Allelefinder

Release Notes

Bug Fixes

- **allele_tools/methods.py**: Corrected the filtered allele numbers. This fix addresses a bug where the filtered allele numbers were not correct.

- **tests/test_9_stec_allele_translate_find.py**: Corrected the filtered allele numbers in the test. This change updates the test to reflect the corrected filtered allele numbers.

How to Upgrade

To upgrade to this version, pull the latest changes from the main branch and rebuild your application.

Known Issues

No known issues at this time.

Changes

Refactor

- Updated the STEC class in `allele_tools/stec.py`. These updates include importing a new function, changing how existing functions are called and handled, and changing some values. These changes improve the functionality and flexibility of the STEC class.

Chore

- Updated the version number to 0.4.6 in `allele_tools/version.py`.
- Decreased the minimum acceptable amino acid allele length for stx2B from 84 to 82 aa in several test files (`tests/test_1_allele_translate_reduce.py`, `tests/test_2_allele_updater.py`, `tests/test_5_stec_allele_find.py`, `tests/test_9_stec_allele_translate_find.py`).
- Updated the expected test results in `tests/test_5_stec_allele_find.py` and `tests/test_9_stec_allele_translate_find.py` to reflect these changes.

Bug Fixes

- None

New Features

- None

Fixes
- Improved gene name handling in `stec.py` for better readability and added additional gene name variations to the `length_dict` in the `translate_reduce` function.
- Corrected gene name handling in `allele_profiler`. The `allele_comprehension` dictionary comprehension in `read_profile` function now keeps the original gene names instead of modifying them. Also, adjusted the indentation in `parseable_blast_outputs` function.
- Adjusted gene name capitalization in `methods.py` to ensure compatibility between protein and gene names. This includes converting gene names to lowercase and adjusting the capitalization of protein names.

Tests
- Updated expected results in `test_5_stec_allele_find.py`, `test_6_stec_aa_allele_find.py`, and `test_9_stec_allele_translate_find.py` to reflect the changes made in the gene and protein naming schemes.

Chores
- Bumped version to 0.4.5 in `version.py` to reflect the new changes made in the gene and protein naming schemes.

Please note that these release notes are based on the commit messages and may not include all changes. For a complete list of changes, please refer to the commit history.

Features
- Renamed the `CONDA_BLD_PATH` environment variable to `CONDA_PKG_PATH` in the GitHub Actions workflow. This change provides a more accurate name for the path where the Conda packages are stored.

Fixes
- Updated the paths in the `anaconda upload` commands and the `actions/upload-artifact` step to use the new `CONDA_PKG_PATH` environment variable. This ensures that these steps are looking in the correct location for the Conda packages.

Chore
- Updated the version number in `allele_tools/version.py` to `0.4.4`.

Features
- Updated the GitHub Actions workflow to include `CONDA_BLD_PATH` environment variable. This change allows the workflow to correctly locate the built Conda packages for upload.
- Added a step in the workflow to install `conda-verify`. This tool provides additional checks on Conda packages.

Fixes
- Updated the file paths in the `anaconda upload` commands to use the `CONDA_BLD_PATH` environment variable. This fixes an issue where the commands were failing because they couldn't find the files.

Miscellaneous
- Updated the version number in `allele_tools/version.py` to `0.4.3`.

Fixes
- Corrected the version replacement in `meta.yaml`. The 'v' prefix from the version string is now removed during the replacement.
- Updated the `anaconda-client` installation step in the GitHub Actions workflow. The path to the `anaconda-client` scripts is now added to the `PATH` environment variable.

Breaking Changes
- The version replacement in `meta.yaml` now removes the 'v' prefix from the version string. This may affect any processes or systems that rely on the previous format of the version string in `meta.yaml`.