Bakta

This is the ninth minor release (v1.9) introducing user-provided feature regions and various minor improvements.

Compatible database scheme version: 5

New features
* Support _a priori_ user-provided feature regions via `--regions` either in Genbank or GFF3 format (currently, only `CDS` features are supported). CDS coordinates are imported, supersede _de novo_ predicted `CDS`, and are subject to the regular internal annotation workflow. To provide functional annotation, as well use `--proteins`: 216 245 247 250 259 (Thanks marade PengfanZhang simone-pignotti thorellk)

Improvements
* Extract & export CRISPR spacer & repeat sequences: 171 249 (Thanks alexweisberg)
* Add support for Pyrodigal v3: 240 244 (Thanks jsgounot)
* Replace HMMER with PyHMMER: 219 (Thanks jhahnfeld)
* Re-activate parallel pyrodigal gene prediction: 252 (Thanks althonos)
* Introduce auxiliary scripts: 246 251 (Thanks AhmedElsherbini)
* Add Podman wrapper script: bd50faabfe7a2cbad7c63f453baae854503a9d46
* Update dependencies to latest versions: 3260441ed181176c71e39125cb58a1e0df69b7dc 33c02f92305c51d3741172d3851bedc7463f83c8 a1d2ffeb465cc9afbb124fe903a877b3ef562d22 b2656722dd5199416b308291c6c7188ccd4f9f58 1a2c48ee177800e21d3ff3e2356fc253407ecd65

Fixes
* Fix PyPI CD: 231
* Add missing `--force` parameter to Docker wrapper script: f39434ed670d1310a144df9defcd3f556e36ffbf
* Fix wrong runtime report: 243

**Full Changelog**: https://github.com/oschwengers/bakta/compare/v1.8.2...v1.9.0

This is the second v1.8 patch release (v1.8.2).

Improvements:
- Replacd HMMER by PyHMMER: https://github.com/oschwengers/bakta/commit/3415e89924dc3699651cc959414f3c7bd5954de7 (Thanks jhahnfeld)
- Refactored & improved CI scripts
- Refactored the code
- Tweaked code to expand required BioPython versions: https://github.com/oschwengers/bakta/commit/6a88c4bbbd2b2f2c7a7fb30f9de4bd2a67a980c0 (Thanks alexweisberg)
- Deactivated `--force` parameter for the current working directory`: https://github.com/oschwengers/bakta/commit/a039bece7a8d76ed0d5cb1eeb94dd01b63d4403d
- Added Pyrodigal to dependency checks: https://github.com/oschwengers/bakta/commit/17bcfc99c48f5c221ee94e5259d52ab0074ad41a

Bug Fixes:
- Fixed and improved the CWL wrapper: 221 229 230 (Thanks bartns & jjkoehorst)

This is the first v1.8 patch release (v1.8.1) catching up an overlooked PR.

Improvements:
- Added all valid expert system hits to the final `dbxrefs` and `JSON` results: 198 199 (Thanks davidtong28)

Important:
199 introduced a breaking change in the JSON data structure of the `feature->expert` section. `expert` was changed from a dictionary (`expert system` -> `hit`) to a flat list of expert hits now having a new `type` field.

This is the eighth minor release (v1.8) introducing a new output option and various minor improvements.

Compatible database scheme version: 5

Improvements:
- Introduced a new `--force` option explicitly allowing to overwrite existing data: 200 (Thanks Dx-wmc)
- Increased sensitivity of protein sequence expert system: 197 (Thanks davidtong28)
- Improved compatibility of FNA output with NCBI Bankit Submission: 201 (Thanks menickname)
- Improved `--plasmid` parameter functionality: 201 https://github.com/oschwengers/bakta/commit/426bfd39c1f83cf8ed240b61be2b867452bcf573
- Introduced output of `bakta_proteins` full annotation results as JSON: 204 (Thanks Rridley7)
- Refactored QC and description of imported genome sequences: https://github.com/oschwengers/bakta/commit/af835b4313d3cb5931d68616d71d0d2623d13afc

Fixes:
- Fixed rare occasions of wrong `5'` / `3'` ("prime") characters in product descriptions: 215 (Thanks axbazin)

This is the seventh minor release (v1.7) introducing a lightweight database version, various gene symbol improvements, and a metagenome mode.

Compatible database scheme version: 5

New features:
- Introduced a lightweight database version: https://github.com/oschwengers/bakta/pull/196 (Thanks tseemann))
- Introduced an operon gene symbol harmonization feature: https://github.com/oschwengers/bakta/pull/190
- Introduced a simple metagenome mode: https://github.com/oschwengers/bakta/issues/191
- Added IS transposase to protein expert system: https://github.com/oschwengers/bakta/issues/10

Improvements:
- Improved CDS gene symbols: https://github.com/oschwengers/bakta/issues/186
- Amended tRNA & rRNA gene symbols: https://github.com/oschwengers/bakta/issues/192
- Amended uppercase ncRNA gene symbols: https://github.com/oschwengers/bakta/issues/194
- Added model IDs and dbxrefs to expert annotation systems: https://github.com/oschwengers/bakta/issues/183 (Thanks davidtong28)
- Updated to Pyrodigal v2.1.0 fixing a bug in the SD motif-detection on reverse contig edges: https://github.com/oschwengers/bakta/commit/599fe709a090331ab6fb7bd3398a5a8ca9899688

Fixes:
- Fixed system-wide db path stored in software volume: https://github.com/oschwengers/bakta/pull/177 (Thanks standage)

This is the first v1.6 patch release (v1.6.1) fixing 2 bugs.

Improvements:
- Deactivated Circos' max contig limit: https://github.com/oschwengers/bakta/commit/0962df7243002875e8126aac85dd55b05034bdb6

Bug fixes:
- Fixed P(y)rodigal `meta` mode for short sequences and provided training files: https://github.com/oschwengers/bakta/issues/175 (Thanks pimarin)
- Fixed an unbound variable in `bakta_plot`: https://github.com/oschwengers/bakta/issues/174 (Thanks Rridley7)