v1.1

What's Changed

• Small fix from black to hackathon_Jan24 by @ens-LCampbell in #278
• Mbarba/lcampbell hack by @MatBarba in #311
• Adding Unit test on assembly module, submodule download.py by @ens-LCampbell in #306
• ENA request: fix new URL + better check by @MatBarba in #323
• Dump GCF accession if provider is RefSeq by @MatBarba in #324
• Reverse default in CLI for ID generation by @MatBarba in #325
• Add unit test for ensembl.io.genomio.genome_metadata.prepare module by @JAlvarezJarreta in #312
• adding duplicated organism metadata to mz genmetaconf by @vsitnik in #327
• Add xref test, fix small bug by @MatBarba in #328
• Test GFF restructure functions by @MatBarba in #317
• Support for miRNA genes by @MatBarba in #330
• Add ensembl.io.genomio.database.factory unit test by @JAlvarezJarreta in #322
• Prepare genome metadata with datasets by @MatBarba in #326
• fixing BioSample typo and adding more RR/MVP related meta_key duplicates by @vsitnik in #331
• Fix for metaconf script by @ens-LCampbell in #335
• CICD when scripts are modified by @MatBarba in #336
• Revert temporary pytest version limit as pytest-workflow has now been fixed by @JAlvarezJarreta in #333
• Fix integrity error report by @MatBarba in #337
• Fix seq compare in integrity by @MatBarba in #338
• Addition of a new sub-module 'status' to assembly module. by @ens-LCampbell in #334
• Allow both translation and transcript ID in cap_protein.fasta by @JAlvarezJarreta in #339
• Set env variable to avoid connection error to OSID by @JAlvarezJarreta in #341
• Simplify code to avoid using flags by @JAlvarezJarreta in #342
• GFF3 simplifier refactoring and tests by @MatBarba in #332
• Update from Hackathon/feb24 by @MatBarba in #329
• Fix description by @MatBarba in #344
• Fix assembly provider for annotation by @MatBarba in #346
• RefSeq gene IDs update by @MatBarba in #345
• Fix after merge by @MatBarba in #347
• Better integrity check by @MatBarba in #343
• Mbarba/load using xref by @MatBarba in #349
• Store RefSeq gene xref by @MatBarba in #348
• Mbarba/disha genbank update by @MatBarba in #350
• primary_transcript as a supported feature and remove TIGRFAM xrefs by @Dishalodha in #351
• Bug fix for assembly tracker by @ens-LCampbell in #352
• Update status.py datasets version - 16.12.1 by @ens-LCampbell in #353
• Set GitLab CI/CD runner tag to ensure the correct job environment by @JAlvarezJarreta in #354
• Disha/hack feb/update tests genbank by @Dishalodha in #321
• Replace ensembl-py tmp_dir fixture by pytest tmp_path by @JAlvarezJarreta in #355
• Add documentaiton badge with quick link to GitHub pages by @JAlvarezJarreta in #357
• Move archive utils to ensembl-py by @JAlvarezJarreta in #356
• Update documentation logo by @JAlvarezJarreta in #361
• Minor updates of our codebase by @JAlvarezJarreta in #359
• Bugfix: keep ensembl.io as the path root by @JAlvarezJarreta in #362
• Bugfix: new logo was wrongly downloaded by @JAlvarezJarreta in #363
• Update fonts to match Ensembl beta's by @JAlvarezJarreta in #364
• Disha/primary transc fix by @Dishalodha in #358
• Remove outdated project layout dir tree by @ens-LCampbell in #365
• Allow mapping mRNA IDs from the Apollo FASTA file to protein IDs by @MatBarba in #366
• External db map fix by @vsitnik in #368
• Keep transcript ID if the gene ID is conserved on a gene with one transcript by @MatBarba in #367
• mRNA without gene by @MatBarba in #369
• Gene segment info from the CDS by @MatBarba in #370
• Add no_fail option to integrity for nextflow to not die by @MatBarba in #371
• Mbarba/match synonym by @MatBarba in #372
• Remove transcript "variant X" when transferring to genes by @MatBarba in #373
• Disha/nextflow notify by @Dishalodha in #379
• Add ensembl-utils and update documentation generation by @JAlvarezJarreta in #380
• Fix mkdocs issues by @JAlvarezJarreta in #382
• Seq_region lrg support by @MatBarba in #241
• Disha/nextflow utils by @Dishalodha in #384
• Disable notification in main nextflow.config by @MatBarba in #386
• Update GenomIO to use ensembl-utils v0.3.0 by @JAlvarezJarreta in #388
• Run canonical transcripts at end of patch build by @MatBarba in #385
• Update code for Biopython 1.84 compatibility by @MatBarba in #391
• Update assembly tracker datasets docker URI to ensemblorg by @ens-LCampbell in #392
• Add ruff checks by @MatBarba in #393

Full Changelog: 1.0...v1.1