Galaxy datatype framework and datatypes
Project description
Overview
The Galaxy models, datatype framework, and datatype implementations.
History
23.1.3 (2023-12-01)
Bug fixes
23.1.2 (2023-11-29)
Bug fixes
Skip change_datatype things if we’re not actually changing the extension by @mvdbeek in #16931
Fix copying metadata to copied job outputs by @mvdbeek in #17007
Assert that DatasetCollectioElement has an associated object by @mvdbeek in #17071
Fix input dates in notifications: consider timezone offset by @davelopez in #17088
Allow relative URLs in broadcasts action links by @davelopez in #17093
Enhancements
Add support for larch datatypes by @patrick-austin in #17080
23.1.1 (2023-10-23)
Bug fixes
Fix bad auto-merge of dev. by @jmchilton in #15386
Merge conflicting db migration branches into one by @jdavcs in #15771
Fix revision scripts, run migrations in CI, add repair option, improve migrations utils by @jdavcs in #15811
Fix anonymous user uploads when vault is configured by @tchaussepiedifb in #15858
Fix nullable deleted column in API Keys table by @davelopez in #15956
Attempt to fix mypy check by @davelopez in #16103
Ensure session is request-scoped for legacy endpoints by @jdavcs in #16207
Update 23.1 release tags for migration scripts by @jdavcs in #16294
Fix tags ownership by @davelopez in #16339
Fix disk usage recalculation for distributed object stores by @mvdbeek in #16380
Fix histories count by @davelopez in #16400
Fix double-encoding notification content by @mvdbeek in #16530
Fixes for conditional subworkflow steps by @mvdbeek in #16632
Copy the collection contents by default when copying a collection by @mvdbeek in #16717
Fix allowlist deserialization in file sources by @mvdbeek in #16729
Fix workflow output display without label by @mvdbeek in #16749
Fix and prevent persisting null file_size by @mvdbeek in #16855
Fix workflow import losing tool_version by @mvdbeek in #16869
Remove more flushes in database operation tools by @mvdbeek in #16875
Fix join condition for nested collection query by @mvdbeek in #16880
Enhancements
Empower Users to Select Storage Destination by @jmchilton in #14073
Add Storage Dashboard visualizations for histories by @davelopez in #14820
Add Storage Management API by @davelopez in #15295
OIDC tokens by @SergeyYakubov in #15300
Expose additional beaker caching backends by @claudiofr in #15349
Add support for visualizing HDF5 datasets. by @jarrah42 in #15394
Towards SQLAlchemy 2.0: drop session autocommit setting by @jdavcs in #15421
Update Python dependencies by @galaxybot in #15435
Update Python dependencies by @galaxybot in #15564
Update database_heartbeat for SA 2.0 compatibility by @jdavcs in #15611
Update supports_skip_locked, supports_returning for SA 2.0 compatibility by @jdavcs in #15633
Add Galaxy Notification System by @davelopez in #15663
Add transactional state to workflow scheduling manager by @jdavcs in #15683
Remove DELETED_NEW job state from code base by @jdavcs in #15690
Fix/Enhance recalculate disk usage API endpoint by @davelopez in #15739
Update Python dependencies by @galaxybot in #15890
FITS data format by @volodymyrss in #15905
Improve display chunk generation for BAMs by @wm75 in #15972
Add History Archival feature by @davelopez in #16003
Code cleanups from ruff and pyupgrade by @nsoranzo in #16035
Add missing fields to HistorySummary schema model by @davelopez in #16041
Dataset chunking tests (and small fixes) by @jmchilton in #16069
Add create_foreign_key migration utility by @jdavcs in #16077
Refactor models enums to eliminate schema dependency on model layer. by @jmchilton in #16080
Use automated naming convention to generate indexes and constraints in database by @jdavcs in #16089
Add zipped mongodb and genenotebook datatypes by @abretaud in #16173
Drop workarounds for old ro-crate-py and docutils versions by @mvdbeek in #16198
bring grids for (published) pages on par with workflows by @martenson in #16209
Add Visium datatype for squidpy and spatialomics tools by @astrovsky01 in #16255
Filter deleted keys from api_keys relationship by @dannon in #16321
Increase CustosAuthnzToken.external_user_id column size by @davelopez in #16818
Other changes
Follow up on object store selection PR. by @jmchilton in #15654
Fix Enums in API docs by @davelopez in #15740
merge release_23.0 into dev by @martenson in #15830
backport of pysam tostring by @martenson in #16822
23.0.6 (2023-10-23)
Bug fixes
23.0.5 (2023-07-29)
Bug fixes
23.0.4 (2023-06-30)
No recorded changes since last release
23.0.3 (2023-06-26)
No recorded changes since last release
23.0.2 (2023-06-13)
No recorded changes since last release
23.0.1 (2023-06-08)
Bug fixes
Display DCE in job parameter component, allow rerunning with DCE input by @mvdbeek in #15744
Fix RO-crate invocation export with complex collections by @davelopez in #15971
Backport Improve display chunk generation for BAMs by @mvdbeek in #16007
Ensure history export contains all expected datasets by @davelopez in #16013
Fix dataype_change not updating HDCA update_time by @mvdbeek in #16099
Fix extended metadata file size handling by @mvdbeek in #16109
Fix implicit converters with optional parameters by @mvdbeek in #16133
Make ctx_rev optional in InstalledToolShedRepository response model by @dannon in #16139
Fix optional fields being validated as missing in ts api by @jmchilton in #16141
Verify existence of default value attribute for user forms fields by @guerler in #16205
20.9.0 (2020-10-15)
First release from the 20.09 branch of Galaxy.
20.5.0 (2020-07-04)
First release from the 20.05 branch of Galaxy.
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