Merge remote-tracking branch 'origin/main' into feat/ipy-magic

.github/workflows/build.yml

@@ -0,0 +1,17 @@
+name: build
+on: [push]
+
+jobs:
+  # build docker container
+  build:
+    runs-on: ubuntu-latest
+    steps:
+
+    - name: checkout files in repo
+      uses: actions/checkout@main
+
+    - name: update jupyter dependencies with repo2docker
+      uses: jupyterhub/repo2docker-action@master
+      with:
+        DOCKER_USERNAME: ltalirz
+        NO_PUSH: true

.github/workflows/push.yml

@@ -0,0 +1,20 @@
+name: push
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  # push to Dockerhub
+  build:
+    runs-on: ubuntu-latest
+    steps:
+
+    - name: checkout files in repo
+      uses: actions/checkout@main
+
+    - name: update jupyter dependencies with repo2docker
+      uses: jupyterhub/repo2docker-action@master
+      with:
+        DOCKER_USERNAME: ltalirz
+        DOCKER_PASSWORD: ${{ secrets.DOCKER_PASSWORD }}

README.md

@@ -1,17 +1,76 @@
-# Run Calculations with an Large Language Model
+# Run Calculations with a Large Language Model
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jan-janssen/comp-mat-sci-llm/HEAD)
 [![Open-with-Voila](https://img.shields.io/badge/Open%20with-Voila-4eafa0.svg)](https://mybinder.org/v2/gh/jan-janssen/comp-mat-sci-llm/main?urlpath=/voila/render/7_voila.ipynb)
+[![Docker](https://img.shields.io/badge/docker-%230db7ed.svg?style=for-the-badge&logo=docker&logoColor=white)](https://hub.docker.com/r/ltalirz/comp-mat-sci-llm)
 
+The computational chemistry and computational materials science community have both developed a great number of 
+simulation tools. Still these tools typically require either rather cryptic input files or at least a fundamental 
+programming experience in a language like Python to control them. Furthermore, many questions are only answered in the 
+documentation, like: 
+* Which physical units does the code use? 
+* Which inputs match to which variables in the equations in the paper? 
+* ...
 
+We address this challenge by developing a Large Language Model (LLM) extension which provides LLM agents to couple the 
+LLM to scientific simulation codes and calculate physical properties from a natural language interface.
+
+## Installation 
+### Via pip 
+While our package is not yet available on the Python Package Index, you can install it directly using:
+```
+pip install git+https://github.com/jan-janssen/comp-mat-sci-llm.git
+```
+The pip package includes optional dependencies for the `mace` model and the `jupyter` integration.  
+
+### Via conda 
+As the conda package is not yet available on Anaconda.org still you can clone the repository and install the 
+dependencies directly from conda using the [environment.yml](environment.yml) file. 
 
-## Set up environment for local development
 Prerequisites:
 - [git](https://git-scm.com/)
 - [conda](https://docs.conda.io/en/latest/miniconda.html)
 
-
-```bash
+ ```bash
 git clone https://github.com/jan-janssen/comp-mat-sci-llm
 cd comp-mat-sci-llm
 conda env create -f environment.yml --name comp-mat-sci-llm
 ```
+
+### As Docker Container 
+Work in Progress 
+
+## Using the package
+The package currently provides two interfaces, one for python / jupyter users to query the large language model directly
+from a python environment and a second web based interface. 
+
+### Python Interface
+```python
+import os
+from llm_compmat import dialog_python
+
+dialog_python(OPENAI_API_KEY=os.getenv("OPENAI_API_KEY", None))
+```
+Here the `OPENAI_API_KEY` environment variable referrers to your [OpenAI API token](https://help.openai.com/en/articles/4936850-where-do-i-find-my-openai-api-key).
+
+### Webbased interface
+The webbased interface can be started using [voila](https://voila.readthedocs.io):
+```
+voila 7_voila.ipynb
+```
+This opens a small application in the webbrowser:
+![voila application](docs/images/voila_screenshot.png)
+
+## Contributors
+* [Yuan Chiang](https://github.com/chiang-yuan)
+* [Giuseppe Fisicaro](https://github.com/giuseppefisicaro)
+* [Jan Janssen](https://github.com/jan-janssen)
+* [Greg Juhasz](https://github.com/gjuhasz)
+* [Sarom Leang](https://github.com/saromleang)
+* [Bernadette Mohr](https://github.com/Bernadette-Mohr)
+* [Utkarsh Pratiush](https://github.com/utkarshp1161)
+* [Francesco Ricci](https://github.com/fraricci)
+* [Leopold Talirz](https://github.com/ltalirz)
+* [Pablo Andres Unzueta](https://github.com/pablo-unzueta)
+* [Trung Vo](https://github.com/btrungvo)
+* [Gabriel Vogel](https://github.com/GaVogel)
+* [Luke Zondagh](https://github.com/Luke-Zondagh)