Python Scientific OS

FastAPI backend equivalent of the TypeScript scientific OS server.

Setup

python -m venv .venv
source .venv/bin/activate
pip install -e .
cp .env.example .env

Add OPENAI_API_KEY and optionally TAVILY_API_KEY to .env.

By default, local development uses SQLite and local file storage, so Docker is optional.

For the full optional stack, install extras:

pip install -e ".[all]"

Package Usage

Install the package in editable mode while developing:

pip install -e .

Install optional Postgres/MinIO support:

pip install -e ".[postgres,s3]"

Build a wheel:

python -m pip wheel . --no-deps -w dist

Install the built wheel:

pip install dist/python_scientific_os-0.1.0-py3-none-any.whl

Start the server

Start the FastAPI server from the project root:

scientific-os-server --reload --port 8000

The API will be available at http://127.0.0.1:8000.

You can also run the app directly with Uvicorn:

uvicorn scientific_os.main:app --reload --port 8000

CLI Chat

With the server running, send a prompt from another terminal:

scientific-os "Create a simple protocol for extracting strawberry DNA."

The CLI prints the response and writes returned IDs, including conversationId and jobId, to stderr. Use that ID to continue the same conversation:

scientific-os \
  --conversation-id 00000000-0000-0000-0000-000000000000 \
  "Make it safer for a classroom demo."

Replace the placeholder UUID with the real conversationId.

You can also pipe prompt text into the CLI:

echo "Create a protocol for testing soil pH." | scientific-os

Use --pretty to print the full JSON response:

scientific-os --pretty "List the protocol sections you generated."

Each chat request is tracked as a job. List recent jobs:

scientific-os --list-jobs

Fetch a single job:

scientific-os --job-id 00000000-0000-0000-0000-000000000000

Filter jobs by status:

scientific-os --list-jobs --status failed

If the server is running somewhere else, pass a custom base URL:

scientific-os --server http://127.0.0.1:8001 "Hello"

Without installing the package, the CLI still works as a module:

python -m scientific_os.cli "Hello"

HTTP Chat

Send a chat request to the local server:

curl -sS http://127.0.0.1:8000/api/chat \
  -H "Content-Type: application/json" \
  -d '{
    "messages": [
      {
        "role": "user",
        "content": "Create a simple protocol for extracting strawberry DNA."
      }
    ]
  }'

To continue a conversation, include the conversationId returned by the previous response:

curl -sS http://127.0.0.1:8000/api/chat \
  -H "Content-Type: application/json" \
  -d '{
    "conversationId": "00000000-0000-0000-0000-000000000000",
    "messages": [
      {
        "role": "user",
        "content": "Make it safer for a classroom demo."
      }
    ]
  }'

Replace the placeholder UUID with the real conversationId.

Chat and protocol search requests are tracked as jobs. List recent jobs over HTTP:

curl -sS http://127.0.0.1:8000/api/jobs

Fetch a single job:

curl -sS http://127.0.0.1:8000/api/jobs/00000000-0000-0000-0000-000000000000

Optional Docker Services

To use Postgres/pgvector and MinIO instead, set these values in .env:

DATABASE_URL=postgresql://myuser:mypassword@localhost:5432/mydb
STORAGE_BACKEND=s3
S3_ENDPOINT=http://localhost:9000
S3_PUBLIC_ENDPOINT=http://localhost:9000

Then start the backing services with docker compose up -d.

The compatible API routes are:

• POST /api/chat
• GET /api/jobs
• GET /api/jobs/{job_id}
• GET /api/conversations
• GET /api/conversations/{conversation_id}
• GET /api/protocols/search
• GET /api/protocols/{protocol_id}