First release of GenomIO!
What's Changed
* updating / adding license comment by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/1
* Mbarba/get redmine by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/2
* Perl to 2.26: don't push to scalar by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/3
* Mbarba/prepare fixes2 by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/5
* The initial commit to add Sphinx setup and slight reconfiguration of its build scripts by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/7
* Mbarba/doc review by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/4
* Mbarba/stable id allocation by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/9
* toying with setuptools by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/8
* Disha/build59update n doc by Dishalodha in https://github.com/Ensembl/ensembl-genomio/pull/11
* piRNA biotype support by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/12
* Updated valid_structures.conf to accout for MAKER2 UTR gene models by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/13
* Addition of IGNORE rules for cases of pseudogenes linked to 3_prime |… by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/15
* by default remove cds from pseudogenes by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/17
* BRC4_genome_loader docs draft by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/16
* Tentative doc for the genome prepare pipeline by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/14
* Disha/valid gene cds exon by Dishalodha in https://github.com/Ensembl/ensembl-genomio/pull/18
* Disha/compare pipeline doc by Dishalodha in https://github.com/Ensembl/ensembl-genomio/pull/19
* Vsitnik new attribs by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/22
* Mbarba/tweaks by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/20
* FlyBase update related fixes by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/27
* Optimize slice cache by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/24
* updating default external_db_map by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/28
* Mbarba/download by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/23
* Mbarba/events by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/25
* Disha/compare comp report by Dishalodha in https://github.com/Ensembl/ensembl-genomio/pull/29
* Mbarba/slurm2 by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/30
* Mbarba/prepare tweaks by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/26
* Mbarba/fix map by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/31
* Mbarba/prepare tweaks by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/33
* Mbarba/mobile genetic element by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/34
* Chunks by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/32
* metaparser script and configs updates related to Prokka loads by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/36
* Fixing LoadGFF3 logging (to avoid ehive db flooding). Not updating stable id if intact. tmRNA added by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/37
* setting max_retry_count to 0 for LoadFunctionalAnnotation stage of BRC4_genome_loader by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/38
* Mbarba/prepare tweaks by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/35
* Mbarba/stats by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/39
* Mbarba/dump events by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/42
* Fix: ignore release to store xref by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/41
* Update chunk_fasta.py by digrigor in https://github.com/Ensembl/ensembl-genomio/pull/43
* Update chunk_fasta.py by digrigor in https://github.com/Ensembl/ensembl-genomio/pull/44
* fill cs_tag from assembly_report only for "assembled-molecule" entries by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/46
* Fix Bio versions to avoid deprecated calls by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/47
* trf wrapper with chunking support to be used with the TRF stage of the DNAFeatures pipeline by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/48
* trf split run documentation update by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/51
* DNA_FEATURES_TRF_SPLIT_TRF_OPTIONS env var for trf_split_run.bash by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/52
* adding some notes on biopython availability for trf_split_run script by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/53
* Lcampbell/agriload p1 by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/54
* Restructure the tree folder of the repository by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/49
* Run `black` over the whole repository by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/55
* Fix BRC4/EBI seq region names by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/56
* adding "gene/intron" to the IGNORE section of valid_structures.conf by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/58
* adding coord_system_level and location gff_metaparser mappings for "chloroplast" by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/59
* fixing default config dir option for BRC4_genome_loader_conf by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/60
* Removed deprecated dependency by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/61
* moving gff_metaparser configuration from scripts to config by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/62
* Mbarba/disha add seq by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/63
* rename manifest_marker -> manifest_maker by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/64
* Mbarba/nextflow merge by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/65
* Mbarba/nextflow merge by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/66
* Manifest stats hackathon-Ahmad & Zahra by ahmadazd in https://github.com/Ensembl/ensembl-genomio/pull/69
* Mbarba/cleanup by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/73
* added BRC4_base_conf by Dishalodha in https://github.com/Ensembl/ensembl-genomio/pull/72
* adding gitlab cicd pipeline configuration by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/75
* Update cicd_gitlab.md doc by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/80
* Update python.gitlab-ci.yml by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/81
* Update cicd_gitlab.md by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/82
* Update python.gitlab-ci.yml by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/83
* Add option out_gene_map to dump by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/77
* Mbarba/prepare addition fix by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/78
* loading exons with coords behind length for circular seq_regions by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/67
* Mbarba/events loader2 by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/74
* Merging Nextflow development into main by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/85
* Disha/nextflow add seq by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/70
* replicating the changes made by Matthieu in nextflow by Dishalodha in https://github.com/Ensembl/ensembl-genomio/pull/87
* Merge tracked genome prepare by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/86
* Merging all Nextflow development into a single branch by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/84
* Mbarba/seq region fix by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/89
* Apply black to all python files by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/90
* Updates and testing additions to CI/CD by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/88
* Resolve missing dependencies by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/91
* NOTICE copyright year check by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/92
* Add license header check by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/94
* Bugfix: bash not available in default docker img by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/95
* Mbarba/cleanup2 by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/96
* lcampbell/genome prepare by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/98
* Migrate license check from Bash to Python by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/97
* Mbarba/cleanup3 by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/99
* Genome prepare and addition prepare modify1 by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/102
* Mbarba/genome prepare fix by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/104
* Final changes to implement working genome_prepare pipeline by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/103
* Mbarba/cleanup4 by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/100
* Test dirs as simple fixture by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/108
* Remove most triggers in CI/CD by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/105
* Add dependabot to our repo by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/109
* adding generic NextFlow installation instructions by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/113
* Bump bcbio-gff from 0.6.7 to 0.7.0 by dependabot in https://github.com/Ensembl/ensembl-genomio/pull/112
* Bump biopython from 1.80 to 1.81 by dependabot in https://github.com/Ensembl/ensembl-genomio/pull/111
* Deprecated UnknownSeq by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/115
* Add coverage badge generation step to make it publicly available by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/110
* Fix README space and test new CI/CD rules by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/116
* Fix CI/CD job trigger issues by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/117
* Mbarba/gff3 improve by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/107
* Process gff3 input only 1 tuple by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/118
* Put modules into subfolders by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/119
* Only deploy GitLab pages for 'main' branch by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/120
* NF install doc and nf dumper pipeline regexp option added by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/121
* not replacing non-ACGTN symbols when loading seq_region data by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/122
* modifying the parser to include tRNA and rRNA in gff by Dishalodha in https://github.com/Ensembl/ensembl-genomio/pull/123
* Mbarba/ez config by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/125
* Set of mixed updates related to yaml documentation and nxf pipe testing by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/124
* Mbarba/fix nxf test by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/126
* Loader fix by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/127
* Mbarba/loader fix fix by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/129
* BRC4_genome_loader: commenting out default queue name to stop overriding env one by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/131
* Add accession to actually run the ncbi stats diff by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/132
* Use genome/io check_json_schema by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/136
* Add ncbi_check option by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/133
* Compare gb id with both refseq and genbank by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/134
* Explicit stats_file path parameter by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/135
* Mbarba/better cache by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/137
* Apply better resources for hungry processes by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/138
* metazoa gen_meta_conf update by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/139
* preserving "cds/parent" rule in metaparser.conf to keep CDSs with no IDs by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/141
* gff_metaparser cds/parent default strategy and metaparser/cds_with_parent_id.patch fixed by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/142
* Mbarba/patch build by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/140
* Mbarba/load gff apply patch by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/144
* Mbarba/patch pipeline by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/143
* add non canonical sites by Dishalodha in https://github.com/Ensembl/ensembl-genomio/pull/145
* Reduce flybase_annotation_id keys length by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/146
* Added CI/CD flat file tests by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/147
* Add data files to GenomIO Python library by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/149
* Add Perl to our CI/CD by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/148
* Apply updates to SLURM profile following conversation with TSC by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/150
* Disha/doc perl by Dishalodha in https://github.com/Ensembl/ensembl-genomio/pull/153
* Include transcript ids to allocate by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/152
* adding "antisense_RNA" transcript type by gnaamati in https://github.com/Ensembl/ensembl-genomio/pull/154
* Mbarba/dump fix by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/151
* Group species params into a meta key by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/157
* Vsitnik/chk integrity no collect by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/160
* Updates to check_json_schmea NXF module & python by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/159
* Collect files is used by other pipelines, fallback by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/162
* Minor folder structure changes by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/163
* Hackathon/download gb by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/164
* Vsitnik/chk integrity no collect by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/165
* Updates to NXF module, and python module related to process_GFF3 by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/166
* Mbarba/addition test by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/167
* Mbarba/genome fix by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/170
* Mbarba/chk integrity no collect 2 by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/171
* fixing bits and resolving prepare_genome issues by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/169
* Disha/hack manifest maker by Dishalodha in https://github.com/Ensembl/ensembl-genomio/pull/161
* Mbarba/stats by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/156
* Fix addition prepare call by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/175
* Mbarba/fix genome prep by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/176
* Mbarba/fix pipeline tests by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/177
* Address some missing elements to control module imports correctly by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/172
* Updates in the Genome prepare pipeline following B67 production by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/174
* Bugfixes and code updated on GenomIO utils by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/178
* Addition of workflow config for sphinx doc generation by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/179
* Change on event to push not PR by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/182
* Added temp file to trigger docs workflow by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/183
* Changes to trigger event of docs workflow by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/184
* More fixes, include on type 'closed', plus format fix by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/185
* Adding empty file to trigger workflow by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/186
* Create temp python test to trigger docs wf by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/187
* Update to YAML to include wildcards on paths by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/188
* Update sphinx_doc_generation.yaml by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/189
* another workflow trigger post yaml update by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/190
* Fix to Sphinx build - Failing to find modules.rst by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/191
* Revert sphinx build to default script/makefile by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/192
* Added new features following B67 production by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/173
* Mbarba/brc mode by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/180
* Mbarba/fix brc mode by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/194
* Test has been split into brc on/off by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/195
* Bugfix: include initial event for each release by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/196
* Migrate from argschema back to argparse by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/193
* Make a explicit CI/CD tag by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/197
* Additional B67 updates by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/198
* Fix tests after moves by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/200
* Mbarba/restructure tests fix2 pipelines by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/201
* Mbarba/restructure by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/211
* Python module restructuring by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/210
* Switch from sphinx to use mkdocs by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/209
* Implement ensembl-py logging events module by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/215
* Lcampbell/assembly_download (includes events) into parents branch genome_stats_compare by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/216
* Fix issues reported by CI/CD by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/217
* Ensembl-py Logging genome_metadata module by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/218
* Lcampbell/genome metadata by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/219
* Merging into parent branch: ens-py logging manifest integrity by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/221
* Implement ensembl-py logging by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/214
* Enable trace file by default with useful field information by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/220
* adding logging to ensembl.io.genomio.fasta.process by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/222
* Mbarba/genbank logging2 by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/213
* Mbarba/logging gff by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/204
* Logging gff fix 2 by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/224
* Adding log to seq_region module by Dishalodha in https://github.com/Ensembl/ensembl-genomio/pull/205
* fixing typo and chunking broken by d5a71fc by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/225
* Updates on our documentation to fix a few minor issues and add new features by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/223
* Mbarba/dumper brc builds by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/212
* Mbarba/logging standard by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/226
* update schema call for dumpers by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/228
* replace when by if, clearer structure by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/229
* Rewrite dumper parameters by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/230
* Move JSON schemas as part of the data files of the Python library by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/227
* Do not create an accession subfolder by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/233
* Rebasing lcampbell/ncbi-datasets with latest main by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/234
* Add singularity definition file recipe folder and ncbi datasets def file by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/236
* Mbarba/core server by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/231
* Mbarba/less check procs by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/232
* Mbarba/stub test by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/235
* fixing issue with RefSeq seq_region synonyms for chuncked assemblies by vsitnik in https://github.com/Ensembl/ensembl-genomio/pull/243
* Use new json validator in ehive dumper by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/244
* Mbarba/nf validation by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/239
* Alternative approach to mock sqlalchemy engine for unittests by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/237
* Update tests tree structure and docstrings by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/245
* Hackathon/dec23 by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/246
* Add exclusion directory list to license header checks by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/252
* A new proposal and approach to store and access test data files by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/253
* Mbarba/stub test dumper by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/238
* Add a db_list file as an option to dump genomes by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/240
* Update BRC4_genome_loader_conf.pm by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/257
* Remove GFFMeta class by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/256
* Update manifest_integrity params by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/258
* updating the container as we require ps for tracing by Dishalodha in https://github.com/Ensembl/ensembl-genomio/pull/260
* Add "hackathon/.+" branches to CI/CD by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/261
* pylint v2.5 is the first one to introduce support for pyproject.toml config by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/262
* Mbarba/hack/merge main by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/266
* Revert code and add bugfix by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/264
* Implement testing of Fasta module by ens-LCampbell in https://github.com/Ensembl/ensembl-genomio/pull/250
* Update minimum versions of main CI/CD and documentation tools by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/267
* Mbarba/hack/fix fasta tests by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/269
* Disha/genbank test update by Dishalodha in https://github.com/Ensembl/ensembl-genomio/pull/268
* GFF3 modules tests by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/254
* Mbarba/fix integrity by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/270
* Add genome stats comparison tests by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/249
* Resolve conflict to prepare merging hackathon/dec23 to main by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/271
* updated LICENSE and README files by sgiorgetti in https://github.com/Ensembl/ensembl-genomio/pull/274
* Fix GFF3 parsing for naked transcripts and CDSs by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/273
* Hackathon/dec23 by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/272
* Make the Python image a CI/CD variable by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/275
* Use module doc for parser description by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/277
* Update stable id pattern in OSID by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/276
* Bump bcbio-gff from 0.7.0 to 0.7.1 by dependabot in https://github.com/Ensembl/ensembl-genomio/pull/281
* Remove --verbose option for black by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/282
* Make perlcritic a manual step in CI/CD by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/283
* Prepare genome publish to BRC dir structure by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/285
* Only generate docs for 'main' and 'hackathon/*' branches by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/287
* Don't fail but write a stats error file by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/288
* Add tests for GFF3 merger by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/284
* Split up ID allocation code and test by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/279
* Add javascript to always have the Copyright up to date in the documentation by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/286
* Add changes in workflow config to trigger rebuild by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/290
* Add unit test for ensembl.io.genomio.genome_stats.dump module by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/280
* Create assert_files fixture by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/289
* Set publish dir for addition pipeline too by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/296
* Fix db_list when not defined by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/294
* Rename BRC seq_region names by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/292
* DBconnection lite by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/295
* Annotation script to update descriptions by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/293
* Hackathon/jan24 by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/298
* Move set_id_prefix to the stable id allocator by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/299
* Mbarba/hack/store gene by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/300
* Fix Dict type by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/304
* Fix ENA API by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/307
* Tweak and exclude synonyms if in xrefs by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/309
* Add mocks for pipeline tests by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/302
* Format outside record loop by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/310
* Add unit test for ensembl.io.genomio.genome_metadata.dump module by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/301
* Add unit test for ensembl.io.genomio.genome_metadata.extend module by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/308
* Disha/hack feb/update extract genbank by Dishalodha in https://github.com/Ensembl/ensembl-genomio/pull/303
* Temporal pytest version restriction by JAlvarezJarreta in https://github.com/Ensembl/ensembl-genomio/pull/313
* Merge main to hackathon by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/314
* Disha/update func anno by Dishalodha in https://github.com/Ensembl/ensembl-genomio/pull/305
* Merge main to hackathon by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/315
* Pytest is too verbose by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/318
* Hackathon/feb24 by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/316
* Plugin with version to not check/update when testing by MatBarba in https://github.com/Ensembl/ensembl-genomio/pull/319
New Contributors
* vsitnik made their first contribution in https://github.com/Ensembl/ensembl-genomio/pull/1
* Dishalodha made their first contribution in https://github.com/Ensembl/ensembl-genomio/pull/11
* digrigor made their first contribution in https://github.com/Ensembl/ensembl-genomio/pull/43
* ahmadazd made their first contribution in https://github.com/Ensembl/ensembl-genomio/pull/69
* dependabot made their first contribution in https://github.com/Ensembl/ensembl-genomio/pull/112
* gnaamati made their first contribution in https://github.com/Ensembl/ensembl-genomio/pull/154
* sgiorgetti made their first contribution in https://github.com/Ensembl/ensembl-genomio/pull/274
**Full Changelog**: https://github.com/Ensembl/ensembl-genomio/commits/1.0