Allelefinder

Features

- **Upload Wheel Distribution as Release Asset**: Added a new step in the GitHub Actions workflow to upload the wheel distribution (.whl file) as a release asset in addition to the source distribution (.tar.gz file). This provides users with more options for installing the package.

- **Include requirements.txt in Source Distribution**: Created a new MANIFEST.in file to include the requirements.txt file in the source distribution. This ensures that the package dependencies are included when the package is installed from the source distribution.

Breaking Changes

- The release assets now include both the source distribution and the wheel distribution. Users who were previously only expecting the source distribution need to be aware of this change.

- The source distribution now includes the requirements.txt file. Users who were previously installing the package without this file need to be aware of this change.

- The version number has been updated to 0.1.9. Users need to update their dependencies if they are specifically using version 0.1.8.

Release Notes

New Features

- **Automated Package Building and Publishing**: We've implemented a new GitHub Actions workflow that automatically builds our Python package and publishes it to PyPI whenever a new release is created. This ensures that our users always have access to the latest version of our software as soon as it's released.

How It Works

- When a new release is created on GitHub, the workflow is triggered.
- The workflow sets up the necessary Python environment and installs the required dependencies.
- It then builds the Python package using `setup.py`.
- The built package is then published to PyPI using the `pypa/gh-action-pypi-publish` action.
- The details of the created release are fetched using the `bruceadams/get-release` action.
- The built package is uploaded as a release asset to the created release using the `actions/upload-release-asset` action.

- Updated CircleCI configuration for improved build and test process.
- Added new dependencies to support additional features.
- Enhanced documentation for better user guidance.
- Expanded and refactored test suite for improved code quality.
- Improved code readability across several modules.
- Updated gene naming scheme to use stx1/stx2 instead of ECs****.
- Added support for allele search of nucleotide query against amino acid database.

Decrease the minimum acceptable length of alleles:

self.length_dict = {
'ECs2973': 82,
'ECs2974': 313,
'ECs1205': 313,
'ECs1206': 84
}

Fix issue with allele naming

Add `allele_concatenate` functionality