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Author SHA1 Message Date
John Davis 09fee6aaad Remove future, autocommit args from session and engine creation 2024-04-05 13:54:39 -04:00
John Davis dcf2d84304 Fix method resolution order for base model class 2024-04-05 13:45:34 -04:00
John Davis 8e75d32ced Use DeclarativeBase as base class 
mypy bug workaround no longer needed as we are no longer specifying a metaclass
 2024-04-05 13:45:34 -04:00
Martin Cech bab7a6a132 Merge pull request #17905 from galaxyproject/dependabot/npm_and_yarn/client/undici-5.28.4 
Bump undici from 5.28.3 to 5.28.4 in /client
 2024-04-05 00:15:25 +02:00
Martin Cech 286092522f Merge branch 'release_24.0' into dev 2024-04-04 15:10:50 -07:00
Martin Cech 1cd9752195 Merge pull request #17895 from martenson/backp 
[24.0] do not show copy button when editing
 2024-04-05 00:00:08 +02:00
Björn Grüning b3ccb040f9 Merge pull request #17647 from itisAliRH/collection-components-refactors 
Collection components refactors
 2024-04-04 20:29:25 +02:00
dependabot[bot] 95e26c34bd Bump undici from 5.28.3 to 5.28.4 in /client 
Bumps [undici](https://github.com/nodejs/undici) from 5.28.3 to 5.28.4.
- [Release notes](https://github.com/nodejs/undici/releases)
- [Commits](https://github.com/nodejs/undici/compare/v5.28.3...v5.28.4)

---
updated-dependencies:
- dependency-name: undici
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
 2024-04-04 17:21:15 +00:00
mvdbeek 6f2a04321d Merge branch 'release_24.0' into dev 2024-04-04 18:55:04 +02:00
mvdbeek d308444f92 Merge branch 'release_23.2' into release_24.0 2024-04-04 18:47:22 +02:00
Marius van den Beek 173b326a76 Merge pull request #17901 from mvdbeek/fix_workflow_saving 
[23.2] Fix saving workflows with freehand_comments only
 2024-04-04 18:45:40 +02:00
Martin Cech cd7de5511d disable instead of hiding 2024-04-04 09:39:23 -07:00
John Chilton 661d93ab2a Merge pull request #17869 from mvdbeek/drop_dummy_replacement 
[24.0] Fix workflow run form failing on certain histories
 2024-04-04 11:06:54 -04:00
Marius van den Beek 46c20cd829 Merge pull request #17899 from mvdbeek/fix_basic_tool_util 
[24.0] Fix conditional Image imports
 2024-04-04 16:44:30 +02:00
mvdbeek b825f798ca Reduce for loop nesting 2024-04-04 16:14:55 +02:00
mvdbeek 023178db2f Fix saving workflows with freehand_comments only 2024-04-04 15:53:33 +02:00
mvdbeek d331cc2339 Fix conditional Image imports 2024-04-04 15:06:18 +02:00
Nicola Soranzo 4a4ead2b5e Merge branch 'release_24.0' into dev 2024-04-04 12:57:27 +01:00
Martin Cech 7aedfa4a67 Merge pull request #17849 from hexylena/rat-hops 
Rename to JupyTool something more searchable (i.e. JupyterLab which includes the substring Jupyter)
 2024-04-04 05:58:22 +02:00
Martin Cech e970ae521e Merge pull request #17898 from nsoranzo/release_24.0_sphinx_rtd_theme_conf_fixes 
[24.0] Fix search and version menu in docs
 2024-04-04 05:54:25 +02:00
Nicola Soranzo ed5b0023ff Fix search and version menu in docs 
The `html_theme_path` option should not be used any more with
sphinx-rtd-theme since it switches off the theme's ability to
automatically enable the sphinxcontrib-jquery extension, i.e.
jQuery is not loaded in the web pages when building the docs with
Sphinx >=6.

xref: https://github.com/readthedocs/sphinx_rtd_theme/issues/1434#issuecomment-1472671651

Also replace the deprecated `canonical_url` theme option with
Sphinx's `html_baseurl`.

xref: https://sphinx-rtd-theme.readthedocs.io/en/stable/configuring.html#confval-canonical_url
 2024-04-04 02:39:52 +01:00
Martin Cech 4827ff89d8 Merge pull request #17896 from mvdbeek/shorten_transaction 
[24.0] Fix deadlock that can occur when changing job state
 2024-04-04 00:17:49 +02:00
John Chilton d8756c6cc3 Merge pull request #17853 from jmchilton/storage_management_within_history 
Enable managing object store usage within a history.
 2024-04-03 15:39:20 -04:00
Marius van den BeekandJohn Davis 2594276b13 Update comments 
Co-authored-by: John Davis <jdavcs@gmail.com>
 2024-04-03 19:39:50 +02:00
mvdbeek 061d4c32db Commit after changing job state 2024-04-03 19:19:40 +02:00
mvdbeek 16e0e4b775 Only update job if state really changed 2024-04-03 19:19:40 +02:00
Martin Cech 4f331e4a70 do not show copy button when editing 2024-04-03 10:16:53 -07:00
Martin Cech 0d3e8cd2b6 Merge pull request #17888 from martenson/no-copy-edit 
do not show published item copy button when editing slug
 2024-04-03 19:14:33 +02:00
John ChiltonandDavid López b7ec41f584 Update client/src/components/User/DiskUsage/Visualizations/HistoryStorageOverview.vue 
Co-authored-by: David López <46503462+davelopez@users.noreply.github.com>
 2024-04-03 13:02:58 -04:00
Marius van den Beek ab2aa7d31c Merge pull request #17892 from mvdbeek/fix_assert_ok 
[24.0] Make `wait_for_history_jobs` look at jobs, not datasets
 2024-04-03 17:20:57 +02:00
Marius van den Beek 28c8b2fdd2 Merge pull request #17866 from kostrykin/verify_imagediff_iou/upstream 
Add `pin_labels` attribute for `image_diff` comparison method
 2024-04-03 17:19:47 +02:00
John Davis af53d03c0a Merge pull request #17778 from jdavcs/dev_sa20 
SQLAlchemy 2.0
 2024-04-03 10:19:00 -04:00
Leonid Kostrykin 8515eed646 Set DEFAULT_PIN_LABELS to None 2024-04-03 15:50:10 +02:00
John Davis 4bb7dd0313 Merge pull request #17894 from jdavcs/24.0_notesfix2 
[24.0] Fix release notes
 2024-04-03 09:34:56 -04:00
Nicola Soranzo 4984523c39 Change test with no outputs to not fail 
``out_3`` has been removed in https://github.com/galaxyproject/galaxy/pull/17874 .
 2024-04-03 13:11:36 +01:00
Nicola Soranzo 1332eb1620 Fix `test_workflow_optional_input_filtering` API test to produce one output again 2024-04-03 13:10:53 +01:00
mvdbeek 8ab16a9f6f Make wait_for_history_jobs look at jobs, not datasets 
That fixes test_optional_workflow_output, which started failing after
https://github.com/galaxyproject/galaxy/pull/17874, which removed the
last static output of `output_filter`, and so there would never be any
active datasets to wait on.
 2024-04-03 13:23:42 +02:00
Marius van den Beek 8139b76401 Merge pull request #17890 from mvdbeek/fix_empty_nested_collection_element_count 
[24.0] Always serialize element_count and populated when listing contents
 2024-04-03 13:13:59 +02:00
mvdbeek 6034a358eb Merge branch 'release_24.0' into dev 2024-04-03 11:21:37 +02:00
mvdbeek 3920f21bc6 Merge branch 'release_23.2' into release_24.0 2024-04-03 11:21:14 +02:00
Marius van den Beek a7398dfb66 Merge pull request #17875 from SaimMomin12/release_23.2 
Added 4dn_pairs and 4dn_pairsam datatypes
 2024-04-03 11:20:36 +02:00
Marius van den Beek 5548b11b0c Merge pull request #17886 from ahmedhamidawan/fix_history_has_owner_function 
[24.0] Fix hasOwner function for histories in client
 2024-04-03 11:15:52 +02:00
mvdbeek f21cbdaa9f Always serialize element_count and populated when listing collection contents 
Fixes https://github.com/galaxyproject/galaxy/issues/17883
 2024-04-03 11:06:47 +02:00
John Davis c0b81c4218 Merge pull request #17889 from jdavcs/24.0_releasenotes_videos 
[24.0] Fix release notes images and videos
 2024-04-02 23:57:29 -04:00
John Davis 9501826257 Fix release notes 
correct links to videos
better images
 2024-04-02 22:28:15 -04:00
John Davis 1df03738da Merge branch 'release_24.0' into dev 
# Conflicts:
#	lib/galaxy/version.py
 2024-04-02 19:07:06 -04:00
John Davis a7f310c163 Start work on 24.0.1.dev0 2024-04-02 19:07:02 -04:00
John Davis 119aaa031f Create version 24.0.0 v24.0.0 2024-04-02 19:06:58 -04:00
Martin Cech 04d3a9f4e1 do not show copy button when editing 2024-04-02 14:17:36 -07:00
John Davis 33505f754d Update version to 24.0.0.dev0 2024-04-02 15:01:44 -04:00