Ensembl-genomio

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

What's Changed
* Add Python build and publication to PyPI pipeline by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/389
* Update ensembl.io.genomio.__version__ to match repository's version by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/395
* bugfix: publish to ensembl-genomio, not ensembl-utils by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/396
* Remove unused dependency and only depend on PyPI libraries by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/397
* Disha/update nextflow utils by Dishalodha in https://github.com/Ensembl/ensembl-genomio/pull/394
* DBconnectionLite update by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/398
* Drop some brc4 modules by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/399
* Move gt container in main config by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/401
* Move singularity enabled in slurm/lsf profiles by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/400
* Update nf-validation to nf-schema by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/402
* Rearrange scripts, drop unused ones by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/404
* Set same behaviour as later Nextflow versions (23.05+) by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/403
* Minor codebase review looking for typos and other missing elements by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/405
* Documentation, badges and version updates by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/406
* Use shields badge for branch checks by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/407


**Full Changelog**: https://github.com/Ensembl/ensembl-genomio/compare/v1.1...v1.2.0