Tools for parsing and storing workflow nodes with support for pyiron and Python functions
Project description
Sim Atlas
Search and discovery platform for simulation nodes — Python functions, workflow definitions, and pyiron nodes used in scientific computing.
Repository layout
sim_atlas/
├── backend/ FastAPI server (sim-atlas-backend)
├── frontend/ Search & discovery SPA, served at /
├── web_ide/ Visual workflow composer SPA, served at /ide
├── toolkit/ Client-side parser & upload library (sim-atlas-toolkit)
└── docs/ Architecture docs and ADRs
How it works
- Researchers run the toolkit on their machine to parse their Python packages and push node metadata to the server.
- The backend stores metadata, generates AI embeddings and AI-refined docstrings on demand, and exposes a REST API and MCP tool.
- The frontend and web_ide are React SPAs built into the backend's static directory and served by it.
Quickstart
1. Clone the repository and install it into a venv
cd <sim-atlas-env>
uv venv --python=3.12
uv pip install sim-atlas
2. Configure and start the backend
cd <sim-atlas-env>
uv run sim-atlas
On the first start the server will create a configuration file in the current working directory if it does not find one.
The API and both SPAs are now available at http://localhost:8000.
3. Generate an API token
Write access (uploading nodes) requires a JWT token:
cd <sim-atlas-env>
uv run sim-atlas-access-token "Your Name" "you@example.com"
export SIM_ATLAS_API_URL=http://localhost:8000/api/v1
export SIM_ATLAS_API_TOKEN=<token>
4. Upload nodes from a Python package
Load the environment with the modules you want to upload. Install the sim-atlas-toolkit into this environment. And upload the module. For example:
uv pip install sim-atlas-toolkit
uv run sim-atlas-upload --recursive filesystem mypackage.mymodule
5. Explore your newely created nodes
Head over to the webinterface and explore the nodes you uploaded:
http://localhost:8000
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