Latest updates

.github/workflows/ci.yml

@@ -29,7 +29,7 @@ jobs:
       - name: Set up uv
         uses: astral-sh/setup-uv@v3
         with:
-          version: "0.4.x"
+          version: "0.5.x"
           enable-cache: true
 
       - name: Install dependencies
@@ -58,7 +58,7 @@ jobs:
       - name: Set up uv
         uses: astral-sh/setup-uv@v3
         with:
-          version: "0.4.x"
+          version: "0.5.x"
           enable-cache: true
 
       - name: Install locked versions of dependencies

.gitignore

@@ -2,6 +2,7 @@
 __pycache__/
 *.py[cod]
 *$py.class
+**.DS_STORE
 
 # C extensions
 *.so
@@ -160,9 +161,24 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
-
-# Test notebook
+src/yellowhammer/yue_test.ipynb
+src/yellowhammer/test.ipynb
 examples/Demo_yue.ipynb
+examples/Demo_yue2.ipynb
 examples/yue_examples
+
+# Test notebook
 examples/FA-Mn-H2PO2.raw
-src/yellowhammer/yue_test.ipynb
+examples/Demo_flagship.ipynb
+examples/HL1-5_5-90_30min.xrdml
+# examples/IMG_1648.jpg
+prompts/deprecated
+examples/llm_trace.txt
+examples/Demo_anthropic.ipynb
+examples/Demo_multimodal.ipynb
+examples/Demo_openai.ipynb
+examples/Demo_pydantic copy.ipynb
+examples/Demo_pydantic.ipynb
+
+# AI generated docs
+MULTIMODAL*

README.md

@@ -6,17 +6,28 @@
 
 </div>
 
-A continuation of the [LLM hackathon](https://www.eventbrite.com/e/llm-hackathon-for-applications-in-materials-and-chemistry-tickets-868303598437) project, [*yeLLowhaMMer: A Multi-modal Tool-calling Agent for Accelerated Research Data Management*](https://github.com/bocarsly-group/llm-hackathon-2024).
+This project is a continuation of [LLM hackathon](https://www.eventbrite.com/e/llm-hackathon-for-applications-in-materials-and-chemistry-tickets-868303598437) project, [*yeLLowhaMMer: A Multi-modal Tool-calling Agent for Accelerated Research Data Management*](https://github.com/bocarsly-group/llm-hackathon-2024).
 
-This repository will explore using the Jupyter AI plugin to provide an agentic interface to [*datalab*](https://github.com/datalab-org/datalab), with the idea of having this as an additional UI that *datalab* users can use to interact with their data, either deployed for their instance, or run locally.
+This repo explores the use of a agentic assistant for [*datalab*](https://github.com/datalab-org/datalab) using Jupyter cell magics as an UI, allowing *datalab* users to interact with the agent during their standard data processing and analysis workflow.
 
-## Initial development tasks
+See the [example notebook](examples/Demo_pydantic.ipynb) for a demonstration.
 
-- [ ] Reproduce the hackathon project with the Jupyter AI plugin, probably by extending the `%%ai` cell magic to something like `%%yellowhammer` that includes the yellowhammer system prompt, and guides through the registration of a *datalab* API key and any provided LLM API keys.
-- [ ] Use yellowhammer to generate API examples for the underlying [*datalab-python-api*](https://github.com/datalab-org/datalab-python-api) package.
+## Current status
+- [x] Port project from langchain to pydantic-AI
+- [x] Create `%%llm` line/cell magic that passes messages to the datalab agent
+- [ ] Agent guides user through the registration of a *datalab* API key and any provided LLM API keys.
+- [x] Write agentic tools for interactions with *datalab* API.
+- [x] Include code-writing tool that can query the underlying API directly with [*datalab-python-api*](https://github.com/datalab-org/datalab-python-api) package.
+- [ ] Update datalab API for direct data retrieval from backend
 - [ ] Consider deploying this as a JupyterHub that *datalab* instances can link to directly.
 - [ ] Integrate the results much more closely into *datalab* itself, i.e., attaching notebooks to the relevant samples, and recording the provenance of AI generated data recording.
 
+## Project structure
+- [`src/yellowhammer/llm_pydantic.py`](src/yellowhammer/llm_pydantic.py): Defines the agent and tools.
+- [`src/yellowhammer/magics.py`](src/yellowhammer/magics.py): Defines Jupyter magic commands.
+- [`prompts`](prompts/): System prompts for each agent
+- [`examples/Demo_pydantic.ipynb`](examples/Demo_pydantic.ipynb): Example notebook demonstrating usage
+
 ## Installation
 
 This repository uses [`uv`](https://docs.astral.sh/uv/) for the entire packaging workflow.