galaxyproject/galaxy v24.2.4

on GitHub

What's Changed

• [24.1] Backport parts of #19659 by @bernt-matthias in #19805
• [24.2] Reduce default framework tool test timeout to 60 seconds by @mvdbeek in #19819
• [24.2] Backport #19810: Fix workflow param tests not updating param type. by @mvdbeek in #19820
• [24.2] Bump up max_peek_size to 50MB by @mvdbeek in #19823
• [24.2] Remove unused client route for standalone wizard interface by @dannon in #19836
• [24.2] Try to recover from recurring activation link error by @jdavcs in #19844
• [24.2] Add spacing between workflow author and invocation count by @ahmedhamidawan in #19849
• [24.2] Point install_requires at requirements.txt file by @mvdbeek in #19864
• [24.2] Handle directories with percents directories with export_remote.xml. by @jmchilton in #19865
• [24.2] Don't collect unnamed outputs twice in extended metadata mode by @mvdbeek in #19868
• [24.0] Check if index exists before creating by @jdavcs in #19873
• [24.2] Publish pre-built client with (point-)release by @mvdbeek in #19879
• [24.2] Lazy-load invocation step jobs as needed by @mvdbeek in #19877
• [24.2] Fix drag and drop for dataset collection elements by @ahmedhamidawan in #19866
• [24.2] Fix various job concurrency limit issues by @mvdbeek in #19824
• [24.2] Fix tabular metadata setting on pulsar with remote metadata by @mvdbeek in #19891
• [24.2] Decode/encode FormDirectory paths to allow spaces (and other characters) by @ahmedhamidawan in #19841
• [24.2] Fix collection builder input states by @mvdbeek in #19797
• [24.0] Drop unused alembic-utils from galaxy-data package requirements by @nsoranzo in #19896
• [24.2] Fix default ordering of items sorted by name by @jdavcs in #19853
• [24.2] Do not reorder options in FormSelect component when multiselect disabled by @jdavcs in #19837
• [24.2] Fix duplicate extensions for data inputs by @ahmedhamidawan in #19903
• [24.2] Skip implicit HDA conversions in DataToolParameter options by @davelopez in #19911
• [24.2] Skip data_meta filter in run form by @mvdbeek in #19895
• [24.2] Let pysam use extra threads available in job by @mvdbeek in #19917
• [24.2] Fix duplicate entries when using drag and drop in multiple mode by @davelopez in #19913
• [24.2] Report TestCaseValidation as linter error for 24.2 and above by @bernt-matthias in #19928
• [24.1] Handle special charater in raw SQL by @jdavcs in #19925
• [24.1] Fix Invenio file source downloads not working with some Invenio instances by @davelopez in #19930
• [24.2] Better interactive tool entry point query by @mvdbeek in #19942
• [24.2] Drop unnecessary job cache job subquery by @mvdbeek in #19945
• [24.2] Use make_fast_zipfile directly by @mvdbeek in #19947
• [24.2] Fix attempt restriction on multiple connections by @mvdbeek in #19948
• [24.2] Sort intersected options by @mvdbeek in #19953
• [23.1] Do not print OIDC access tokens to the logs by @kysrpex in #19966
• [24.2] Renew OIDC access tokens using valid refresh tokens by @kysrpex in #19967
• [24.2] Fix bug in psa-authnz redirect handling by @dannon in #19968
• [24.2] Add missing job state history entry for queued state by @mvdbeek in #19977
• [24.2] Restrict job cache to terminal jobs (and other fixes) by @mvdbeek in #19978
• [24.2] Fix dynamic filter option access when building command line by @mvdbeek in #19982
• [24.2] Do not display default labels obscuring selectable options in a vue-multiselect component by @jdavcs in #19981
• [24.2] ChatGXY Error Handling by @dannon in #19987
• [24.2] Always set copy_elements to true by @mvdbeek in #19985
• [24.2] Update selectable object stores after adding or editing them by @davelopez in #19992
• [24.2] Fix various parameter validation issues. by @jmchilton in #19949
• [24.2] Ensure job states are fetched in invocation view by @ahmedhamidawan in #20010
• [24.2] Fix edit permission for datasets delete button in storage dashboard overview by location by @itisAliRH in #20066
• [24.2] Job cache backports by @mvdbeek in #20078
• [24.2] Skip param_value filter if ref value is runtime value by @mvdbeek in #20144
• [24.2] Fix edam selenium test by @mvdbeek in #20134
• [24.2] Fix DataCollectionParameterModel factory by @mvdbeek in #20164
• [24.2] Update dev package version in meta package by @natefoo in #20159
• [23.1] Renew access tokens from PSA using valid refresh tokens by @kysrpex in #20040
• [24.0] Fix invocation failure dataset reference by @mvdbeek in #20200
• [24.2] Fix #19515 - invalid citation handling changed with 24.2. by @jmchilton in #19716
• [24.2] Conditionally import from galaxy.config in galaxy.model.mapping if TYPE_CHECKING by @natefoo in #20209
• [24.0] Fall back to name in job summary if no input label given by @mvdbeek in #20258
• [24.1] Refactor display_as URL generation for UCSC links and fix to remove double slashes in URL by @natefoo in #20239
• [24.2] Fix WF Run RO-Crate logo width in Firefox by @davelopez in #20305
• [24.2] Fix searching roles in admin UI by @jdavcs in #20394
• [24.2] Fix unit tests returning values by @nsoranzo in #20413
• [24.2] Fix mull_targets() with mamba 2.x by @nsoranzo in #20416
• [24.2] Skip validation of expression.json input in workflow parameter validator by @mvdbeek in #20412
• [24.2] Fix mulled-search --destination quay, add index reuse by @natefoo in #20107
• [24.2] Prevent running datatype autodetect on purged datasets by @mvdbeek in #20479
• [24.2] Fix legacy get_metadata_file controller route by @mvdbeek in #20477
• [24.2] Make response header values strings by @mvdbeek in #20475
• [24.2] Link workflow invocation outputs upon importing invocation by @mvdbeek in #20485
• [24.2] Make optional edam-ontology in datatypes registry optional by @natefoo in #20492

Full Changelog: v24.2.3...v24.2.4