v1.5.0

What's Changed

• Update database.factory.main() function to test all its contents by @JAlvarezJarreta in #449
• Update GenomIO to avoid too many positional arguments by @JAlvarezJarreta in #450
• Add new module for DB meta data querying by @ens-LCampbell in #451
• Refactor genome_metadata dump module by @ens-LCampbell in #453

Full Changelog: v1.4.0...v1.5.0

v1.4.0

What's Changed

• Remove patch build nextflow modules by @JAlvarezJarreta in #444
• Remove patch_build scripts by @Dishalodha in #446
• Use parents feature instead of loop for subparsers by @JAlvarezJarreta in #447
• Bugfix and output param name change by @ens-LCampbell in #448

Full Changelog: v1.3.2...v1.4.0

v1.3.2

What's Changed

• Manifest tests by @MatBarba in #434
• Old brc4 minor fixes by @MatBarba in #443
• Refactor assembly.status module by @JAlvarezJarreta in #433
• Reconfigure how containers are used in nextflow pipelines by @ens-LCampbell in #442

Full Changelog: V1.3.1...v1.3.2

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

V1.3.1

What's Changed

• Fix for mkdocs deployment by @ens-LCampbell in #440
• Bugfix mkdocs, minor version change (v1.3.1) by @ens-LCampbell in #441

Full Changelog: v1.3.0...V1.3.1

v1.2.0

What's Changed

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

Full Changelog: v1.1...v1.2.0

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

v1.0

First release of GenomIO!

What's Changed

• updating / adding license comment by @vsitnik in #1
• Mbarba/get redmine by @MatBarba in #2
• Perl to 2.26: don't push to scalar by @MatBarba in #3
• Mbarba/prepare fixes2 by @MatBarba in #5
• The initial commit to add Sphinx setup and slight reconfiguration of its build scripts by @ens-LCampbell in #7
• Mbarba/doc review by @MatBarba in #4
• Mbarba/stable id allocation by @MatBarba in #9
• toying with setuptools by @vsitnik in #8
• Disha/build59update n doc by @Dishalodha in #11
• piRNA biotype support by @vsitnik in #12
• Updated valid_structures.conf to accout for MAKER2 UTR gene models by @ens-LCampbell in #13
• Addition of IGNORE rules for cases of pseudogenes linked to 3_prime |… by @ens-LCampbell in #15
• by default remove cds from pseudogenes by @MatBarba in #17
• BRC4_genome_loader docs draft by @vsitnik in #16
• Tentative doc for the genome prepare pipeline by @MatBarba in #14
• Disha/valid gene cds exon by @Dishalodha in #18
• Disha/compare pipeline doc by @Dishalodha in #19
• Vsitnik new attribs by @vsitnik in #22
• Mbarba/tweaks by @MatBarba in #20
• FlyBase update related fixes by @vsitnik in #27
• Optimize slice cache by @MatBarba in #24
• updating default external_db_map by @vsitnik in #28
• Mbarba/download by @MatBarba in #23
• Mbarba/events by @MatBarba in #25
• Disha/compare comp report by @Dishalodha in #29
• Mbarba/slurm2 by @MatBarba in #30
• Mbarba/prepare tweaks by @MatBarba in #26
• Mbarba/fix map by @MatBarba in #31
• Mbarba/prepare tweaks by @MatBarba in #33
• Mbarba/mobile genetic element by @MatBarba in #34
• Chunks by @vsitnik in #32
• metaparser script and configs updates related to Prokka loads by @vsitnik in #36
• Fixing LoadGFF3 logging (to avoid ehive db flooding). Not updating stable id if intact. tmRNA added by @vsitnik in #37
• setting max_retry_count to 0 for LoadFunctionalAnnotation stage of BRC4_genome_loader by @vsitnik in #38
• Mbarba/prepare tweaks by @MatBarba in #35
• Mbarba/stats by @MatBarba in #39
• Mbarba/dump events by @MatBarba in #42
• Fix: ignore release to store xref by @MatBarba in #41
• Update chunk_fasta.py by @digrigor in #43
• Update chunk_fasta.py by @digrigor in #44
• fill cs_tag from assembly_report only for "assembled-molecule" entries by @vsitnik in #46
• Fix Bio versions to avoid deprecated calls by @MatBarba in #47
• trf wrapper with chunking support to be used with the TRF stage of the DNAFeatures pipeline by @vsitnik in #48
• trf split run documentation update by @vsitnik in #51
• DNA_FEATURES_TRF_SPLIT_TRF_OPTIONS env var for trf_split_run.bash by @vsitnik in #52
• adding some notes on biopython availability for trf_split_run script by @vsitnik in #53
• Lcampbell/agriload p1 by @JAlvarezJarreta in #54
• Restructure the tree folder of the repository by @JAlvarezJarreta in #49
• Run black over the whole repository by @JAlvarezJarreta in #55
• Fix BRC4/EBI seq region names by @MatBarba in #56
• adding "gene/intron" to the IGNORE section of valid_structures.conf by @vsitnik in #58
• adding coord_system_level and location gff_metaparser mappings for "chloroplast" by @vsitnik in #59
• fixing default config dir option for BRC4_genome_loader_conf by @vsitnik in #60
• Removed deprecated dependency by @JAlvarezJarreta in #61
• moving gff_metaparser configuration from scripts to config by @vsitnik in #62
• Mbarba/disha add seq by @MatBarba in #63
• rename manifest_marker -> manifest_maker by @MatBarba in #64
• Mbarba/nextflow merge by @MatBarba in #65
• Mbarba/nextflow merge by @MatBarba in #66
• Manifest stats hackathon-Ahmad & Zahra by @ahmadazd in #69
• Mbarba/cleanup by @MatBarba in #73
• added BRC4_base_conf by @Dishalodha in #72
• adding gitlab cicd pipeline configuration by @vsitnik in #75
• Update cicd_gitlab.md doc by @vsitnik in #80
• Update python.gitlab-ci.yml by @vsitnik in #81
• Update cicd_gitlab.md by @vsitnik in #82
• Update python.gitlab-ci.yml by @vsitnik in #83
• Add option out_gene_map to dump by @MatBarba in #77
• Mbarba/prepare addition fix by @MatBarba in #78
• loading exons with coords behind length for circular seq_regions by @vsitnik in #67
• Mbarba/events loader2 by @MatBarba in #74
• Merging Nextflow development into main by @JAlvarezJarreta in #85
• Disha/nextflow add seq by @MatBarba in #70
• replicating the changes made by Matthieu in nextflow by @Dishalodha in #87
• Merge tracked genome prepare by @MatBarba in #86
• Merging all Nextflow development into a single branch by @JAlvarezJarreta in #84
• Mbarba/seq region fix by @MatBarba in #89
• Apply black to all python files by @MatBarba in #90
• Updates and testing additions to CI/CD by @JAlvarezJarreta in #88
• Resolve missing dependencies by @JAlvarezJarreta in #91
• NOTICE copyright year check by @JAlvarezJarreta in #92
• Add license header check by @JAlvarezJarreta in #94
• Bugfix: bash not available in default docker img by @JAlvarezJarreta in #95
• Mbarba/cleanup2 by @MatBarba in #96
• lcampbell/genome prepare by @ens-LCampbell in #98
• Migrate license check from Bash to Python by @JAlvarezJarreta in #97
• Mbarba/cleanup3 by @MatBarba in #99
• Genome prepare and addition prepare modify#1 by @ens-LCampbell in #102
• Mbarba/genome prepare fix by @MatBarba in #104
• Final changes to implement working genome_prepare pipeline by @ens-LCampbell in #103
• Mbarba/cleanup4 by @MatBarba in #100
• Test dirs as simple fixture by @MatBarba in #108
• Remove most triggers in CI/CD by @JAlvarezJarreta in #105
• Add dependabot to our repo by @jalva...