The core of the Jax-Geneweaver Python library
Project description
Geneweaver Core
The Geneweaver Core Python library provides shared foundational functionality for the Geneweaver project. It is a dependency of all other Geneweaver Python libraries, and is not intended to be used directly.
Installation
The Geneweaver Core library is available on PyPI and can be installed with pip:
pip install geneweaver-core
If you are using Poetry, you can add the Geneweaver Core library to your project with:
poetry add geneweaver-core
Overview
This package is structured so as to share an import path with other geneweaver
packages. This allows you to install
the package and import it without having to worry about the package name. For example, if you install the geneweaver-core
package, as well as the geneweaver-db
package, you can import the geneweaver
package and access both libraries:
from geneweaver import core, db
The Geneweaver Core library provides the following functionality:
-
geneweaver.core.schema
: Pydantic schema definitions -
geneweaver.core.enum
: Enumerations -
geneweaver.core.config
: Configuration managementGeneweaverBaseSettings
: Base Settings class to inherit from for your own package's configuration classesGeneweaverCoreSettings
: Configuration class for Geneweaver Core settings
-
geneweaver.core.exc
: Geneweaver shared exceptionsGeneweaverException
: Base exception class for GeneweaverGeneweaverError
: Base error class for GeneweaverGeneweaverWarning
: Base warning class for Geneweaver
-
geneweaver.core.pase
: Geneweaver file parsing functionalitybatch
: Functions for parsing a batch filescore
: Functions for parsing a scorecsv
: Functions for parsing a CSV filexlsx
: Functions for parsing an Excel fileenum
: Enumerations for file parsingexceptions
: Exceptions for file parsingutils
: Utility functions for file parsing
Planned Functionality
geneweaver.core.logging
: Shared logging managementgeneweaver.core.utils
: Shared utility functions
Acknowledgements
This project was developed by the Computational Systems and Synthetic Biology Center at the Jackson Laboratory in conjunction with the Baylor University Computational Biology and Bioinformatics Program.
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