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 @JAlvarezJarreta in #109
• adding generic NextFlow installation instructions by @vsitnik in #113
• Bump bcbio-gff from 0.6.7 to 0.7.0 by @dependabot in #112
• Bump biopython from 1.80 to 1.81 by @dependabot in #111
• Deprecated UnknownSeq by @MatBarba in #115
• Add coverage badge generation step to make it publicly available by @JAlvarezJarreta in #110
• Fix README space and test new CI/CD rules by @JAlvarezJarreta in #116
• Fix CI/CD job trigger issues by @JAlvarezJarreta in #117
• Mbarba/gff3 improve by @MatBarba in #107
• Process gff3 input only 1 tuple by @MatBarba in #118
• Put modules into subfolders by @MatBarba in #119
• Only deploy GitLab pages for 'main' branch by @JAlvarezJarreta in #120
• NF install doc and nf dumper pipeline regexp option added by @vsitnik in #121
• not replacing non-ACGTN symbols when loading seq_region data by @vsitnik in #122
• modifying the parser to include tRNA and rRNA in gff by @Dishalodha in #123
• Mbarba/ez config by @MatBarba in #125
• Set of mixed updates related to yaml documentation and nxf pipe testing by @ens-LCampbell in #124
• Mbarba/fix nxf test by @MatBarba in #126
• Loader fix by @vsitnik in #127
• Mbarba/loader fix fix by @MatBarba in #129
• BRC4_genome_loader: commenting out default queue name to stop overriding env one by @vsitnik in #131
• Add accession to actually run the ncbi stats diff by @MatBarba in #132
• Use genome/io check_json_schema by @MatBarba in #136
• Add ncbi_check option by @MatBarba in #133
• Compare gb id with both refseq and genbank by @MatBarba in #134
• Explicit stats_file path parameter by @MatBarba in #135
• Mbarba/better cache by @MatBarba in #137
• Apply better resources for hungry processes by @MatBarba in #138
• metazoa gen_meta_conf update by @vsitnik in #139
• preserving "cds/parent" rule in metaparser.conf to keep CDSs with no IDs by @vsitnik in #141
• gff_metaparser cds/parent default strategy and metaparser/cds_with_parent_id.patch fixed by @vsitnik in #142
• Mbarba/patch build by @MatBarba in #140
• Mbarba/load gff apply patch by @MatBarba in #144
• Mbarba/patch pipeline by @MatBarba in #143
• add non canonical sites by @Dishalodha in #145
• Reduce flybase_annotation_id keys length by @JAlvarezJarreta in #146
• Added CI/CD flat file tests by @JAlvarezJarreta in #147
• Add data files to GenomIO Python library by @JAlvarezJarreta in #149
• Add Perl to our CI/CD by @JAlvarezJarreta in #148
• Apply updates to SLURM profile following conversation with TSC by @JAlvarezJarreta in #150
• Disha/doc perl by @Dishalodha in #153
• Include transcript ids to allocate by @MatBarba in #152
• adding "antisense_RNA" transcript type by @gnaamati in #154
• Mbarba/dump fix by @MatBarba in #151
• Group species params into a meta key by @MatBarba in #157
• Vsitnik/chk integrity no collect by @vsitnik in #160
• Updates to check_json_schmea NXF module & python by @ens-LCampbell in #159
• Collect files is used by other pipelines, fallback by @MatBarba in #162
• Minor folder structure changes by @JAlvarezJarreta in #163
• Hackathon/download gb by @MatBarba in #164
• Vsitnik/chk integrity no collect by @vsitnik in #165
• Updates to NXF module, and python module related to process_GFF3 by @ens-LCampbell in #166
• Mbarba/addition test by @MatBarba in #167
• Mbarba/genome fix by @MatBarba in #170
• Mbarba/chk integrity no collect 2 by @MatBarba in #171
• fixing bits and resolving prepare_genome issues by @vsitnik in #169
• Disha/hack manifest maker by @Dishalodha in #161
• Mbarba/stats by @MatBarba in #156
• Fix addition prepare call by @MatBarba in #175
• Mbarba/fix genome prep by @MatBarba in #176
• Mbarba/fix pipeline tests by @MatBarba in #177
• Address some missing elements to control module imports correctly by @JAlvarezJarreta in #172
• Updates in the Genome prepare pipeline following B67 production by @JAlvarezJarreta in #174
• Bugfixes and code updated on GenomIO utils by @JAlvarezJarreta in #178
• Addition of workflow config for sphinx doc generation by @ens-LCampbell in #179
• Change on event to push not PR by @ens-LCampbell in #182
• Added temp file to trigger docs workflow by @ens-LCampbell in #183
• Changes to trigger event of docs workflow by @ens-LCampbell in #184
• More fixes, include on type 'closed', plus format fix by @ens-LCampbell in #185
• Adding empty file to trigger workflow by @ens-LCampbell in #186
• Create temp python test to trigger docs wf by @ens-LCampbell in #187
• Update to YAML to include wildcards on paths by @ens-LCampbell in #188
• Update sphinx_doc_generation.yaml by @ens-LCampbell in #189
• another workflow trigger post yaml update by @ens-LCampbell in #190
• Fix to Sphinx build - Failing to find modules.rst by @ens-LCampbell in #191
• Revert sphinx build to default script/makefile by @ens-LCampbell in #192
• Added new features following B67 production by @JAlvarezJarreta in #173
• Mbarba/brc mode by @MatBarba in #180
• Mbarba/fix brc mode by @MatBarba in #194
• Test has been split into brc on/off by @MatBarba in #195
• Bugfix: include initial event for each release by @JAlvarezJarreta in #196
• Migrate from argschema back to argparse by @JAlvarezJarreta in #193
• Make a explicit CI/CD tag by @JAlvarezJarreta in #197
• Additional B67 updates by @JAlvarezJarreta in #198
• Fix tests after moves by @MatBarba in #200
• Mbarba/restructure tests fix2 pipelines by @MatBarba in #201
• Mbarba/restructure by @MatBarba in #211
• Python module restructuring by @JAlvarezJarreta in #210
• Switch from sphinx to use mkdocs by @ens-LCampbell in #209
• Implement ensembl-py logging events module by @ens-LCampbell in #215
• Lcampbell/assembly_download (includes events) into parents branch genome_stats_compare by @ens-LCampbell in #216
• Fix issues reported by CI/CD by @JAlvarezJarreta in #217
• Ensembl-py Logging genome_metadata module by @ens-LCampbell in #218
• Lcampbell/genome metadata by @ens-LCampbell in #219
• Merging into parent branch: ens-py logging manifest integrity by @ens-LCampbell in #221
• Implement ensembl-py logging by @ens-LCampbell in #214
• Enable trace file by default with useful field information by @JAlvarezJarreta in #220
• adding logging to ensembl.io.genomio.fasta.process by @vsitnik in #222
• Mbarba/genbank logging2 by @MatBarba in #213
• Mbarba/logging gff by @MatBarba in #204
• Logging gff fix 2 by @MatBarba in #224
• Adding log to seq_region module by @Dishalodha in #205
• fixing typo and chunking broken by d5a71fc by @vsitnik in #225
• Updates on our documentation to fix a few minor issues and add new features by @JAlvarezJarreta in #223
• Mbarba/dumper brc builds by @MatBarba in #212
• Mbarba/logging standard by @MatBarba in #226
• update schema call for dumpers by @MatBarba in #228
• replace when by if, clearer structure by @MatBarba in #229
• Rewrite dumper parameters by @MatBarba in #230
• Move JSON schemas as part of the data files of the Python library by @JAlvarezJarreta in #227
• Do not create an accession subfolder by @MatBarba in #233
• Rebasing lcampbell/ncbi-datasets with latest main by @ens-LCampbell in #234
• Add singularity definition file recipe folder and ncbi datasets def file by @ens-LCampbell in #236
• Mbarba/core server by @MatBarba in #231
• Mbarba/less check procs by @MatBarba in #232
• Mbarba/stub test by @MatBarba in #235
• fixing issue with RefSeq seq_region synonyms for chuncked assemblies by @vsitnik in #243
• Use new json validator in ehive dumper by @MatBarba in #244
• Mbarba/nf validation by @MatBarba in #239
• Alternative approach to mock sqlalchemy engine for unittests by @JAlvarezJarreta in #237
• Update tests tree structure and docstrings by @JAlvarezJarreta in #245
• Hackathon/dec23 by @ens-LCampbell in #246
• Add exclusion directory list to license header checks by @JAlvarezJarreta in #252
• A new proposal and approach to store and access test data files by @JAlvarezJarreta in #253
• Mbarba/stub test dumper by @MatBarba in #238
• Add a db_list file as an option to dump genomes by @MatBarba in #240
• Update BRC4_genome_loader_conf.pm by @ens-LCampbell in #257
• Remove GFFMeta class by @JAlvarezJarreta in #256
• Update manifest_integrity params by @ens-LCampbell in #258
• updating the container as we require ps for tracing by @Dishalodha in #260
• Add "hackathon/.+" branches to CI/CD by @JAlvarezJarreta in #261
• pylint v2.5 is the first one to introduce support for pyproject.toml config by @JAlvarezJarreta in #262
• Mbarba/hack/merge main by @MatBarba in #266
• Revert code and add bugfix by @JAlvarezJarreta in #264
• Implement testing of Fasta module by @ens-LCampbell in #250
• Update minimum versions of main CI/CD and documentation tools by @JAlvarezJarreta in #267
• Mbarba/hack/fix fasta tests by @MatBarba in #269
• Disha/genbank test update by @Dishalodha in #268
• GFF3 modules tests by @MatBarba in #254
• Mbarba/fix integrity by @MatBarba in #270
• Add genome stats comparison tests by @JAlvarezJarreta in #249
• Resolve conflict to prepare merging hackathon/dec23 to main by @MatBarba in #271
• updated LICENSE and README files by @sgiorgetti in #274
• Fix GFF3 parsing for naked transcripts and CDSs by @MatBarba in #273
• Hackathon/dec23 by @MatBarba in #272
• Make the Python image a CI/CD variable by @JAlvarezJarreta in #275
• Use module doc for parser description by @MatBarba in #277
• Update stable id pattern in OSID by @MatBarba in #276
• Bump bcbio-gff from 0.7.0 to 0.7.1 by @dependabot in #281
• Remove --verbose option for black by @JAlvarezJarreta in #282
• Make perlcritic a manual step in CI/CD by @JAlvarezJarreta in #283
• Prepare genome publish to BRC dir structure by @MatBarba in #285
• Only generate docs for 'main' and 'hackathon/*' branches by @JAlvarezJarreta in #287
• Don't fail but write a stats error file by @MatBarba in #288
• Add tests for GFF3 merger by @MatBarba in #284
• Split up ID allocation code and test by @MatBarba in #279
• Add javascript to always have the Copyright up to date in the documentation by @JAlvarezJarreta in #286
• Add changes in workflow config to trigger rebuild by @JAlvarezJarreta in #290
• Add unit test for ensembl.io.genomio.genome_stats.dump module by @JAlvarezJarreta in #280
• Create assert_files fixture by @MatBarba in #289
• Set publish dir for addition pipeline too by @MatBarba in #296
• Fix db_list when not defined by @MatBarba in #294
• Rename BRC seq_region names by @MatBarba in #292
• DBconnection lite by @MatBarba in #295
• Annotation script to update descriptions by @MatBarba in #293
• Hackathon/jan24 by @MatBarba in #298
• Move set_id_prefix to the stable id allocator by @MatBarba in #299
• Mbarba/hack/store gene by @MatBarba in #300
• Fix Dict type by @MatBarba in #304
• Fix ENA API by @MatBarba in #307
• Tweak and exclude synonyms if in xrefs by @MatBarba in #309
• Add mocks for pipeline tests by @MatBarba in #302
• Format outside record loop by @MatBarba in #310
• Add unit test for ensembl.io.genomio.genome_metadata.dump module by @JAlvarezJarreta in #301
• Add unit test for ensembl.io.genomio.genome_metadata.extend module by @JAlvarezJarreta in #308
• Disha/hack feb/update extract genbank by @Dishalodha in #303
• Temporal pytest version restriction by @JAlvarezJarreta in #313
• Merge main to hackathon by @MatBarba in #314
• Disha/update func anno by @Dishalodha in #305
• Merge main to hackathon by @MatBarba in #315
• Pytest is too verbose by @MatBarba in #318
• Hackathon/feb24 by @MatBarba in #316
• Plugin with version to not check/update when testing by @MatBarba in #319

New Contributors

• @vsitnik made their first contribution in #1
• @Dishalodha made their first contribution in #11
• @digrigor made their first contribution in #43
• @ahmadazd made their first contribution in #69
• @dependabot made their first contribution in #112
• @gnaamati made their first contribution in #154
• @sgiorgetti made their first contribution in #274

Full Changelog: https://github.com/Ensembl/ensembl-genomio/commits/1.0