Add Python examples, How to Use, and Data License to FastAPI docs

[Copilot]

The API lacked usage documentation, code examples, and license information in the Swagger UI — making it difficult for users to get started or understand data provenance.

Changes

• app/core/config.py: Expanded DESCRIPTION to clearly explain what CLEAN is and what the API exposes.

• app/main.py: Added three new markdown sections to the FastAPI app description (visible at /api/v1/docs):

  • How to Use — Base URL, endpoint list, and orientation for new users.
  • Python Examples — Six requests-based snippets covering common query patterns:
    • Search by organism / EC number
    • Filter by confidence score and curation status
    • CSV download
    • Typeahead suggestions
    • EC number lookup
  • Data License — CC BY 4.0 for UniProt data, required citation for CLEAN predictions (Yu et al., Science 2023), MIT for API source.

Example snippet (search by organism)

import requests

BASE_URL = "https://fastapi.cleandb.mmli2.ncsa.illinois.edu/api/v1"

response = requests.get(f"{BASE_URL}/search", params={"organism": "Homo sapiens"})
response.raise_for_status()
data = response.json()
for record in data["data"]:
    print(record["uniprot"], record["predicted_ec"])

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• openenzymedb-api.platform.moleculemaker.org
  • Triggering command: /home/REDACTED/work/_temp/ghcca-node/node/bin/node /home/REDACTED/work/_temp/ghcca-node/node/bin/node --enable-source-maps /home/REDACTED/work/_temp/copilot-developer-action-main/dist/index.js (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

Original prompt

---

This section details on the original issue you should resolve

<issue_title>Examples, How To Use, License</issue_title>
<issue_description>As a user, I would like to have access to the following related to the CLEANDB-API:

1. Example Queries for FASTAPI: Similar to what we have had present for OpenEnzyme Database
   here under "Python Examples": https://openenzymedb-api.platform.moleculemaker.org/api/v1/docs

2. Basic "How to Use" Instructions, to be added to the front-end FAQ Page, as part of an "API" tab: https://cleandb.frontend.staging.mmli2.ncsa.illinois.edu/about

Similar to what we have present for OpenEnzymeDB, here: https://openenzymedb.platform.moleculemaker.org/about/api
and here: https://openenzymedb-api.platform.moleculemaker.org/api/v1/docs

3. Basic License Page for the API,

Similar to what we have present for OpenEnzymeDB here, under "data license": https://openenzymedb-api.platform.moleculemaker.org/api/v1/docs

and here: https://openenzymedb.platform.moleculemaker.org/about/license</issue_description>

<agent_instructions>As a user, I would like to have access to the following related to the CLEANDB-API:

Example Queries for FASTAPI: Similar to what we have had present for OpenEnzyme Database
here under "Python Examples": https://openenzymedb-api.platform.moleculemaker.org/api/v1/docs

Basic "How to Use" Instructions, to be added to the front-end FAQ Page, as part of an "API" tab: https://cleandb.frontend.staging.mmli2.ncsa.illinois.edu/about

Similar to what we have present for OpenEnzymeDB, here: https://openenzymedb.platform.moleculemaker.org/about/api
and here: https://openenzymedb-api.platform.moleculemaker.org/api/v1/docs

Basic License Page for the API,
Similar to what we have present for OpenEnzymeDB here, under "data license": https://openenzymedb-api.platform.moleculemaker.org/api/v1/docs

and here: https://openenzymedb.platform.moleculemaker.org/about/license</agent_instructions>

Comments on the Issue (you are @copilot in this section)

• Fixes Examples, How To Use, License #12

---

✨ Let Copilot coding agent set things up for you — coding agent works faster and does higher quality work when set up for your repo.