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8139 Commits
Author SHA1 Message Date
mvdbeek 6f2a04321d Merge branch 'release_24.0' into dev 2024-04-04 18:55:04 +02:00
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
Nicola Soranzo 4a4ead2b5e Merge branch 'release_24.0' into dev 2024-04-04 12:57:27 +01:00
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
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 406c22e980 Merge branch 'release_24.0' into dev 2024-04-02 18:18:53 +01:00
mvdbeek 626baad567 Refactor RuntimeValue utils for re-use 
Moving this to tools.parameters.workflow_utils avoids a circular
dependency when importing is_runtime_value in
tools.parameters.dynamic_options.
 2024-04-02 19:10:20 +02:00
mvdbeek 55029be8eb Avoid get_initial_value when we have a tool state 
It's not guaranteed this will always work, and it's unnecessary if
we have e.g. `ConnectedValue` in a workflow context.
 2024-04-02 19:10:20 +02:00
mvdbeek 969e995a9b Add test tool w/ dynamic select in conditional 
Include this in a workflow, and notice that the run form breaks
if the history contains a dataset that trips up the dynamic parameter.
 2024-04-02 19:10:20 +02:00
John Davis f52d35bf7f Use NullPool for sqlite engines 
This restores the behavior under SQLAlchemy 1.4
(Note that we set the pool for sqlite only if it's not an in-memory db
 2024-04-02 10:08:53 -04:00
John Davis 28fd6ad99b Fix package mypy errors 2024-04-02 10:08:53 -04:00
John Davis 78a77d934a Mypy: typing errors, misc. fixes 2024-04-02 10:08:53 -04:00
John Davis 511816e51d Mypy: type-ignore: scoped_session vs. install_model_session 
We use the disctinction for DI.
 2024-04-02 10:08:53 -04:00
John Davis f1579e13de Fix typing error: use Session instead of scoped_session 
No need to pass around scoped_session as arguments
 2024-04-02 10:08:53 -04:00
John Davis fb018c54bc Fix SA2.0 error: use Row._mapping for keyed attribute access 
Ref: https://docs.sqlalchemy.org/en/20/changelog/migration_20.html#result-rows-act-like-named-tuples
 2024-04-02 10:08:53 -04:00
M Bernt e1ec2c8b28 Update test/functional/tools/output_filter.xml 2024-04-02 09:46:55 +02:00
M Bernt ae594c18bc Add back test output 2024-04-02 09:46:55 +02:00
Matthias Bernt 46abd27123 make test a bit more specific 2024-04-02 09:46:55 +02:00
Matthias Bernt 6687cdc3ca adapt output filter test 
- remove the output that is always present
- add a test that has no outputs
 2024-04-02 09:46:22 +02:00
Leonid Kostrykin cdfc3f0e57 Add pin_labels attribute for image_diff comparison method 2024-03-29 12:01:34 +01:00
John Chilton 383057d9b8 Linting fix. 2024-03-27 13:25:50 -04:00
John Chilton 77ef4a3896 objectstores storage management (UI+API) 2024-03-27 10:22:59 -04:00
Matthias Bernt af612e9342 add linting for valid EDAM terms 2024-03-26 09:40:15 +01:00
mvdbeek 06a07bb295 Merge branch 'release_24.0' into dev 2024-03-21 19:08:38 +01:00
John Davis 7af9c3d127 Merge pull request #17728 from jmchilton/history_update_bug 
[24.0] Fix source history update_time being updated when importing a public history
 2024-03-21 12:35:02 -04:00
Marius van den Beek 429c63e856 Merge pull request #17797 from kostrykin/tifffile 
Add support for floating point TIFF files in verification of image-based tool outputs
 2024-03-20 15:54:22 +01:00
mvdbeek cd16d19d8a Merge branch 'release_24.0' into dev 2024-03-20 15:50:39 +01:00
Leonid Kostrykin 45a819ebc8 Adds tifffile support for image assertions 2024-03-20 10:12:17 +01:00
Leonid Kostrykin 4fffff6db6 Add float TIFF test case (fails with Pillow) 2024-03-19 22:03:34 +01:00
Marius van den Beek 020bfcdec8 Merge pull request #17777 from mvdbeek/fix_copy_of_hda_not_getting_metadata 
[24.0] Also set extension and metadata on copies of job outputs when finishing job
 2024-03-19 19:53:03 +01:00
mvdbeek 113430fd45 Merge branch 'release_24.0' into dev 2024-03-19 11:43:15 +01:00
mvdbeek 6f08b9fc9c Add unit test for updating output hda copies 2024-03-19 10:41:16 +01:00
Ahmed Awan 7eb3cc9059 allow exact query search (surrounded by quotes) in grids 
Users can bypass the client filtering by surrounding their raw search query by quotes and sending the unprocessed filter to the backend.
 2024-03-18 14:44:02 -05:00
John Chilton e67bff7349 Why doesn't the update bug appear at the model level? 2024-03-18 10:10:54 -04:00
mvdbeek 8bdf4b71d7 Merge branch 'release_24.0' into dev 2024-03-18 11:32:36 +01:00
Martin Cech 4b1b600139 fix oidc logout test 
which relied on receiving 400
 2024-03-16 17:46:08 -07:00
Leonid Kostrykin fc67b20444 Fix bug in assert_has_image_n_labels 2024-03-15 14:16:06 +01:00
Marius van den Beek e2b67da82c Merge pull request #17581 from kostrykin/files_assertions_images 
Add content assertion XML tags for test output verification using images
 2024-03-13 13:08:55 +01:00
Leonid Kostrykin 8a81593c53 Rename has_image_labels to has_image_n_labels 2024-03-13 09:34:34 +00:00
Leonid Kostrykin 5964f72dfc Rename assertion attribute value 2024-03-13 07:28:48 +00:00
Dannon a62177e525 Merge pull request #17653 from galaxybot/dev_auto_update_dependencies 
Update Python dependencies
 2024-03-12 14:32:25 -05:00
John Chilton 0a3e222e62 Merge pull request #17655 from bernt-matthias/topic/lint-bio.tools 
tool linter: check for valid bio.tools entries
 2024-03-12 13:43:48 -04:00
Nicola Soranzo 330599c70f Fixes for new errors from ruff 0.3.2 2024-03-12 11:06:57 +00:00
John Davis 728bbeb296 Merge pull request #17654 from nsoranzo/ruff_C4_pyupgrade 
Code cleanups from ruff and pyupgrade
 2024-03-11 15:21:30 -04:00
Matthias Bernt 3dae54a672 make it a warning 2024-03-11 15:23:52 +01:00
mvdbeek 74766a3fb5 Merge branch 'release_24.0' into dev 2024-03-11 12:02:17 +01:00
mvdbeek 3dbc2c6760 Merge branch 'release_23.2' into release_24.0 2024-03-11 11:55:56 +01:00
Matthias Bernt 4e1a6d3b94 tool tinter: check for valid bio.tools entries 2024-03-11 11:47:55 +01:00
Leonid Kostrykin fb7bbaaa83 Rename delta to eps for float-based assertions (#1) 
* Rename `delta` to `eps` for float-based assertions

* Fix tests
 2024-03-11 11:31:23 +01:00