init release commit

.github/workflows/pytest.yml

@@ -0,0 +1,46 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python application
+
+on:
+  push:
+    tags:
+      - requires_test
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+      with:
+          lfs: 'true'
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+    - uses: actions/cache@v3
+      id: cache
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.*') }}
+        restore-keys: | 
+          ${{ runner.os }}-pip-
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest
+        pip install pytest-timeout
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Test with pytest
+      env:
+        OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
+      run: |
+       pip install '.[streamlit]'
+       pytest tests --timeout=400

.github/workflows/test_and_deploy.yaml

@@ -62,7 +62,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: "3.x"
+          python-version: "3.9"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

.gitignore

@@ -43,3 +43,8 @@ share/python-wheels/
 .installed.cfg
 *.egg
 MANIFEST
+
+
+*.pyc
+__pycache__/
+*~

.streamlit/config.toml

@@ -0,0 +1,9 @@
+[browser]
+gatherUsageStats = true
+
+[theme]
+primaryColor="#ea4461"
+backgroundColor="#000000"
+secondaryBackgroundColor="#5a165a"
+textColor="#ffffff"
+font="monospace"

Makefile

@@ -0,0 +1,4 @@
+export streamlit_app=True
+app:
+
+	streamlit run app.py --server.fileWatcherType none 

README.md

@@ -1,29 +1,23 @@
 <p align="center">
-<img src="https://images.squarespace-cdn.com/content/v1/57f6d51c9f74566f55ecf271/733ec9c2-52bc-4fcb-aefb-1516d0a50c19/amadeuslogo.png?format=1500w" width="95%">
+<img src="https://images.squarespace-cdn.com/content/v1/57f6d51c9f74566f55ecf271/8555eac6-6af0-4538-bda4-c1a8a2c7bed8/amadeusgpt_logo.png?format=1500w" width="95%">
 </p>
 
 🪄 **We turn natural language descriptions of behaviors into machine-executable code.**
 
 - We use large language models (LLMs) to bridge natural language and behavior analysis.
-- This work is accepted to **NeuRIPS2023!** 
-- For more details, check out our arXiv preprint version **[AmadeusGPT: a natural language interface for interactive animal behavioral analysis](https://arxiv.org/abs/2307.04858)** by [Shaokai Ye](https://github.com/yeshaokai), [Jessy Lauer](https://github.com/jeylau), [Mu Zhou](https://github.com/zhoumu53), [Alexander Mathis](https://github.com/AlexEMG) & [Mackenzie W. Mathis](https://github.com/MMathisLab).
-
+- This work is accepted to **NeuRIPS2023!** Read the paper, [AmadeusGPT: a natural language interface for interactive animal behavioral analysis](https://www.google.com/search?q=amadeusgpt+openreview&sca_esv=590699485&rlz=1C5CHFA_enCH1059CH1060&ei=K1N6ZaHdKvmrur8PosOOkAo&ved=0ahUKEwjhnta83I2DAxX5le4BHaKhA6IQ4dUDCBE&uact=5&oq=amadeusgpt+openreview&gs_lp=Egxnd3Mtd2l6LXNlcnAiFWFtYWRldXNncHQgb3BlbnJldmlldzIHECEYoAEYCjIHECEYoAEYCki2HVDfAliOHHACeACQAQGYAYMDoAHaGaoBCDEuMTEuMS40uAEDyAEA-AEBwgIFECEYqwLCAggQABiABBiiBMICCBAAGIkFGKIE4gMEGAEgQYgGAQ&sclient=gws-wiz-serp#:~:text=AmadeusGPT%3A%20a%20natural,net%20%E2%80%BA%20pdf)
 - Like this project? Please consider giving us a star ⭐️!
 
-## Demo AmadeusGPT🎻
-
-  - 🔮 App: [https://amadeusgpt.kinematik.ai/](https://amadeusgpt.kinematik.ai/)
-
-  - We thank [Kinematik AI](https://kinematik.ai/) for partnering with us on hosting the demo. This is an academic research project demo 💕
-
-https://github.com/AdaptiveMotorControlLab/AmadeusGPT/assets/28102185/61bc447c-29d4-4295-91be-23e5a7f10386
-
-- Please note that you need an [openAI API key](https://platform.openai.com/account/api-keys), which you can easily create [here](https://platform.openai.com/account/api-keys).
+## Install & Run AmadeusGPT🎻
 
-## License 
-
-  AmadeusGPT is license under the Apache-2.0 license.
-  -  Please note several key dependencies have their own licensing. Please carefully check the license information for [DeepLabCut](https://github.com/DeepLabCut/DeepLabCut) (LGPL-3.0 license), [SAM](https://github.com/facebookresearch/segment-anything) (Apache-2.0 license), [CEBRA](https://github.com/AdaptiveMotorControlLab/CEBRA) (Non-Commercial), etc...
+- AmadeusGPT is a Python package hosted on pypi. You can create a virtual env (conda, etc, see below*) or Docker and run:
+```python
+pip install amadeusgpt[streamlit]
+```
+- If you want the demo, you will also need demo files that are supplied in our repo (see below**), so please git clone the repo. Then, to launch the Demo App execute:
+```python
+make app
+```
 
 ## Citation
 
@@ -37,8 +31,33 @@ https://github.com/AdaptiveMotorControlLab/AmadeusGPT/assets/28102185/61bc447c-2
       year={2023},
       url={https://openreview.net/forum?id=9AcG3Tsyoq},
 ```
+- arXiv preprint version **[AmadeusGPT: a natural language interface for interactive animal behavioral analysis](https://arxiv.org/abs/2307.04858)** by [Shaokai Ye](https://github.com/yeshaokai), [Jessy Lauer](https://github.com/jeylau), [Mu Zhou](https://github.com/zhoumu53), [Alexander Mathis](https://github.com/AlexEMG) & [Mackenzie W. Mathis](https://github.com/MMathisLab).
+
+### Install tips
+- *Make a new conda env: `conda create --name amadeusGPT` then run `conda activate amadeusGPT` or you can also use our supplied conda if you git cloned the repo: `conda env create -f amadesuGPT.yml` then pip install amadeusGPT once created/lauched.
+- **Git clone this repo: so please open a terminal, we recommend to download into Documents (so type `cd Documents`) and run `git clone https://github.com/AdaptiveMotorControlLab/AmadeusGPT.git` Then go into the dir (`cd AmadeusGPT`)
+- If you want to use SAM, you need to download the weights. Otherwise you will see the following message in the app: `Cannot find SAM checkpoints. Skipping SAM`. Download them and add to "static" directory: wget https://dl.fbaipublicfiles.com/segment_anything/sam_vit_b_01ec64.pth
+
+###  Install trouble shooting:
+- If you hit an error during installing on an M1/M2 Macbook with installing HDF5, run `conda install h5py` in your conda env.
+- If you launch the app and get an ffmpeg error, `RuntimeError: No ffmpeg exe could be found. Install ffmpeg on your system, or set the IMAGEIO_FFMPEG_EXE environment variable.` try running `conda install ffmpeg`.
+- If you have an M1/M2 chip and use CEBRA within AmadeusGPT, and you get this error: `RuntimeError: Device type MPS is not supported for torch.Generator() api` run `pip install --update torch`
+
+## Hosted Demo:
+
+  - 🔮 App: [https://amadeusgpt.kinematik.ai/](https://amadeusgpt.kinematik.ai/)
+  - Please note that you need an [openAI API key](https://platform.openai.com/account/api-keys), which you can easily create [here](https://platform.openai.com/account/api-keys).
+
+https://github.com/AdaptiveMotorControlLab/AmadeusGPT/assets/28102185/61bc447c-29d4-4295-91be-23e5a7f10386
+
+## License 
+
+AmadeusGPT is license under the Apache-2.0 license.
+  -  🚨 Please note several key dependencies have their own licensing. Please carefully check the license information for [DeepLabCut](https://github.com/DeepLabCut/DeepLabCut) (LGPL-3.0 license), [SAM](https://github.com/facebookresearch/segment-anything) (Apache-2.0 license), [CEBRA](https://github.com/AdaptiveMotorControlLab/CEBRA) (Non-Commercial), etc...
+
 
 ## News
+- 🤩 Dec 2023, code released!
 - 🔥 Our work was accepted to NeuRIPS2023
 - 🧙‍♀️ Open-source code coming in the fall of 2023
 - 🔮 arXiv paper and demo released July 2023

__init__.py

@@ -0,0 +1 @@
+

amadeusgpt/__init__.py

@@ -1 +1,2 @@
-
+from amadeusgpt.implementation import AnimalBehaviorAnalysis
+from amadeusgpt.main import AMADEUS

amadeusgpt/amadeus_security.py

@@ -0,0 +1,26 @@
+import ast
+
+
+class IllegaActionError(Exception):
+    def __init__(self, message):
+        super().__init__(message)
+
+
+class LoopChecker(ast.NodeVisitor):
+    def visit_While(self, node):
+        raise IllegaActionError("Dangerous! Infinite or long loop detected: while loop")
+
+    def visit_Call(self, node):
+        if isinstance(node.func, ast.Name) and node.func.id == "range":
+            if len(node.args) > 0 and isinstance(node.args[0], ast.Num):
+                loop_count = node.args[0].n
+                if loop_count > 1000:
+                    raise IllegaActionError(
+                        "Dangerous! Infinite or long loop detected: range() loop"
+                    )
+        self.generic_visit(node)
+
+
+def check_code(code):
+    tree = ast.parse(code)
+    LoopChecker().visit(tree)

amadeusgpt/brains/__init__.py

@@ -0,0 +1,6 @@
+from .base import BaseBrain
+from .diagnosis import DiagnosisBrain
+from .explainer import ExplainerBrain
+from .code_generator import CodeGenerationBrain
+from .self_debug import SelfDebugBrain
+from .rephraser import RephraserBrain