mini-classyfire 0.1.0

A lightweight, zero-dependency ClassyFire wrapper

Mini-Classyfire

A lightweight, zero-dependency Python client and CLI tool designed to batch-process and extract high-resolution chemical taxonomy classifications from the ClassyFire API.

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Key Features

• Zero Dependencies: Built entirely on Python's native standard library (urllib, json, csv). No external heavy frameworks required.
• Defensive Parsing Architecture: Dynamically inspects and normalizes unpredictable API schema variations (e.g., handling fields like molecular_framework or alternative_parents when they dynamically alternate between plain strings, nested dictionaries, or arrays).
• High-Resolution Taxonomy Capture: Extracts deep structural metadata, including direct_parent, subclass, and molecular_framework, rather than just top-level categories.
• Strict Upstream Rate-Limiting: Features an integrated throttling guard capped at ~6.6 requests per second to strictly honor ClassyFire's upstream limit (<10 req/s), preventing IP blocking or 429 Too Many Requests faults.
• Progressive Disk Flushing: Writes outputs to a structured CSV file row-by-row in real-time. If a network disruption occurs mid-batch, data fetched up to that exact second is safely preserved on disk.

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Project Architecture

mini_classifier/
│
├── src/
│   └── mini_classyfire/
│       ├── __init__.py
│       └── client.py
│
├── main.py
├── compounds.txt
└── pyproject.toml

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Usage

Run the bulk processor by passing an input text file containing one InChIKey per line:

Command Line Interface (CLI)

python main.py -f compounds.txt

Optional Arguments

You can explicitly override the default output destination using the -o or --output flag: Bash

python main.py -f compounds.txt -o custom_output_report.csv

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2. The LICENSE File

Create a separate text file named exactly LICENSE (no extension) in your root directory and paste this standard MIT text inside it. The placeholder name completely masks your real identity while granting open-source permissions:

MIT License

Copyright (c) 2026

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.