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Author SHA1 Message Date
mvdbeek 2c19e16994 Assert dynamic tool error message specificity 2025-09-01 17:36:10 +02:00
mvdbeek 60d12acb7d Serialize step tool_uuid as string, not UUID class instance 2025-09-01 17:36:10 +02:00
mvdbeek 8272fbf7a8 Display error message in custom tool editor 2025-09-01 17:36:09 +02:00
mvdbeek 4cf80afcaa Fix invocation step view with custom tools 2025-09-01 17:36:09 +02:00
mvdbeek 612d9fdb75 Fix tool form updates custom tools 2025-09-01 17:36:09 +02:00
mvdbeek 826be2ba83 Use literal block quotes 2025-09-01 17:36:09 +02:00
mvdbeek ec186820cc Rebuild openapi schema 2025-09-01 17:36:09 +02:00
mvdbeek 4d75e3b066 Default to skip if data style unspecified 2025-09-01 17:36:08 +02:00
mvdbeek 0308f25b43 Implement templatable configfiles for yaml tools 2025-09-01 17:36:08 +02:00
mvdbeek b801dfe94b Fix tool form loading 2025-09-01 17:36:08 +02:00
mvdbeek 1848693e9c Add button to deactivate user defined tool 2025-09-01 17:36:08 +02:00
Nicola Soranzo 5777a716dd Merge pull request #20841 from galaxybot/dev_auto_update_dependencies 
Update Python dependencies
 2025-08-30 18:20:25 +01:00
galaxybot d49bc365c4 Update Python dependencies 
by running `make update-dependencies`.
 2025-08-30 03:16:24 +00:00
Ahmed Hamid Awan 3b68c38af0 Merge pull request #20837 from ahmedhamidawan/fix_workflow_success_lint_error 
Fix lint error in `WorkflowRunSuccess`
 2025-08-29 15:10:07 -05:00
mvdbeek 30af8fb6ea Merge branch 'release_25.0' into dev 2025-08-29 20:00:19 +02:00
mvdbeek 4225e4b0fa Merge branch 'release_24.2' into release_25.0 2025-08-29 19:59:33 +02:00
Ahmed Awan 9408c4e9cb Fix lint error in WorkflowRunSuccess 
This was caused in https://github.com/galaxyproject/galaxy/pull/20797#issuecomment-3237586999
 2025-08-29 12:56:41 -05:00
Marius van den Beek 4ea216f0e1 Merge pull request #20836 from mvdbeek/include_user_agent 
[24.2] Include galaxy user agent in data source tools
 2025-08-29 19:40:44 +02:00
mvdbeek 541d70acf6 Include galaxy user agent in data source tools 
Closes https://github.com/galaxyproject/galaxy/issues/20833
 2025-08-29 17:22:28 +02:00
Nicola Soranzo dcd415a293 Merge pull request #20834 from bernt-matthias/bump-directory-converters 
Bump requirement of directory converters
 2025-08-29 16:55:41 +02:00
Alireza Heidari 56dc017e6f Merge pull request #20797 from guerler/refactor_webhooks 
Remove Backbone dependency from webhook wrappers
 2025-08-29 14:57:37 +02:00
Matthias Bernt d76747df7d bump requirement of directory converters 
with conda I get

```
Traceback (most recent call last):
  File "<string>", line 1, in <module>
    from galaxy.util.compression_utils import CompressedFile; CompressedFile('/tmp/tmp3v2nuot4/files/a/9/7/dataset_a97aebb4-46f7-47a9-b418-11ff1deeed74.dat').extract('.')
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/berntm/miniforge3/envs/__galaxy-util@23.2.1/lib/python3.13/site-packages/galaxy/util/compression_utils.py", line 29, in <module>
    from .checkers import (
    ...<2 lines>...
    )
  File "/home/berntm/miniforge3/envs/__galaxy-util@23.2.1/lib/python3.13/site-packages/galaxy/util/checkers.py", line 20, in <module>
    from galaxy.util.image_util import image_type
  File "/home/berntm/miniforge3/envs/__galaxy-util@23.2.1/lib/python3.13/site-packages/galaxy/util/image_util.py", line 3, in <module>
    import imghdr
ModuleNotFoundError: No module named 'imghdr'
```
 2025-08-29 13:03:00 +02:00
John Chilton b186d0e9d5 Merge pull request #20829 from jmchilton/collection_operation_icons 
Migrate icon defs in CollectionOperations.vue to best practices.
 2025-08-28 12:52:48 -04:00
John Chilton 0088f13b74 Migrate icon defs in CollectionOperations to best practices. 2025-08-28 10:30:36 -04:00
John Chilton fcb5e414da Merge pull request #20805 from davelopez/add_huggingface_file_source 
Add Hugging Face 🤗 file source and user-defined template
 2025-08-28 09:36:32 -04:00
Marius van den Beek 49ef7aadac Merge pull request #20823 from mvdbeek/precommit_config_ignore_json_yaml 2025-08-28 15:30:26 +02:00
Marius van den Beek 543de69bf3 Merge pull request #20826 from nsoranzo/fixes_from_cwl 
Small improvements for running CWL tools
 2025-08-28 09:15:20 +02:00
Marius van den Beek 4f41fe3b88 Merge pull request #20824 from nsoranzo/doc_fixes 
Update 2 docs pages
 2025-08-28 09:12:44 +02:00
Nicola Soranzo 1a721fbc22 Get tool versions instead of the whole tool panel to check tool presence 2025-08-27 19:51:39 +01:00
Nicola Soranzo 2293a085bc Log exception if converting toolbox to dict fails 2025-08-27 19:51:38 +01:00
Nicola SoranzoandMarius van den Beek be6a0dee57 Drop unnecessary "just" 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2025-08-27 19:18:20 +01:00
Aysam Guerler b49e4355a8 Merge pull request #20771 from ahmedhamidawan/fix_and_refactor_tours 
Modernize and Refactor Tour components
 2025-08-27 20:55:25 +03:00
Nicola Soranzo a802727c33 Update docs on debugging tests within GitHub actions 
Subsets were replaced with shards in commit 992edaa8b4 .
 2025-08-27 16:33:43 +01:00
Nicola Soranzo 7fa47d4ba6 Update Python instructions for admins 2025-08-27 16:30:39 +01:00
mvdbeek a2d11cef42 Ignore yaml and json in prettier pre-commit hook 
The .prettierignore file appears to not be respected,
but I think this is the only relevant discrepancy with .prettierignore,
as we either won't change the remaining files or they're already in
.gitignore.
 2025-08-27 16:10:41 +02:00
Marius van den Beek 9b35015f28 Merge pull request #20822 from mvdbeek/webpack_dev_server_fix 
Fix webpack dev server detection
 2025-08-27 15:30:39 +02:00
mvdbeek 9f0be71efd Update pre-commit sample for newer prettier 2025-08-27 15:23:03 +02:00
Marius van den Beek 65d634e347 Update client/webpack.config.js 2025-08-27 15:10:45 +02:00
mvdbeek ae6c504e3e Fix webpack dev server detection 2025-08-27 15:06:24 +02:00
Ahmed Awan 3fd9b12f44 cache tours to make runTour also work 
This exists solely for the `tour_generator` webhook as of now. We are going to be refactoring and changing that from a webhook to core functionality, so we have also commented out the selenium that tests "Tool Describing Tours".
 2025-08-26 14:05:24 -05:00
Ahmed Awan 1721497f31 prevent localStorage persistentRef from being string null/undefined 2025-08-26 12:23:26 -05:00
guerler 68ebc87c44 Fix masthead webhook request method 2025-08-26 20:04:10 +03:00
guerler 7892a28944 Update masthead webhook loading 2025-08-26 20:04:10 +03:00
guerler 31d0f63b87 Modernize webhook wrappers, remove backbone dependency 2025-08-26 20:04:10 +03:00
guerler c32097c1fe Import only appendScriptStyle in webhooks 2025-08-26 20:04:09 +03:00
Ahmed AwanandAysam Guerler 568429e076 add tourStore that keeps track of a running tour 
We mount `TourRunner` in `App.vue` instead of `Analysis.vue`, because this way we can have a tour run across all routes (even workflow editor, published views etc.).

Note that an entire page reload resets the store still...

Co-authored-by: Aysam Guerler <aysam.guerler@gmail.com>
 2025-08-26 10:37:01 -05:00
Ahmed Awan 13094f558d use GLink and API types in TourList 2025-08-26 10:36:01 -05:00
Ahmed Awan 279ae4a17d modernize TourStep component 2025-08-26 10:35:59 -05:00
Ahmed Awan 04afe32001 add waiting for element indicator when waiting on a CSS element 2025-08-26 10:35:20 -05:00
Ahmed Awan 0b61328a70 rename tour end button from "Cancel" to "End Tour" 2025-08-26 10:35:20 -05:00