Binette

What's Changed

This release contains no specific changes to the codebase, but includes final changes to the JOSS paper (PR 26) and also updates and fixes minor details in the tutorial section of the documentation (PR 27 & 28).


**Full Changelog**: https://github.com/genotoul-bioinfo/Binette/compare/v1.0.2...v1.0.3

What's Changed

- **New Tutorial**: Added a tutorial that walks through how to use Binette with real data. (from PR 23 )
- **Better Bin Set Naming**: Improved how bin set names are inferred from input directories or tables. (from PR 25)

- **New Output Files**:
- The directory `input_bins_quality_reports` is now created in the output repository, which stores quality reports for the initial bin sets. This helps compare how much Binette improves the bins compare to the input bins. (from PR 25)

- **Refactoring**:
- Cleaned up some typing issues flagged by Pylance.
- Switched from `os.path` to `pathlib` for better path handling.

**Full Changelog**: https://github.com/genotoul-bioinfo/Binette/compare/v1.0.1...v1.0.2

What's Changed

* Improve error management to provide clear message when the contigs input and bin tables do not match. (PR 12, issue 11)
* FASTA file selection in the bin directory is now based on file extensions. Previously, all files in the directory were expected to be bins in FASTA format. The extensions to search for can be specified with `--fasta_extensions`. By default, `fasta`, `.fna`, and `.fa` are considered. (Added in PR 16, issue 14)
* Added more unit tests to increase test coverage.

**Full Changelog**: https://github.com/genotoul-bioinfo/Binette/compare/v1.0.0...v1.0.1

First official release of Binette. :rocket:

**Full Changelog**: https://github.com/genotoul-bioinfo/Binette/compare/v0.1.7...1.0.0

* Added unit tests and coverage (4).
* Introduced documentation hosted on Read the Docs: https://binette.readthedocs.io (#5).
* Implemented a workflow to automate the publication of Binette on PyPI (5).

**Full Changelog**: https://github.com/genotoul-bioinfo/Binette/compare/v0.1.6...v0.1.7

A minor change in how to retrieve binette version in binette.py to fix error in bioconda recipe: https://github.com/bioconda/bioconda-recipes/pull/42477