ivoryos 0.1.17__tar.gz → 0.1.19__tar.gz

{ivoryos-0.1.17 → ivoryos-0.1.19}/LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2023-2024 Ivory Zhang | Hein Lab
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-THE SOFTWARE.
+MIT License
+
+Copyright (c) 2023-2024 Ivory Zhang | Hein Lab
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

{ivoryos-0.1.17 → ivoryos-0.1.19}/MANIFEST.in

@@ -1,8 +1,8 @@
-graft ivoryos/static
-graft ivoryos/templates
-graft ivoryos/routes
-global-exclude *.pyc
-
-# exclude examples
-prune ivoryos/example
+graft ivoryos/static
+graft ivoryos/templates
+graft ivoryos/routes
+global-exclude *.pyc
+
+# exclude examples
+prune ivoryos/example
 prune ivoryos/docs

{ivoryos-0.1.17/ivoryos.egg-info → ivoryos-0.1.19}/PKG-INFO

@@ -1,178 +1,174 @@
-Metadata-Version: 2.2
-Name: ivoryos
-Version: 0.1.17
-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
-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
-Dynamic: author
-Dynamic: author-email
-Dynamic: description
-Dynamic: description-content-type
-Dynamic: home-page
-Dynamic: license
-Dynamic: requires-dist
-Dynamic: summary
-
-[![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)
-
-![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/ivoryos.png)
-# ivoryOS: interoperable Web UI for self-driving laboratories (SDLs)
-"plug and play" web UI extension for flexible SDLs.
-
-## Table of Contents
-- [Description](#description)
-- [System requirements](#system-requirements)
-- [Installation](#installation)
-- [Instructions for use](#instructions-for-use)
-- [Demo](#demo)
-- [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). 
-This web UI aims to ease up the control of any Python-based SDLs by displaying functions and parameters for initialized modules dynamically. 
-The modules can be hardware API, high-level functions, or experiment workflow.
-With the least modification of the current workflow, user can design, manage and execute their experimental designs and monitor the execution process. 
-
-## System requirements
-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 >=3.7 for best compatibility.
-### Python dependencies
-This software is compatible with the latest versions of all dependencies. 
-- bcrypt~=4.0
-- Flask-Login~=0.6
-- Flask-Session~=0.8
-- Flask-SocketIO~=5.3
-- Flask-SQLAlchemy~=3.1
-- SQLAlchemy-Utils~=0.41
-- Flask-WTF~=1.2
-- python-dotenv==1.0.1
-- openai (optional ~=1.53)
-- ax-platform (optional ~=0.3 or ~=0.4 for Python>=3.9)
-
-## Installation
-```bash
-pip install ivoryos
-```
-or
-```bash
-git clone https://gitlab.com/heingroup/ivoryos.git
-cd ivoryos
-pip install -e .
-```
-
-The installation may take 10 to 30 seconds to install. The installation time may vary and take up to several minutes, depending on the network speed, computer performance, and virtual environment settings.
-
-## Instructions for use
-### Quick start
-In your SDL script, use `ivoryos(__name__)`. 
-```python
-import ivoryos
-
-ivoryos.run(__name__)
-```
-### Login
-Create an account and login (local database)
-### 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.
-
-
-### Additional settings
-#### 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.
-
-#### 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.
-
-```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
-ivoryos.run(__name__, logger="logger name")
-```
-or
-```python
-ivoryos.run(__name__, logger=["logger 1", "logger 2"])
-```
-#### Offline (design without hardware connection)
-After one successful connection, a blueprint will be automatically saved and made accessible without hardware connection. In a new Python script in the same directory, use `ivoryos.run()` to start offline mode.
-
-```python
-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`,
-addresses will be available on terminal.
-```Python
-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
-
-### Deck function and web form 
-![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/demo.gif)
-
-### Text-to-code demo
-![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/text-to-code.gif)
-
-### Directory structure
-
-When you run the application for the first time, it will automatically create the following folders and files in the same directory:
-
-- **`ivoryos_data/`**: Main directory for application-related data.
-  - **`ivoryos_data/config_csv/`**: Contains iteration configuration files in CSV format.
-  - **`ivoryos_data/llm_output/`**: Stores raw prompt generated for the large language model.
-  - **`ivoryos_data/pseudo_deck/`**: Contains pseudo-deck `.pkl` files for offline access.
-  - **`ivoryos_data/results/`**: Used for storing results or outputs during workflow execution.
-  - **`ivoryos_data/scripts/`**: Holds Python scripts compiled from the visual programming script design.
-
-- **`default.log`**: Log file that captures application logs.
-- **`ivoryos.db`**: Database file that stores application data locally.
-
-
-### Demo video
-Intro + Tutorial + Demo with PurPOSE platform
-https://youtu.be/dFfJv9I2-1g 
-
-
-## Authors and Acknowledgement
-Ivory Zhang, Lucy Hao
-
-Authors acknowledge all former and current Hein Lab members for their valuable suggestions. 
+Metadata-Version: 2.1
+Name: ivoryos
+Version: 0.1.19
+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
+Platform: UNKNOWN
+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)
+
+![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/ivoryos.png)
+# ivoryOS: interoperable Web UI for self-driving laboratories (SDLs)
+"plug and play" web UI extension for flexible SDLs.
+
+## Table of Contents
+- [Description](#description)
+- [System requirements](#system-requirements)
+- [Installation](#installation)
+- [Instructions for use](#instructions-for-use)
+- [Demo](#demo)
+- [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). 
+This web UI aims to ease up the control of any Python-based SDLs by displaying functions and parameters for initialized modules dynamically. 
+The modules can be hardware API, high-level functions, or experiment workflow.
+With the least modification of the current workflow, user can design, manage and execute their experimental designs and monitor the execution process. 
+
+## System requirements
+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 >=3.7 for best compatibility.
+### Python dependencies
+This software is compatible with the latest versions of all dependencies. 
+- bcrypt~=4.0
+- Flask-Login~=0.6
+- Flask-Session~=0.8
+- Flask-SocketIO~=5.3
+- Flask-SQLAlchemy~=3.1
+- SQLAlchemy-Utils~=0.41
+- Flask-WTF~=1.2
+- python-dotenv==1.0.1
+- openai (optional ~=1.53)
+- ax-platform (optional ~=0.3 or ~=0.4 for Python>=3.9)
+
+## Installation
+```bash
+pip install ivoryos
+```
+or
+```bash
+git clone https://gitlab.com/heingroup/ivoryos.git
+cd ivoryos
+pip install -e .
+```
+
+The installation may take 10 to 30 seconds to install. The installation time may vary and take up to several minutes, depending on the network speed, computer performance, and virtual environment settings.
+
+## Instructions for use
+### Quick start
+In your SDL script, use `ivoryos(__name__)`. 
+```python
+import ivoryos
+
+ivoryos.run(__name__)
+```
+### Login
+Create an account and login (local database)
+### 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.
+
+
+### Additional settings
+#### 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.
+
+#### 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.
+
+```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
+ivoryos.run(__name__, logger="logger name")
+```
+or
+```python
+ivoryos.run(__name__, logger=["logger 1", "logger 2"])
+```
+#### Offline (design without hardware connection)
+After one successful connection, a blueprint will be automatically saved and made accessible without hardware connection. In a new Python script in the same directory, use `ivoryos.run()` to start offline mode.
+
+```python
+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`,
+addresses will be available on terminal.
+```Python
+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
+
+### Deck function and web form 
+![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/demo.gif)
+
+### Text-to-code demo
+![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/text-to-code.gif)
+
+### Directory structure
+
+When you run the application for the first time, it will automatically create the following folders and files in the same directory:
+
+- **`ivoryos_data/`**: Main directory for application-related data.
+  - **`ivoryos_data/config_csv/`**: Contains iteration configuration files in CSV format.
+  - **`ivoryos_data/llm_output/`**: Stores raw prompt generated for the large language model.
+  - **`ivoryos_data/pseudo_deck/`**: Contains pseudo-deck `.pkl` files for offline access.
+  - **`ivoryos_data/results/`**: Used for storing results or outputs during workflow execution.
+  - **`ivoryos_data/scripts/`**: Holds Python scripts compiled from the visual programming script design.
+
+- **`default.log`**: Log file that captures application logs.
+- **`ivoryos.db`**: Database file that stores application data locally.
+
+
+### Demo video
+Intro + Tutorial + Demo with PurPOSE platform
+https://youtu.be/dFfJv9I2-1g 
+
+
+## Roadmap
+
+- [x] Allow plugin pages ✅  
+- [ ] pause, resume, abort current and pending workflows
+- [ ] snapshot version control
+- [ ] dropdown input
+- [ ] show line number option
+
+
+## Authors and Acknowledgement
+Ivory Zhang, Lucy Hao
+
+Authors acknowledge all former and current Hein Lab members for their valuable suggestions. 
+
+