https://github.com/thejacksonlaboratory/geneweaver-core

The core library for GeneWeaver projects.
https://github.com/thejacksonlaboratory/geneweaver-core

analysis functional-genomics genomic-data-science genomics schemas

Last synced: 2 months ago
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The core library for GeneWeaver projects.

• Host: GitHub
• URL: https://github.com/thejacksonlaboratory/geneweaver-core
• Owner: TheJacksonLaboratory
• License: apache-2.0
• Created: 2023-11-15T18:08:50.000Z (almost 2 years ago)
• Default Branch: main
• Last Pushed: 2025-04-30T15:41:39.000Z (6 months ago)
• Last Synced: 2025-04-30T16:39:11.663Z (6 months ago)
• Topics: analysis, functional-genomics, genomic-data-science, genomics, schemas
• Language: Python
• Homepage: https://geneweaver.org
• Size: 429 KB
• Stars: 2
• Watchers: 6
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

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README

          
# Geneweaver Core

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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:

```bash

pip install geneweaver-core

```

If you are using Poetry, you can add the Geneweaver Core library to your project with:

```bash

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:

```python

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 management

  * `GeneweaverBaseSettings`: Base Settings class to inherit from for your own package's configuration classes

  * `GeneweaverCoreSettings`: Configuration class for Geneweaver Core settings

* `geneweaver.core.exc`: Geneweaver shared exceptions

  * `GeneweaverException`: Base exception class for Geneweaver

  * `GeneweaverError`: Base error class for Geneweaver

  * `GeneweaverWarning`: Base warning class for Geneweaver

* `geneweaver.core.pase`: Geneweaver file parsing functionality

  * `batch`: Functions for parsing a batch file

  * `score`: Functions for parsing a score

  * `csv`: Functions for parsing a CSV file

  * `xlsx`: Functions for parsing an Excel file

  * `enum`: Enumerations for file parsing

  * `exceptions`: Exceptions for file parsing

  * `utils`: Utility functions for file parsing

#### Planned Functionality

* `geneweaver.core.logging`: Shared logging management

* `geneweaver.core.utils`: Shared utility functions