scigantic

scigantic turns a dataset name into a notebook. Give it a Hugging Face dataset (owner/repo) or a Scigantic archive id and it opens a page on scigantic.com where the dataset is mounted read-only inside a hosted JupyterLab with a starter notebook. The same package can list and stream the files of a Hugging Face dataset locally over hf://, so you can look before you launch.

Install

pip install scigantic

Local streaming needs huggingface_hub:

pip install "scigantic[hf]"

Python 3.9 or newer. The base package has no dependencies.

python -m scigantic works the same as the scigantic command.

Open a dataset in the browser

Command line:

scigantic open hf:openadmet/cyp-challenge-train-test

This prints https://scigantic.com/hf/openadmet/cyp-challenge-train-test and opens it in your default browser. Add --no-browser to print the URL only, or --json to call the resolve API and print its reply (the archive id, and whether this request created it).

Python:

import scigantic

url = scigantic.url_for("openadmet/cyp-challenge-train-test")  # no network
scigantic.open("openadmet/cyp-challenge-train-test")  # opens the browser
info = scigantic.resolve("openadmet/cyp-challenge-train-test")  # {"archiveId": ..., "created": ...}

Accepted references: hf:owner/repo, hf://datasets/owner/repo, owner/repo, a https://huggingface.co/datasets/... URL (with or without a file path), a Scigantic archive id, or a https://scigantic.com/archive/<id> URL.

Inside a Jupyter kernel scigantic.open() shows the URL as a clickable link instead of trying to open a browser on the kernel's machine.

The first request for a dataset creates its catalog entry. Later requests return the existing one. If the dataset cannot be served, resolve raises SciganticError whose reason is one of private, gated, disabled, not_found, license, too_large, invalid_repo, rate_limited or upstream_error. Network errors and 502/503/504 answers are retried three times before reason is network or error; a 429 carries retry_after in seconds when the API sent one.

Stream files locally with hf://

scigantic files hf:openadmet/cyp-challenge-train-test

from scigantic import hf

hf.files("openadmet/cyp-challenge-train-test")
# ['README.md', 'cyp-challenge-TRAIN_inhibition.csv', ...]

with hf.open("openadmet/cyp-challenge-train-test", "cyp-challenge-TRAIN_inhibition.csv") as f:
    head = f.read(4096)

Reads go through huggingface_hub.HfFileSystem as HTTP range requests, so nothing is downloaded in full. Hugging Face rate limits apply. files, open and info take revision= and token=. A gated or missing repository raises SciganticError with reason gated or not_found, the same codes the hosted path uses.

Catalog search

scigantic search "mass spectrometry"
scigantic info 15b4d4e6-d24e-5344-9789-9501cded9c3c

scigantic.catalog.search(query, limit=10) and scigantic.catalog.get(archive_id) expose the same read-only API from Python.

What the hosted notebook requires

The landing page and the catalog API need no account. Running the notebook needs a free Scigantic account. Only public Hugging Face datasets with a permissive licence are served (for example MIT, Apache-2.0, CC BY, CC0, ODC). Private, gated and disabled repositories, and datasets whose card carries no recognised licence, are refused with the reason above and a link back to the source.

Configuration and exit codes

Setting	Effect
SCIGANTIC_API_URL, --api-url	catalog API base, default https://api.scigantic.com
SCIGANTIC_SITE_URL, --site-url	landing page base, default https://scigantic.com
--timeout	seconds per API request, default 10

Exit codes: 0 success; 1 the catalog refused or could not be reached (the reason is printed to stderr); 2 the reference could not be parsed.

Licence

MIT. See LICENSE.