6. Changelog¶

6.1. Version 0.23.0 (August 2026)¶

Containers

Added recipes: repeatmasker 4.2.2 and 4.2.4, seqkit 2.13.0, seqtk 1.5.0, barrnap 1.10.6, cufflinks 2.2.1, hicexplorer 3.7.6.
repeatmasker 4.2.4 is 43% smaller than 4.2.2 (290 MB against 511 MB) for the same Dfam 4.0 coverage, mostly by stripping the debug symbols that conda-forge and bioconda ship in their shared libraries. It also fixes RepeatProteinMask, which no earlier image could run, and pins the RepeatMasker version: the image published as 4.2.2 actually contains 4.2.4.
DupMasker is no longer advertised for repeatmasker. It requires a duplicon library that is not distributed any more, so it never worked.

Bug fixes

damona build created its temporary image in damona.cfg, a file rather than a directory, and failed with NotADirectoryError.
Listing an environment crashed when its bin/ directory held files Damona did not create, such as hand-made symbolic links. Those are now detected and skipped.

Performance

damona stats queried Zenodo once per software, which is slow and hits the API rate limit. Lookups are now batched (40 records per request) and cached for 24h.

Documentation

Per-software README.md files are generated; an optional NOTES.md next to a recipe is now appended to them, so hand-written caveats survive regeneration.
Reworked the user and developer guides, moved the changelog out of the README, and declared support for Python 3.11 and 3.12.

CLI & User Experience

Added a rich footer to damona --help with author, documentation, issues, and Zenodo links.
Added a welcome box displayed on first damona invocation in each shell session (bash, zsh, fish).
Removed redundant info from the help docstring and shell welcome message.
Removed the debug message "Using Damona executable: …" from shell scripts.
Improved damona search with fallback recommendation for bundled binaries.

Registry & New Recipes

Added new recipes: spades 4.1.0, kallisto 0.51.1, pbmm2 1.16.99, STAR 2.7.11b, nextdenovo 2.5.2, deepvariant 1.10.0, diamond 2.1.24, pbsv 2.11.0, bamqc, idr 2.1.0, unicycler 0.5.1, bioconvert 1.2.0.
Added broken flag to mark buggy releases (hidden from search but still installable).

Documentation

Updated damona --help and damona search bwa screenshots in README and user guide.
Fixed Sphinx warnings in doc/conf.py: removed deprecated get_html_theme_path, unsupported theme options, added sphinx_click extension, updated source_suffix format.
Updated and improved README files for individual recipes.