Version 3.3.3 - Variation Dataset Enhancements & Updater Critical Bug Fixes

RELEASE NOTES - Version 3.3.3

Release Date: 2024-10-22

New Features and Updates

• Added required attributes to support variation datasets

Bug Fixes

• Fixed geneset updates, and cores that match the assembly exactly.accession, organism.biosample, genebuild.provider_*, genebuild.last_geneset_update will be refused.
• Dataset_attributes that are NULL, "", "NULL" are not loaded.
• Updates to assembly through re-upload is depricated
• Dataset_attributes that are NULL, "", "NULL" are not loaded by the metadata updater.

Breaking Changes

• Removed Force core db load flag from the updater

3.0.1: Merge pull request #99 from Ensembl/feature/python_3_10

RELEASE NOTES - Version 3.0.1

Release Date: 2024-09-20

New Features and Updates

• Python Version Updated: Upgraded Python version from 3.8.3 to 3.10.14.
• Travis CI Environment: Updated the Travis CI build environment to Ubuntu Focal (20.04).
• Ensembl-py Library: Upgraded ensembl-py dependency to version 2.1.

Bug Fixes

• Fixed compatibility issues with Python 3.10.x.
• Resolved issues with the older version of ensembl-py to support new API features.

Breaking Changes

• Dropped support for Python versions older than 3.8.
• Ensured compatibility of third-party libraries with Python 3.10.

2.1.0a1

What's Changed

• update get genome query to try to fix slowness issues. by @marcoooo in #76
• Updated some queries to speed up process. Attempt to fix tests locall… by @marcoooo in #77
• Reintroduce reflection in build. by @marcoooo in #78
• Bugfix/assembly by @vinay-ebi in #79
• Updates/dataset factory updater by @dpopleton in #80
• Feature/restored status enum by @marcoooo in #81
• Minor Fix for taxid scope by @dpopleton in #82
• Feature/release status by @marcoooo in #84

Full Changelog: 2.0.1a1...2.1.0a1

2.0.1a1

What's Changed

• genome factory for new metadata db and test cases adde by @vinay-ebi in #75
• Feature/dataset factory by @dpopleton in #70

Full Changelog: 2.0.0a3...2.0.1a1

2.0.0a3

What's Changed

• Moved reflection package yagrc to test. by @marcoooo in #74

Full Changelog: 2.0.0a2...2.0.0a3

2.0.0a2

What's Changed

• Updated Schema with is_circular and type for assembly_sequence ✨ ✅ by @dpopleton in #52
• Feature/post mvp updates by @dpopleton in #55
• Bugfixes/retro compatibility by @marcoooo in #56
• Feature/new genome logic by @dpopleton in #57
• Feature/genome UUID manager by @dpopleton in #58
• Features/merge services by @marcoooo in #59
• [gRPC] Add GetReleaseVersionByUUID endpoint by @bilalebi in #61
• [gRPC] Replace ensembl_name with production_name for GetGenomeUUID endpoint by @bilalebi in #60
• Features/ftp links by @sanjay-boddu in #63
• [gRPC] Fix ALLOW_UNRELEASED and add logging by @bilalebi in #62
• Annual copyright update 2024 by @marcoooo in #64
• Changed FTP method retrieval method and default to ensembl annotati… by @marcoooo in #65
• [gRPC/API] Add dataset_type to ftp links endpoint response by @bilalebi in #66
• Feature/update alt accession by @marcoooo in #69
• Features/ftp links updated testsample by @marcoooo in #67
• Update FTP path for good :-) (or not) by @marcoooo in #71
• Update FTP path for good ... twice by @marcoooo in #72
• Added server reflection to services + quick tests by @marcoooo in #73

New Contributors

• @sanjay-boddu made their first contribution in #63

Full Changelog: 1.3.2...2.0.0a2

1.3.2

What's Changed

• Ensured that the name of assembly sequences is assembly_sequence_name… by @dpopleton in #47
• Checksum name incorrect by @andrewyatz in #46
• Fixed the typo in the original typo fix by @marcoooo in #49
• Update VERSION by @marcoooo in #50
• Features/dbconnection latest py by @marcoooo in #53
• Update genome model by @vinay-ebi in #51

New Contributors

• @andrewyatz made their first contribution in #46

Full Changelog: 1.3.0...1.3.2

1.1.1a2

What's Changed

• Added assembly schema changes by @dpopleton in #30
• Features/updater refactor by @dpopleton in #32
• Features/schema changes by @dpopleton in #33
• First version of get_popular_organism (list + counts) by @marcoooo in #34
• Improve code logic and add fetch genome by ensembl and assembly name by @bilalebi in #31
• Features/attributes parlence best by @dpopleton in #35
• fix fetching of unreleased genomes and unreleased datasets from new m… by @vinay-ebi in #37
• Fetch unreleased data only if required internally (API changes) by @bilalebi in #36

New Contributors

• @bilalebi made their first contribution in #31

Full Changelog: 1.1.1a1...1.1.1a2

1.1.1a1

What's Changed

• fetch multiple genomes with in operator by @vinay-ebi in #28
• Features/uuids assembly organism by @marcoooo in #29

Full Changelog: 1.1.0...1.1.1a1

1.1.0

What's Changed

• Features/updates dependencies by @marcoooo in #25
• default filter for dataset_topic changed to dataset_name by @vinay-ebi in #27
• Features/fixtures refactored by @marcoooo in #26

Full Changelog: 1.0.1...1.1.0