Breakfast

What's Changed
* Bump all deps, including python (>=3.11,<3.13) by matthuska in https://github.com/rki-mf1/breakfast/pull/24


**Full Changelog**: https://github.com/rki-mf1/breakfast/compare/v0.4.4...v0.4.5

This also required tweaking the python dependency to only allow 3.9 and 3.10 (rather than >= 3.9), because of scipy.

This is due to both bioconda and conda-forge not supporting Python 3.10 yet. See https://github.com/bioconda/bioconda-recipes/pull/35488 for details.

What's Changed
* Require Python 3.10+ only instead of 3.9 and 3.10 by matthuska in https://github.com/rki-mf1/breakfast/pull/16


**Full Changelog**: https://github.com/rki-mf1/breakfast/compare/v0.4.0...v0.4.1

What's Changed
* Add contributing docs (CONTRIBUTING.md) and update the README.md by matthuska in https://github.com/rki-mf1/breakfast/pull/7
* Feature/speedup submat batches by denisbeslic tweaked by matthuska in https://github.com/rki-mf1/breakfast/pull/9
* Create output cache dir if it doesn't exist. by matthuska in https://github.com/rki-mf1/breakfast/pull/15
* Add more tests for filtering mutations, more specific var-type options, option for controlling number of parallel threads (--jobs) by matthuska in https://github.com/rki-mf1/breakfast/pull/14
* Add nextclade DNA test data denisbeslic


**Full Changelog**: https://github.com/rki-mf1/breakfast/compare/v0.3.3...v0.4.0

Tiny fix to handle empty values in the column we are using as features (main the covsonar dna_profile column right now). Was causing a crash.