ivoryos 1.2.0b1__tar.gz → 1.2.2__tar.gz

{ivoryos-1.2.0b1 → ivoryos-1.2.2}/PKG-INFO

@@ -1,13 +1,26 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: ivoryos
-Version: 1.2.0b1
+Version: 1.2.2
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
-Home-page: https://gitlab.com/heingroup/ivoryos
-Author: Ivory Zhang
-Author-email: ivoryzhang@chem.ubc.ca
+Author-email: Ivory Zhang <ivoryzhang@chem.ubc.ca>
 License: MIT
+Project-URL: Homepage, https://gitlab.com/heingroup/ivoryos
+Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: bcrypt
+Requires-Dist: Flask-Login
+Requires-Dist: Flask-Session
+Requires-Dist: Flask-SocketIO
+Requires-Dist: Flask-SQLAlchemy
+Requires-Dist: Flask-WTF
+Requires-Dist: SQLAlchemy-Utils
+Requires-Dist: python-dotenv
+Requires-Dist: astor; python_version < "3.9"
+Provides-Extra: optimizer
+Requires-Dist: ax-platform; extra == "optimizer"
+Requires-Dist: baybe; extra == "optimizer"
+Dynamic: license-file
 
 [![Documentation Status](https://readthedocs.org/projects/ivoryos/badge/?version=latest)](https://ivoryos.readthedocs.io/en/latest/?badge=latest)
 [![PyPI version](https://img.shields.io/pypi/v/ivoryos)](https://pypi.org/project/ivoryos/)
@@ -39,7 +52,7 @@ With the least modification of the current workflow, user can design, manage and
 This software is developed and tested using Windows. This software and its dependencies are compatible across major platforms: Linux, macOS, and Windows. Some dependencies (Flask-SQLAlchemy) may require additional setup.
 
 ### Python Version
-Python >=3.10 for best compatibility. Python >=3.7 without Ax.
+Python >=3.10 for the best compatibility. Python >=3.7 without Ax.
 ### Python dependencies
 This software is compatible with the latest versions of all dependencies. 
 - bcrypt~=4.0
@@ -50,7 +63,9 @@ This software is compatible with the latest versions of all dependencies.
 - SQLAlchemy-Utils~=0.41
 - Flask-WTF~=1.2
 - python-dotenv==1.0.1
-- ax-platform (optional ~=0.4 for Python>=3.9)
+- ax-platform (optional 1.0 for Python>=3.10)
+- baybe (optional)
+
 
 ## Installation
 ```bash
@@ -74,43 +89,60 @@ import ivoryos
 ivoryos.run(__name__)
 ```
 ### Login
-Create an account and login (local database)
+Create an account and login (local database with bcrypt password)
 ### Features
-- **Direct control**: direct function calling _Device_ tab
-- **Workflow design and iteration**:
-  - **Design**: add function to canvas in _Design_ tab. click `Compile and Run` button to go to the execution page
-  - **Execution**: configure iteration methods and parameters in _Compile/Run_ tab. 
-  - **Database**: manage workflows in _Library_ tab.
-- **Info page**: additional info in _About_ tab.
+- **Direct control**: direct function calling _Devices_ tab
+- **Workflows**:
+  - **Design Editor**: drag/add function to canvas in _Design_ tab. click `Compile and Run` button to go to the execution configuration page
+  - **Execution Config**: configure iteration methods and parameters in _Compile/Run_ tab. 
+  - **Design Library**: manage workflow scripts in _Library_ tab.
+  - **Workflow Data**: Execution records are in _Data_ tab.
 
 [//]: # (![Discord]&#40;https://img.shields.io/discord/1313641159356059770&#41;)
 
 [//]: # (![PyPI - Downloads]&#40;https://img.shields.io/pypi/dm/ivoryos&#41;)
 
 
-### Additional settings (not actively maintained)
-#### AI assistant
-To streamline the experimental design on SDLs, we also integrate Large Language Models (LLMs) to interpret the inspected functions and generate code according to task descriptions.
+### Additional settings
+[//]: # (#### AI assistant)
 
-#### Enable LLMs with [OpenAI API](https://github.com/openai/openai-python)
-1. Create a `.env` file for `OPENAI_API_KEY`
-```
-OPENAI_API_KEY="Your API Key"
-```
-2. In your SDL script, define model, you can use any GPT models.
+[//]: # (To streamline the experimental design on SDLs, we also integrate Large Language Models &#40;LLMs&#41; to interpret the inspected functions and generate code according to task descriptions.)
 
-```python
-ivoryos.run(__name__, model="gpt-3.5-turbo")
-```
+[//]: # ()
+[//]: # (#### Enable LLMs with [OpenAI API]&#40;https://github.com/openai/openai-python&#41;)
 
-#### Enable local LLMs with [Ollama](https://ollama.com/)
-1. Download Ollama.
-2. pull models from Ollama
-3. In your SDL script, define LLM server and model, you can use any models available on Ollama.
+[//]: # (1. Create a `.env` file for `OPENAI_API_KEY`)
 
-```python
-ivoryos.run(__name__, llm_server="localhost", model="llama3.1")
-```
+[//]: # (```)
+
+[//]: # (OPENAI_API_KEY="Your API Key")
+
+[//]: # (```)
+
+[//]: # (2. In your SDL script, define model, you can use any GPT models.)
+
+[//]: # ()
+[//]: # (```python)
+
+[//]: # (ivoryos.run&#40;__name__, model="gpt-3.5-turbo"&#41;)
+
+[//]: # (```)
+
+[//]: # ()
+[//]: # (#### Enable local LLMs with [Ollama]&#40;https://ollama.com/&#41;)
+
+[//]: # (1. Download Ollama.)
+
+[//]: # (2. pull models from Ollama)
+
+[//]: # (3. In your SDL script, define LLM server and model, you can use any models available on Ollama.)
+
+[//]: # ()
+[//]: # (```python)
+
+[//]: # (ivoryos.run&#40;__name__, llm_server="localhost", model="llama3.1"&#41;)
+
+[//]: # (```)
 
 #### Add additional logger(s)
 ```python
@@ -135,7 +167,7 @@ ivoryos.run(__name__)
 
  * Running on all addresses (0.0.0.0)
  * Running on http://127.0.0.1:8000
- * Running on http://xxx.xx.xx.xxx:8000
+ * Running on http://0.0.0.0:8000
 
 ### Deck function and web form 
 ![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/demo.gif)
@@ -163,6 +195,8 @@ When you run the application for the first time, it will automatically create th
 - [x] dropdown input ✅  
 - [x] show line number option ✅  
 - [ ] snapshot version control
+- [ ] optimizer-agnostic
+- [ ] check batch-config file compatibility
 
 ## Citing
 
@@ -203,4 +237,4 @@ For an additional perspective related to the development of the tool, please see
 ## Authors and Acknowledgement
 Ivory Zhang, Lucy Hao
 
-Authors acknowledge all former and current Hein Lab members for their valuable suggestions. 
+Authors acknowledge Telescope Innovations, Hein Lab members for their valuable suggestions and contributions.

ivoryos-1.2.0b1/ivoryos.egg-info/PKG-INFO → ivoryos-1.2.2/README.md

@@ -1,14 +1,3 @@
-Metadata-Version: 2.1
-Name: ivoryos
-Version: 1.2.0b1
-Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
-Home-page: https://gitlab.com/heingroup/ivoryos
-Author: Ivory Zhang
-Author-email: ivoryzhang@chem.ubc.ca
-License: MIT
-Description-Content-Type: text/markdown
-License-File: LICENSE
-
 [![Documentation Status](https://readthedocs.org/projects/ivoryos/badge/?version=latest)](https://ivoryos.readthedocs.io/en/latest/?badge=latest)
 [![PyPI version](https://img.shields.io/pypi/v/ivoryos)](https://pypi.org/project/ivoryos/)
 ![License](https://img.shields.io/pypi/l/ivoryos)
@@ -39,7 +28,7 @@ With the least modification of the current workflow, user can design, manage and
 This software is developed and tested using Windows. This software and its dependencies are compatible across major platforms: Linux, macOS, and Windows. Some dependencies (Flask-SQLAlchemy) may require additional setup.
 
 ### Python Version
-Python >=3.10 for best compatibility. Python >=3.7 without Ax.
+Python >=3.10 for the best compatibility. Python >=3.7 without Ax.
 ### Python dependencies
 This software is compatible with the latest versions of all dependencies. 
 - bcrypt~=4.0
@@ -50,7 +39,9 @@ This software is compatible with the latest versions of all dependencies.
 - SQLAlchemy-Utils~=0.41
 - Flask-WTF~=1.2
 - python-dotenv==1.0.1
-- ax-platform (optional ~=0.4 for Python>=3.9)
+- ax-platform (optional 1.0 for Python>=3.10)
+- baybe (optional)
+
 
 ## Installation
 ```bash
@@ -74,43 +65,60 @@ import ivoryos
 ivoryos.run(__name__)
 ```
 ### Login
-Create an account and login (local database)
+Create an account and login (local database with bcrypt password)
 ### Features
-- **Direct control**: direct function calling _Device_ tab
-- **Workflow design and iteration**:
-  - **Design**: add function to canvas in _Design_ tab. click `Compile and Run` button to go to the execution page
-  - **Execution**: configure iteration methods and parameters in _Compile/Run_ tab. 
-  - **Database**: manage workflows in _Library_ tab.
-- **Info page**: additional info in _About_ tab.
+- **Direct control**: direct function calling _Devices_ tab
+- **Workflows**:
+  - **Design Editor**: drag/add function to canvas in _Design_ tab. click `Compile and Run` button to go to the execution configuration page
+  - **Execution Config**: configure iteration methods and parameters in _Compile/Run_ tab. 
+  - **Design Library**: manage workflow scripts in _Library_ tab.
+  - **Workflow Data**: Execution records are in _Data_ tab.
 
 [//]: # (![Discord](https://img.shields.io/discord/1313641159356059770))
 
 [//]: # (![PyPI - Downloads](https://img.shields.io/pypi/dm/ivoryos))
 
 
-### Additional settings (not actively maintained)
-#### AI assistant
-To streamline the experimental design on SDLs, we also integrate Large Language Models (LLMs) to interpret the inspected functions and generate code according to task descriptions.
+### Additional settings
+[//]: # (#### AI assistant)
 
-#### Enable LLMs with [OpenAI API](https://github.com/openai/openai-python)
-1. Create a `.env` file for `OPENAI_API_KEY`
-```
-OPENAI_API_KEY="Your API Key"
-```
-2. In your SDL script, define model, you can use any GPT models.
+[//]: # (To streamline the experimental design on SDLs, we also integrate Large Language Models (LLMs) to interpret the inspected functions and generate code according to task descriptions.)
 
-```python
-ivoryos.run(__name__, model="gpt-3.5-turbo")
-```
+[//]: # ()
+[//]: # (#### Enable LLMs with [OpenAI API](https://github.com/openai/openai-python))
 
-#### Enable local LLMs with [Ollama](https://ollama.com/)
-1. Download Ollama.
-2. pull models from Ollama
-3. In your SDL script, define LLM server and model, you can use any models available on Ollama.
+[//]: # (1. Create a `.env` file for `OPENAI_API_KEY`)
 
-```python
-ivoryos.run(__name__, llm_server="localhost", model="llama3.1")
-```
+[//]: # (```)
+
+[//]: # (OPENAI_API_KEY="Your API Key")
+
+[//]: # (```)
+
+[//]: # (2. In your SDL script, define model, you can use any GPT models.)
+
+[//]: # ()
+[//]: # (```python)
+
+[//]: # (ivoryos.run(__name__, model="gpt-3.5-turbo"))
+
+[//]: # (```)
+
+[//]: # ()
+[//]: # (#### Enable local LLMs with [Ollama](https://ollama.com/))
+
+[//]: # (1. Download Ollama.)
+
+[//]: # (2. pull models from Ollama)
+
+[//]: # (3. In your SDL script, define LLM server and model, you can use any models available on Ollama.)
+
+[//]: # ()
+[//]: # (```python)
+
+[//]: # (ivoryos.run(__name__, llm_server="localhost", model="llama3.1"))
+
+[//]: # (```)
 
 #### Add additional logger(s)
 ```python
@@ -135,7 +143,7 @@ ivoryos.run(__name__)
 
  * Running on all addresses (0.0.0.0)
  * Running on http://127.0.0.1:8000
- * Running on http://xxx.xx.xx.xxx:8000
+ * Running on http://0.0.0.0:8000
 
 ### Deck function and web form 
 ![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/demo.gif)
@@ -163,6 +171,8 @@ When you run the application for the first time, it will automatically create th
 - [x] dropdown input ✅  
 - [x] show line number option ✅  
 - [ ] snapshot version control
+- [ ] optimizer-agnostic
+- [ ] check batch-config file compatibility
 
 ## Citing
 
@@ -203,4 +213,4 @@ For an additional perspective related to the development of the tool, please see
 ## Authors and Acknowledgement
 Ivory Zhang, Lucy Hao
 
-Authors acknowledge all former and current Hein Lab members for their valuable suggestions. 
+Authors acknowledge Telescope Innovations, Hein Lab members for their valuable suggestions and contributions.

{ivoryos-1.2.0b1 → ivoryos-1.2.2}/ivoryos/__init__.py

@@ -1,8 +1,11 @@
 import os
 import sys
+import uuid
 from typing import Union
 
-from flask import Flask, redirect, url_for, g, Blueprint
+from flask import Flask, redirect, url_for, g, Blueprint, session
+from flask_login import AnonymousUserMixin
+
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
 
 from ivoryos.config import Config, get_config
@@ -90,6 +93,23 @@ def create_app(config_class=None):
         """
         g.logger = logger
         g.socketio = socketio
+        session.permanent = False
+        # DEMO_MODE: Simulate logged-in user per session
+        if app.config.get("DEMO_MODE", False):
+            if "demo_user_id" not in session:
+                session["demo_user_id"] = f"demo_{str(uuid.uuid4())[:8]}"
+
+            class SessionDemoUser(AnonymousUserMixin):
+                @property
+                def is_authenticated(self):
+                    return True
+
+                def get_id(self):
+                    return session.get("demo_user_id")
+
+            login_manager.anonymous_user = SessionDemoUser
+
+
 
     @app.route('/')
     def redirect_to_prefix():
@@ -101,6 +121,7 @@ def create_app(config_class=None):
         text = ' '.join(word for word in name.split('_'))
         return text.capitalize()
 
+    # app.config.setdefault("DEMO_MODE", False)
     return app
 
 

{ivoryos-1.2.0b1 → ivoryos-1.2.2}/ivoryos/config.py

@@ -43,6 +43,7 @@ class TestingConfig(Config):
 
 class DemoConfig(Config):
     DEBUG = False
+    DEMO_MODE = True
     SQLALCHEMY_DATABASE_URI = 'sqlite:///:memory:'
     OUTPUT_FOLDER = os.path.join(os.path.abspath(os.curdir), '/tmp/ivoryos_data')
     CSV_FOLDER = os.path.join(OUTPUT_FOLDER, 'config_csv/')

ivoryos-1.2.2/ivoryos/optimizer/ax_optimizer.py

@@ -0,0 +1,164 @@
+# optimizers/ax_optimizer.py
+from typing import Dict
+
+
+
+from ivoryos.optimizer.base_optimizer import OptimizerBase
+from ivoryos.utils.utils import install_and_import
+
+class AxOptimizer(OptimizerBase):
+    def __init__(self, experiment_name, parameter_space, objective_config, optimizer_config=None):
+        try:
+            from ax.api.client import Client
+        except ImportError as e:
+            install_and_import("ax", "ax-platform")
+            raise ImportError("Please install Ax with pip install ax-platform to use AxOptimizer. Attempting to install Ax...")
+        super().__init__(experiment_name, parameter_space, objective_config, optimizer_config)
+
+        self.client = Client()
+        # 2. Configure where Ax will search.
+        self.client.configure_experiment(
+            name=experiment_name,
+            parameters=self._convert_parameter_to_ax_format(parameter_space)
+        )
+        # 3. Configure the objective function.
+        self.client.configure_optimization(objective=self._convert_objective_to_ax_format(objective_config))
+        if optimizer_config:
+            self.client.set_generation_strategy(self._convert_generator_to_ax_format(optimizer_config))
+        self.generators = self._create_generator_mapping()
+
+    @staticmethod
+    def _create_generator_mapping():
+        """Create a mapping from string values to Generator enum members."""
+        from ax.modelbridge import Generators
+        return {member.value: member for member in Generators}
+
+    def _convert_parameter_to_ax_format(self, parameter_space):
+        """
+        Converts the parameter space configuration to Baybe format.
+        :param parameter_space: The parameter space configuration.
+        [
+            {"name": "param_1", "type": "range", "bounds": [1.0, 2.0], "value_type": "float"},
+            {"name": "param_2", "type": "choice", "bounds": ["a", "b", "c"], "value_type": "str"},
+            {"name": "param_3", "type": "range", "bounds": [0 10], "value_type": "int"},
+        ]
+        :return: A list of Baybe parameters.
+        """
+        from ax import RangeParameterConfig, ChoiceParameterConfig
+        ax_params = []
+        for p in parameter_space:
+            if p["type"] == "range":
+                ax_params.append(
+                    RangeParameterConfig(
+                        name=p["name"],
+                        bounds=tuple(p["bounds"]),
+                        parameter_type=p["value_type"]
+                    ))
+            elif p["type"] == "choice":
+                ax_params.append(
+                    ChoiceParameterConfig(
+                        name=p["name"],
+                        values=p["bounds"],
+                        parameter_type=p["value_type"],
+                    )
+                )
+        return ax_params
+
+    def _convert_objective_to_ax_format(self, objective_config: list):
+        """
+        Converts the objective configuration to Baybe format.
+        :param parameter_space: The parameter space configuration.
+        [
+            {"name": "obj_1", "minimize": True, "weight": 1},
+            {"name": "obj_2", "minimize": False, "weight": 2}
+        ]
+        :return: Ax objective configuration. "-cost, utility"
+        """
+        objectives = []
+        for obj in objective_config:
+            obj_name = obj.get("name")
+            minimize = obj.get("minimize", True)
+            weight = obj.get("weight", 1)
+            sign = "-" if minimize else ""
+            objectives.append(f"{sign}{weight} * {obj_name}")
+        return ", ".join(objectives)
+
+    def _convert_generator_to_ax_format(self, optimizer_config):
+        """
+        Converts the optimizer configuration to Ax format.
+        :param optimizer_config: The optimizer configuration.
+        :return: Ax generator configuration.
+        """
+        from ax.generation_strategy.generation_node import GenerationStep
+        from ax.generation_strategy.generation_strategy import GenerationStrategy
+        generators = self._create_generator_mapping()
+        step_1 = optimizer_config.get("step_1", {})
+        step_2 = optimizer_config.get("step_2", {})
+        step_1_generator = step_1.get("model", "Sobol")
+        step_2_generator = step_2.get("model", "BOTorch")
+        generator_1 = GenerationStep(model=generators.get(step_1_generator), num_trials=step_1.get("num_samples", 5))
+        generator_2 = GenerationStep(model=generators.get(step_2_generator), num_trials=step_2.get("num_samples", -1))
+        return GenerationStrategy(steps=[generator_1, generator_2])
+
+    def suggest(self, n=1):
+        trial_index, params = self.client.get_next_trials(1).popitem()
+        self.trial_index = trial_index
+        return params
+
+    def observe(self, results):
+        self.client.complete_trial(
+            trial_index=self.trial_index,
+            raw_data=results
+        )
+
+    @staticmethod
+    def get_schema():
+        return {
+            "parameter_types": ["range", "choice"],
+            "multiple_objectives": True,
+            # "objective_weights": True,
+            "optimizer_config": {
+                "step_1": {"model": ["Sobol", "Uniform", "Factorial", "Thompson"], "num_samples": 5},
+                "step_2": {"model": ["BoTorch", "SAASBO", "SAAS_MTGP", "Legacy_GPEI", "EB", "EB_Ashr", "ST_MTGP", "BO_MIXED", "Contextual_SACBO"]}
+            },
+        }
+
+    def append_existing_data(self, existing_data):
+        """
+        Append existing data to the Ax experiment.
+        :param existing_data: A dictionary containing existing data.
+        """
+        from pandas import DataFrame
+        if not existing_data:
+            return
+        if isinstance(existing_data, DataFrame):
+            existing_data = existing_data.to_dict(orient="records")
+        parameter_names = [i.get("name") for i in self.parameter_space]
+        objective_names = [i.get("name") for i in self.objective_config]
+        for name, value in existing_data.items():
+            # First attach the trial and note the trial index
+            parameters = {name: value for name in existing_data if name in parameter_names}
+            trial_index = self.client.attach_trial(parameters=parameters)
+            raw_data = {name: value for name in existing_data if name in objective_names}
+            # Then complete the trial with the existing data
+            self.client.complete_trial(trial_index=trial_index, raw_data=raw_data)
+
+
+if __name__ == "__main__":
+    # Example usage
+    optimizer = AxOptimizer(
+        experiment_name="example_experiment",
+        parameter_space=[
+            {"name": "param_1", "type": "range", "bounds": [0.0, 1.0], "value_type": "float"},
+            {"name": "param_2", "type": "choice", "bounds": ["a", "b", "c"], "value_type": "str"}
+        ],
+        objective_config=[
+            {"name": "objective_1", "minimize": True},
+            {"name": "objective_2", "minimize": False}
+        ],
+        optimizer_config={
+            "step_1": {"model": "Sobol", "num_samples": 5},
+            "step_2": {"model": "BoTorch"}
+        }
+    )
+    print(optimizer._create_generator_mapping())

ivoryos-1.2.2/ivoryos/optimizer/base_optimizer.py

@@ -0,0 +1,65 @@
+### ivoryos/optimizers/base.py
+
+from abc import ABC, abstractmethod
+
+
+
+class OptimizerBase(ABC):
+    def __init__(self, experiment_name:str, parameter_space: list, objective_config: dict, optimizer_config: dict):
+        """
+        :param experiment_name: arbitrary name
+        :param parameter_space: list of parameter names
+        [
+            {"name": "param_1", "type": "range", "bounds": [1.0, 2.0], "value_type": "float"},
+            {"name": "param_2", "type": "choice", "bounds": ["a", "b", "c"], "value_type": "str"},
+            {"name": "param_3", "type": "range", "bounds": [0 10], "value_type": "int"},
+        ]
+        :param objective_config: objective configuration
+                [
+            {"name": "obj_1", "minimize": True, "weight": 1},
+            {"name": "obj_2", "minimize": False, "weight": 1}
+        ]
+        :param optimizer_config: optimizer configuration
+        optimizer_config={
+            "step_1": {"model": "Random", "num_samples": 10},
+            "step_2": {"model": "BOTorch"}
+        }
+        """
+        self.experiment_name = experiment_name
+        self.parameter_space = parameter_space
+        self.objective_config = objective_config
+        self.optimizer_config = optimizer_config
+
+    @abstractmethod
+    def suggest(self, n=1):
+        pass
+
+    @abstractmethod
+    def observe(self, results: dict):
+        """
+        observe
+        :param results: {"objective_name": "value"}
+        """
+        pass
+
+    @abstractmethod
+    def append_existing_data(self, existing_data):
+        pass
+
+    @staticmethod
+    def get_schema():
+        """
+        Returns a template for the optimizer configuration.
+        """
+        return {
+            "parameter_types": ["range", "choice"],
+            "multiple_objectives": True,
+            # "objective_weights": True,
+            "optimizer_config": {
+                "step_1": {"model": [], "num_samples": 10},
+                "step_2": {"model": []}
+            },
+        }
+
+
+