Common tools for all the repos at Dayhoff Labs
Project description
dayhoff-tools
A set of small, sharp tools for everyone at Dayhoff. Hosted on PyPi, so you can Poetry or pip install like everything else.
Installation
The base package includes minimal dependencies required for core CLI functionality (like job running):
pip install dayhoff-tools
# or
uv add dayhoff-tools
# or, for the special case of installing it in the DHT repo itself,
uv pip install -e .[full]
Optional Dependencies
You can install extra sets of dependencies using brackets. Available groups are:
core: Includes common data science and bioinformatics tools (biopython,boto3,docker,fair-esm,h5py,questionary).dev: Includes development and testing tools (black,pytest,pandas,numpy,torch, etc.).all: Includes all dependencies from bothcoreanddev.
Examples:
# Install with core dependencies
pip install 'dayhoff-tools[core]'
poetry add 'dayhoff-tools[core]'
# Install with all dependencies
pip install 'dayhoff-tools[all]'
poetry add 'dayhoff-tools[all]'
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