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AIBS Informatics Core

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Overview

The AIBS Informatics Core library provides a collection of core functionalities and utilities for various projects at the Allen Institute for Brain Science. This library includes modules for handling environment configurations, data models, executors, and various utility functions.

Features

  • Collections - Specialized collection classes including DeepChainMap, Tree, ValidatedStr, and various enum base classes
  • Environment - EnvBase for creating isolated namespaces based on environment type and name
  • Models - Base classes for data serialization/deserialization using Pydantic
  • Executors - Base classes for creating and running task executors with input/output validation
  • Utils - Comprehensive utility functions for file operations, logging, hashing, JSON handling, and more

Quick Start

Installation

pip install aibs-informatics-core

Basic Usage

from aibs_informatics_core.env import EnvBase

# Create an environment namespace
env_base = EnvBase('dev-projectX')
env_base.prefixed('my_resource', 'blue')  # 'dev-projectX-my_resource-blue'

Modules

Module Description
Collections Collection classes and utilities (DeepChainMap, Tree, ValidatedStr, enums)
Env Environment configuration and namespace management
Executors Base executor classes and CLI utilities
Models Data model base classes and serialization protocols
Utils Utility functions for file operations, logging, hashing, and more

Contributing

Any and all PRs are welcome. Please see CONTRIBUTING.md for more information.

License

This software is licensed under the Allen Institute Software License, which is the 2-clause BSD license plus a third clause that prohibits redistribution and use for commercial purposes without further permission. For more information, please visit Allen Institute Terms of Use.