Ensembl-genomio

What's Changed
* Add ps for genomio container by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/454
* Adding CICD trigger to allow non versioned release genomio container builds by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/455
* Update commit tag format when rebuilding docker containers by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/457
* Sync add-version with main (updated CICD container trigger) by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/458
* Add --version to every entry point by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/456


**Full Changelog**: https://github.com/Ensembl/ensembl-genomio/compare/v1.5.0...v1.6.0

What's Changed
* Update database.factory.main() function to test all its contents by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/449
* Update GenomIO to avoid too many positional arguments by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/450
* Add new module for DB meta data querying by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/451
* Refactor genome_metadata dump module by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/453


**Full Changelog**: https://github.com/Ensembl/ensembl-genomio/compare/v1.4.0...v1.5.0

What's Changed
* Remove patch build nextflow modules by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/444
* Remove patch_build scripts by Dishalodha in https://github.com/Ensembl/ensembl-genomio/pull/446
* Use parents feature instead of loop for subparsers by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/447
* Bugfix and output param name change by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/448


**Full Changelog**: https://github.com/Ensembl/ensembl-genomio/compare/v1.3.2...v1.4.0

What's Changed
* Manifest tests by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/434
* Old brc4 minor fixes by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/443
* Refactor assembly.status module by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/433
* Reconfigure how containers are used in nextflow pipelines by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/442


**Full Changelog**: https://github.com/Ensembl/ensembl-genomio/compare/V1.3.1...v1.3.2

What's Changed
* Fix for mkdocs deployment by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/440
* Bugfix mkdocs, minor version change (v1.3.1) by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/441


**Full Changelog**: https://github.com/Ensembl/ensembl-genomio/compare/v1.3.0...V1.3.1

What's Changed
* Rebase lcampbell/scripts_cleanup branch with main branch by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/409
* Convert chunk fasta script to module and remove gff3_extract_annotation entry point by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/408
* Dump with container by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/387
* Update/Fixes to container Dumper pipeline by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/412
* Dealing with bcbio-gff update to 0.7.1, using strand as a part of the location obj by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/414
* recovering after bcbio update from 1-based to 0-based starts by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/416
* Fix process name and mysql arguments by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/415
* fixing transposable_element JSON path in metaparser configs by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/417
* Bcbio update recovery by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/418
* Test manifest generate by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/411
* Test update description by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/410
* Mbarba/simpler acc by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/413
* adding ignored signatures to valid_structures by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/425
* Drop seq_region_name script, obsolete by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/421
* Add mysql optional dependencies relying on ensembl-utils tag by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/423
* Fix assert_called by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/426
* Upgrade to ensembl-py 2.1 by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/427
* Bugfix: run push commits on main branch by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/429
* genomio.fasta.chunk fixed, refactored, tests added by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/430
* Require type hints in every method and function by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/431
* Fix URL in README by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/432
* Mbarba/test seqregion dump by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/420
* Update gff3overlap branch with main by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/435
* Transform standalone gff-overlaps.py script to module by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/422
* Black-ify overlaps fix cicd by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/436
* Upgrade ensembl-py to 2.1.2 to fix seq_region dump bug by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/437
* Tests for seq_region/prepare by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/424
* Revert relative paths to absolute paths so they work properly in pypi by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/438
* Increase genomio version to 1.3.0 by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/439


**Full Changelog**: https://github.com/Ensembl/ensembl-genomio/compare/v1.2.0...v1.3.0