mondolib

Python library for Mondo.

Prerequisites

1. OAK Currently in order to understand how to use or code with this library you should understand the basics of OAK

2. Inputs The intended input of this lib is generally the editors file.

We recommend that this is converted into sqlite first for speed

robot convert -i mondo-edit.obo -o mondo-edit.owl
poetry run semsql make --docker mondo-edit.db

See the Makefile and tests/input for an example file

Installation

No PyPI yet

from this repo, do a

poetry install

If Poetry is not already installed, follow these instructions:

• create a virual environment (venv or conda)
• activate the virtual environment
• run pipx install poetry
  • install pipx (as needed) following these details
• clone the mondolib repo
• run poetry install from within mondolib directory Note: this repo is known to work with Python 3.9 (and may also work with 3.10 or 3.11 or 3.12) as of 21-Mar-2024.

Modules

QC

This has intentionally bespoke and mondo-unique checks