v1.3.0

What's Changed

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

Full Changelog: v1.2.0...v1.3.0