Binette

What's Changed

* Fix intermittent error caused by how Binette handles the pyfastx index. (Issue 49, PR 52).

**Full Changelog**: https://github.com/genotoul-bioinfo/Binette/compare/v1.1.0...v1.1.1

What's Changed

- Updated Binette dependencies to align with CheckM2 v1.1.0 (44). Binette now runs on Python 3.12 (previously 3.8) and uses Diamond >=2.1 (previously 2.0.4), fixing 13.
- Changed license from MIT to GNU GPL to comply with CheckM2's licensing terms (44).
- Fixed pyfastx index setup for the contig FASTA file when writing final bins (45).

**Full Changelog**: https://github.com/genotoul-bioinfo/Binette/compare/v1.0.5...v1.1.0

What's Changed

- **Fix an error when writing input bin metrics:** Resolved an issue where identical input bins from different bin sets were not properly dereplicated when writing metrics, producing an unscored bin error. The dereplicated bins are now exclusively used, ensuring accurate tracking and avoiding such errors. (Reported in issues 34 and 39, fixed in PR 36)
- **Fix incorrect input proteins management:** When dealing with input protein file, Binette was not expecting proteins from unbinned contigs. The input protein file is now filtered to exclude genes from unbinned contigs, ensuring only protein data from contigs within the input bins is used. (See PR 37, reported in issue 35)
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Additional Updates
- Temporary files in `<outdir>/temporary_files/` are now compressed, optimizing storage. (PR 37)
- The `pyfastx` index for contig files is stored in `<outdir>/temporary_files/` instead of alongside the assembly file, ensuring cleaner directory management. (PR 37)

**Full Changelog**: https://github.com/genotoul-bioinfo/Binette/compare/v1.0.4...v1.0.5

What's Changed

- **Possibility to provide precomputed gene sequences**: You can now use the `--genes` argument to provide precomputed protein sequences, bypassing the gene-calling step. (See PR 31, requested in issue 30, [documentation](https://binette.readthedocs.io/en/latest/usage.html#providing-precomputed-protein-sequences))
- **Code formatting with Black**: Added the Black formatter to ensure a consistent and clean codebase. (PR 32)

**Full Changelog**: https://github.com/genotoul-bioinfo/Binette/compare/v1.0.3...v1.0.4

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