v1.0.4

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)
• Code formatting with Black: Added the Black formatter to ensure a consistent and clean codebase. (PR #32)

Full Changelog: v1.0.3...v1.0.4

Binette v1.0.3

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: v1.0.2...v1.0.3

Binette v1.0.2

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: v1.0.1...v1.0.2

Binette v1.0.1

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: v1.0.0...v1.0.1

Binette v1.0.0

First official release of Binette. 🚀

Full Changelog: v0.1.7...1.0.0

Binette v0.1.7

• 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: v0.1.6...v0.1.7

Binette v0.1.6

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

Add usage and fix minor issue in N50 and length of bins in final bin table

This minor release includes the addition of a comprehensive usage section in the README.md, which aims to facilitate the usage of Binette (#2 ).
Additionally, it addresses a minor issue where the N50 and length values of the bin reported in the final bin table were incorrectly set to None.

Improve install

Minor release

• Simplify install of checkm2 using conda.
• Fix import bug
• update Readme accordingly

Binette v0.1.3

Add some github actions to check binette installation.
Follow checkm2 v1.0.2 release.