1.0

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...