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41797 Commits
Author SHA1 Message Date
Nicola Soranzo d95f823b3f Merge branch 'release_24.2' into release_25.0 2025-07-07 16:06:01 +01:00
Nicola Soranzo 777ec1ef42 Merge branch 'release_24.1' into release_24.2 2025-07-07 16:00:41 +01:00
David LópezandMarius van den Beek bad87c198a Add comment for version constraint 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2025-07-07 15:33:21 +02:00
davelopez acd6798198 Update redis version constraint to allow only minor updates 2025-07-07 15:06:46 +02:00
Marius van den Beek b2e75709c6 Merge pull request #20596 from davelopez/25.0_fix_invalid_workflow_uuid 
[25.0] Prevent importing workflows with invalid step UUID
 2025-07-04 18:38:12 +02:00
John Davis 8711543bb8 Do not set attribute on a namedtuple 2025-07-03 16:29:55 -04:00
David LópezandNicola Soranzo 1708721eab Refactor test to simplify assertion 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2025-07-03 14:07:42 +02:00
davelopez a773285183 Clarify exception message for invalid UUID version 4 2025-07-03 13:36:48 +02:00
davelopez 7318b85469 Add test for invalid UUID v4 format in workflow steps 2025-07-03 13:33:06 +02:00
davelopez 8ca67561b0 Validate UUID v4 format for workflow steps on import 2025-07-03 10:21:56 +02:00
davelopez 5b6c478789 Add utility function to validate UUID v4 format 2025-07-03 10:20:43 +02:00
mvdbeek 66266f39f8 Don't fail volume mount construction for tool_directory-less tools 
Dev's hate this one simple trick: https://github.com/galaxyproject/usegalaxy-playbook/blob/4963808ac295ef49b786f619b5b659d158e0be0b/env/main/group_vars/galaxyservers/vars.yml#L133
 2025-07-02 16:54:26 +02:00
mvdbeek 0cf6540485 Merge branch 'release_24.2' into release_25.0 2025-07-02 16:37:04 +02:00
John Chilton cb97a19aef Merge pull request #20582 from mvdbeek/apply_rules_fix 
[24.2] Fix apply rules ownership check
 2025-07-02 10:23:44 -04:00
Marius van den Beek cb93c7b976 Merge pull request #20502 from davelopez/add_redis_conditional_dependency 
[25.0] Add redis conditional dependency
 2025-07-01 10:58:00 -04:00
mvdbeek 06498946fc Fix apply rules ownership check 2025-06-28 14:59:17 -04:00
Nate Coraor c5fb942ef2 Don't assume cwd = job directory when running prepare dirs 2025-06-27 13:39:45 -04:00
Nate Coraor 8f5147488a Version split requests-unixsocket 2025-06-25 15:21:48 -04:00
Nate Coraor 161ce32729 Upgrade requests-unixsocket for requests compatibility 2025-06-25 15:07:55 -04:00
Marius van den Beek 89b37a6701 Merge pull request #20545 from mvdbeek/fix_user_defined_tool_extension 
[25.0] Fix restricting user defined tool input datasets extensions
 2025-06-23 09:22:50 -04:00
davelopez f3ae4b2fd5 Improve Redis URL validation in conditional dependencies check 2025-06-23 11:28:31 +02:00
davelopez 74a4f30c5b Fix format 2025-06-23 09:17:07 +02:00
mvdbeek 462955599b Fix extension parsing for yaml tools 2025-06-22 19:22:59 -04:00
Marius van den Beek 6fe8a7bf6d Merge pull request #20464 from mvdbeek/drop_num_unique_values 
[25.0] Remove ``num_unique_values`` tiff metadata element
 2025-06-22 08:32:30 +02:00
Nicola Soranzo 4b1558b284 Move definition of DatasetCollectionDescriptionT before its use 
Fix the following error on py37-test_galaxy_packages_for_pulsar tests:

```
FAILED tests/tool_util/test_input_models.py::test_input_collection_type - pydantic.errors.PydanticUserError: `ParsedTool` is not fully defined; you should define `DatasetCollectionDescriptionT`, then call `ParsedTool.model_rebuild()`.
```

Backport of commit bb87560d8f .
 2025-06-21 17:37:26 +01:00
Marius van den BeekandNicola Soranzo e0d3ebc110 Make redis check a little more specific 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2025-06-21 11:00:05 +02:00
Nate Coraor 751b52f1ec Start work on 25.0.2.dev0 2025-06-20 16:37:11 -04:00
Nate Coraor 5915a88342 Create version 25.0.1 2025-06-20 16:37:07 -04:00
Nate Coraor 7899dfbfbc Bump Gravity to 1.1.1 2025-06-20 11:44:22 -04:00
Nicola Soranzo cc26ab7834 Merge branch 'release_24.2' into release_25.0 2025-06-20 13:00:45 +01:00
Nicola Soranzo 36ef67be1f Merge branch 'release_24.1' into release_24.2 2025-06-20 13:00:05 +01:00
Nicola Soranzo c96792693c Merge branch 'release_24.0' into release_24.1 2025-06-20 12:55:50 +01:00
Marius van den Beek a55b61c5b4 Merge pull request #20524 from bernt-matthias/users 
[24.2] Do not expose user info to non authenticated users
 2025-06-20 12:21:33 +02:00
Marius van den Beek 94ed4a6a9b Merge pull request #20531 from natefoo/config-script-fixes 
[25.0] Fix `galaxy-config` script, move install to `galaxy-dependencies` in app package
 2025-06-20 09:46:11 +02:00
Marius van den Beek a594358d91 Merge pull request #20527 from natefoo/isa-rwval-0.10.11 
[25.0] Pin isa-rwval 0.10.11, drop conditional import handling
 2025-06-20 09:43:07 +02:00
Nate Coraor 6a887e0aff Fix galaxy-config script, move install to galaxy-dependencies in app package 2025-06-19 16:58:43 -04:00
Marius van den Beek cb4d73917b Merge pull request #20529 from nsoranzo/release_25.0_fix_tool-util_pkg 
[25.0] Fix import of ``galaxy.tool_util.cwl`` module
 2025-06-19 22:45:28 +02:00
Nicola Soranzo 0764567b21 Fix import of `galaxy.tool_util.cwl` module 
when cwltool is not installed.

Fix:

```
Traceback (most recent call last):
  File "/home/conda/feedstock_root/build_artifacts/galaxy-tool-util_1750355530639/test_tmp/run_test.py", line 11, in <module>
    import galaxy.tool_util.cwl
  File "/home/conda/feedstock_root/build_artifacts/galaxy-tool-util_1750355530639/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/python3.9/site-packages/galaxy/tool_util/cwl/__init__.py", line 2, in <module>
    from .parser import (
  File "/home/conda/feedstock_root/build_artifacts/galaxy-tool-util_1750355530639/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/python3.9/site-packages/galaxy/tool_util/cwl/parser.py", line 122, in <module>
    class ToolProxy(metaclass=ABCMeta):
  File "/home/conda/feedstock_root/build_artifacts/galaxy-tool-util_1750355530639/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/python3.9/site-packages/galaxy/tool_util/cwl/parser.py", line 127, in ToolProxy
    tool: process.Process,
AttributeError: 'NoneType' object has no attribute 'Process'
```
 2025-06-19 20:32:43 +01:00
Nicola Soranzo fdf931b954 Fix new `test_index_anon` API test 2025-06-19 20:01:47 +01:00
Nate Coraor fd41e726e1 Pin isa-rwval 0.10.11, drop conditional import handling 2025-06-19 14:12:25 -04:00
Matthias Bernt 98ddca1e11 fixup 2025-06-19 19:34:52 +02:00
Matthias Bernt 79d08a4d2f Merge branch 'users' of https://github.com/bernt-matthias/galaxy into users 2025-06-19 19:09:02 +02:00
Matthias Bernt b71eaaf437 try to add test 2025-06-19 18:58:01 +02:00
M BerntandNicola Soranzo 14ab0e22b8 Raise exception for unauthenicated users 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2025-06-19 18:27:34 +02:00
Matthias Bernt 4b7afea7da never exopose user info to non authenticated users 
fixes https://github.com/galaxyproject/galaxy/issues/20505

should be fine is non-authenticated users can't share anything
(not sure about this)
 2025-06-19 16:21:35 +02:00
Nicola Soranzo f4b5e74c91 Merge pull request #20520 from mvdbeek/gravity_1_1_0 
[25.0] Bump gravity dependency to 1.1.0
 2025-06-19 15:07:02 +01:00
Marius van den Beek e95a55907f Merge pull request #20516 from natefoo/web-client-static-fixes 
[25.0] Fixes for static handling and the web_client package
 2025-06-19 11:18:23 +02:00
mvdbeek d95d07b059 Bump gravity dependency to 1.1.0 
So that the next package release will use
https://github.com/galaxyproject/gravity/releases/tag/v1.1.0.
I want to use this in planemo.
 2025-06-19 10:29:09 +02:00
mvdbeek 43feb0efb3 Merge branch 'release_24.2' into release_25.0 2025-06-19 10:17:22 +02:00
Marius van den Beek 044442bdfb Merge pull request #20511 from mvdbeek/fix_too_strict_validation 
[24.2] Relax validation of XML test assertion parsing
 2025-06-19 10:15:16 +02:00