heingroup/ivoryos/-/blob/main/community/examples/abstract_sdl_example/abstract_sdl.py)
 
 ---
 
 ## Roadmap
 
-- [x] Allow plugin pages ✅  
-- [x] pause, resume, abort current and pending workflows ✅
 - [ ] dropdown input 
 - [ ] snapshot version control
-- [ ] optimizer-agnostic
 - [ ] check batch-config file compatibility
 
 ---
 
+## Contributing
+
+We welcome all contributions — from core improvements to new drivers, plugins, and real-world use cases.
+See `CONTRIBUTING.md` for details and let us know you're interested: https://forms.gle/fPSvw5LEGrweUQUH8
+
+---
+
 ## Citing
 
+<details>
+<summary>Click to see citations</summary>
+
 If you find this project useful, please consider citing the following manuscript:
 
 > Zhang, W., Hao, L., Lai, V. et al. [IvoryOS: an interoperable web interface for orchestrating Python-based self-driving laboratories.](https://www.nature.com/articles/s41467-025-60514-w) Nat Commun 16, 5182 (2025).
@@ -196,6 +256,8 @@ For an additional perspective related to the development of the tool, please see
   url          = {https://communities.springernature.com/posts/behind-ivoryos-empowering-scientists-to-harness-self-driving-labs-for-accelerated-discovery}
 }
 ```
+</details>
+
 ---
 ## 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-1.4.4.dist-info/RECORD

@@ -0,0 +1,119 @@
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