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Author SHA1 Message Date
Ahmed Awan dfd897b0f3 [25.0] Fix css alignment styling of login page 2025-06-10 10:51:26 -05:00
Nicola Soranzo 2e663169e5 Merge branch 'release_24.2' into release_25.0 2025-06-09 21:50:24 +01:00
Nicola Soranzo 1155081c20 Merge pull request #20419 from mvdbeek/update_pulsar_galaxy_lib 
[25.0] Update pulsar-galaxy-lib to 0.15.8
 2025-06-09 21:47:49 +01:00
John Chilton ddc07c9075 Merge pull request #20412 from mvdbeek/fix_validators_from_expression_json 
[24.2] Skip validation of expression.json input in workflow parameter validator
 2025-06-09 14:50:54 -04:00
John Chilton b986a92c54 Merge pull request #20414 from mvdbeek/fix_cheetah_app_access_python_3_13 
[25.0] Fix $app attribute access in cheetah templates
 2025-06-09 14:49:27 -04:00
mvdbeek 29088af250 Update pulsar-galaxy-lib to 0.15.8 
Fixes https://github.com/galaxyproject/pulsar/issues/392
 2025-06-09 19:41:29 +02:00
Marius van den Beek c3e93a8752 Merge pull request #20417 from mvdbeek/rerun_fix 
[25.0] Fix job rerun with tool version change
 2025-06-09 15:53:48 +02:00
mvdbeek 4f545f424d Fix job rerun with tool version change 
Fixes https://github.com/galaxyproject/galaxy/issues/20337, broken in https://github.com/galaxyproject/galaxy/pull/20259
 2025-06-09 12:16:26 +02:00
mvdbeek d61d3fed03 Fix $app attribute access in cheetah templates 
Fixes https://github.com/galaxyproject/galaxy/issues/20365,
which occurs only on Python 3.13 on datasets that can be visualized by a
display application.
 2025-06-09 11:55:43 +02:00
Nicola Soranzo 90fad91813 Merge branch 'release_24.2' into release_25.0 2025-06-08 21:47:42 +01:00
Marius van den Beek 323d47e827 Merge pull request #20416 from nsoranzo/release_24.2_fix_mull_targets_mamba 
[24.2] Fix ``mull_targets()`` with mamba 2.x
 2025-06-08 20:51:56 +02:00
Nicola Soranzo 252a7fd72c Fix type annotation for NumPy 2.3.0 
Fix the following issues in py313-test_galaxy_packages :

```
galaxy/tool_util/verify/asserts/image.py:763: error: Incompatible types in
assignment (expression has type "list[Any]", variable has type
"ndarray[tuple[Any, ...], dtype[Any]]")  [assignment]
            present_labels = [label for label in present_labels if label i...
                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~...
galaxy/tool_util/verify/asserts/image.py:770: error: Incompatible types in
assignment (expression has type "list[Any]", variable has type
"ndarray[tuple[Any, ...], dtype[Any]]")  [assignment]
        present_labels = [label for label in present_labels if label not i...
                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~...
galaxy/tool_util/verify/asserts/image.py:773: error: Incompatible return value
type (got
"tuple[ndarray[tuple[Any, ...], dtype[Any]], ndarray[tuple[Any, ...], dtype[Any]]]",
expected "tuple[ndarray[tuple[Any, ...], dtype[Any]], list[Any]]")
[return-value]
        return im_arr, present_labels
               ^~~~~~~~~~~~~~~~~~~~~~
```
 2025-06-08 14:04:56 +01:00
Nicola Soranzo 162fe28318 Fix `mull_targets()` with mamba 2.x 
Fix mulled unit test test/unit/tool_util/mulled/test_mulled_build.py::test_mulled_build_files_cli[True] :

```
use_mamba = True
tmpdir = local('/tmp/pytest-of-runner/pytest-0/test_mulled_build_files_cli_Tr0')

    @pytest.mark.parametrize("use_mamba", [False, True])
    @external_dependency_management
    def test_mulled_build_files_cli(use_mamba: bool, tmpdir) -> None:
        singularity_image_dir = tmpdir.mkdir("singularity image dir")
        target = build_target("zlib", version="1.2.13", build="h166bdaf_4")
        involucro_context = InvolucroContext(involucro_bin=os.path.join(tmpdir, "involucro"))
        exit_code = mull_targets(
            [target],
            involucro_context=involucro_context,
            command="build-and-test",
            singularity=True,
            use_mamba=use_mamba,
            singularity_image_dir=singularity_image_dir,
        )
>       assert exit_code == 0
E       assert 1 == 0

...

[Jun  7 08:40:09] SERR error    libmamba Expected environment not found at prefix: /usr/local
[Jun  7 08:40:09] SERR critical libmamba Aborting.
```

Upstream issue: https://github.com/mamba-org/mamba/issues/3845 .
Fixed upstream in https://github.com/mamba-org/mamba/pull/3919 ,
released in mamba 2.2.0 .

Also:
- Improve type annotations
- Replace `FALLBACK_LINE_TUPLE` namedtuple with `Target` dataclass
 2025-06-07 23:06:31 +01:00
Nicola Soranzo 2c41fefdce Merge branch 'release_24.2' into release_25.0 2025-06-07 18:00:47 +01:00
Nicola Soranzo bc0acd7f98 Merge pull request #20413 from nsoranzo/fix_package_tests 
[24.2] Fix unit tests returning values
 2025-06-07 09:30:14 +01:00
Nicola Soranzo 6eaf865073 Fix unit tests returning values 
These break with pytest 8.4.0, see
https://docs.pytest.org/en/stable/changelog.html#pytest-8-4-0-2025-06-02

Fix the following errors in test_galaxy_packages tests:

```
FAILED tests/tool_shed/test_hg_util.py::test_add_file_and_commmit_changeset - Failed: Expected None, but test returned local('/tmp/pytest-of-runner/pytest-7/test_add_file_and_commmit_chan0/test.txt'). Did you mean to use `assert` instead of `return`?
FAILED tests/tool_shed/test_hg_util.py::test_add_dir_and_commit_changeset - Failed: Expected None, but test returned local('/tmp/pytest-of-runner/pytest-7/test_add_dir_and_commit_change0/abc'). Did you mean to use `assert` instead of `return`?
```

Also:
- Replace legacy `tmpdir` fixtures with `tmp_path`.
- Improve type annotations.
 2025-06-06 20:25:39 +01:00
mvdbeek a50f890bd5 Skip validation of expression.json input in workflow parameter validator 2025-06-06 18:19:34 +02:00
Marius van den Beek 8db845b7ca Merge pull request #20397 from ahmedhamidawan/no_waiting_for_ok_state 
[25.0] Prevent waiting for history item state to be ok in uploader
 2025-06-06 13:15:32 +02:00
Marius van den Beek 1bf6f51610 Merge pull request #20405 from martenson/admin-jobs 
[25.0] Fixes for the admin jobs interface
 2025-06-06 12:49:59 +02:00
Martin Cech 93e1446e4c Merge pull request #20400 from bernt-matthias/fix_20395 
[25.0] Add job config variable for singularity `--contain`
 2025-06-06 08:42:21 +02:00
Ahmed Awan 04602c3b84 wait for add items button to enable; no need to switch to create tab 
The test would fail because the add items to collection button's disabled/enabled state was not being detected, and hence, we would manually switch tabs and the items would not even have been added to the list yet. Now, we wait for the button to enable, and then adding the items automatically switches tab to Create.
 2025-06-05 14:09:23 -05:00
Ahmed Awanandmvdbeek 58561002d5 No need to wait for item hids, waiting for the button itself is better 
Co-authored-by: mvdbeek <m.vandenbeek@gmail.com>
 2025-06-05 11:40:03 -05:00
John Chilton 37e14a6519 Merge pull request #20403 from jmchilton/fix_collection_types 
[25.0] Bug fix: allow any collection type in FormCollectionType.
 2025-06-05 09:45:06 -04:00
Martin Cech a7a61f1815 client format lint 2025-06-05 11:53:19 +02:00
Martin Cech 7ea330c8d7 clarify admin help for jobs page 2025-06-05 11:48:57 +02:00
Martin Cech 7d9155d38f drop description for a hidden form element 2025-06-05 11:36:18 +02:00
Martin Cech 1f5a808e9a fix the filtering for "unfinished jobs" to all non-terminal 
do not mention cutoff when all unfinished are displayed
drop mention of regex for search, that is not implemented
 2025-06-05 11:29:07 +02:00
M Bernt 0ed6442318 Add missing comments 2025-06-05 09:33:11 +02:00
M BerntandNicola Soranzo 704f0620f5 Doc improvements 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2025-06-05 09:31:28 +02:00
Ahmed Hamid Awan c645edaa8a Merge pull request #20401 from davelopez/25.0_fix_form_select_input_sorting 
[25.0] Fix form select input sorting
 2025-06-04 14:35:31 -05:00
M BerntandNate Coraor a71d4dd0db Fix sample config 
Co-authored-by: Nate Coraor <nate@bx.psu.edu>
 2025-06-04 21:03:38 +02:00
John Chilton a2f556974f Bug fix: allow any collection type in FormCollectionType. 2025-06-04 14:05:48 -04:00
Marius van den Beek f29fe3a96e Merge pull request #20399 from dannon/fix-toolshed-tool-icons 
[25.0] Fix toolshed-installed tool icons
 2025-06-04 19:42:31 +02:00
davelopez cad00b6861 Adapt sorting and value assignment in FormData tests 2025-06-04 19:06:37 +02:00
davelopez 7551e87a1b Preserve the order of selected values in FormSelect currentValue 2025-06-04 19:04:46 +02:00
Matthias Bernt 964a62bb2c add job config for singularity --contain 
also move doc to yaml config job config file
 2025-06-04 18:53:10 +02:00
Dannon Baker 7ee1d3c480 Add tests for tool icon endpoint handling simple and toolshed tool IDs 2025-06-04 12:10:48 -04:00
Ahmed Awan c2974fe61c remove wait for upload state alert 2025-06-04 10:38:54 -05:00
Dannon Baker 8217fd1435 Encode tool IDs in icon URLs to handle special characters 
This ensures toolshed tool IDs with slashes and other special characters
are properly escaped when constructing the icon endpoint URL.
 2025-06-04 11:16:52 -04:00
Dannon Baker 97fb170e82 Fix tool icon endpoint to handle toolshed tool IDs with slashes 
Changed the FastAPI route parameter from {tool_id} to {tool_id:path} to
properly capture complex tool identifiers containing forward slashes.
 2025-06-04 11:06:16 -04:00
Dannon 86ecd96552 Merge pull request #20317 from guerler/fix_display_window_manager 
[25.0] Avoid displaying dataset tab view in window manager
 2025-06-04 10:43:39 -04:00
Marius van den Beek fa97351fe2 Merge pull request #20396 from dannon/reduce_bundle_size 
[25.0] Force Monaco into a separate bundle
 2025-06-04 11:48:43 +02:00
davelopez f6bf604bab Do not sort FormData values by HID 2025-06-04 11:33:01 +02:00
Marius van den Beek 695dc84298 Merge pull request #20276 from guerler/fix_interactive_activity 
[25.0] Fix interactive activity highlighting
 2025-06-04 10:02:39 +02:00
Dannon Baker 7212c2c8e1 Positive conditionals and the early return for the isolated exceptional case are clearer and easier to follow than the multiple negative conditions 
(discussed on call, was mentioned we could dump this part)
 2025-06-03 22:44:04 -04:00
Ahmed Awan d096f53969 add close button for split collection creator in workflow run 
For the case where we have multiple collection type options for a collection input, the form data context button is not a toggle; as in it doesn't show/hide the creator. Therefore, added a close button to the side.
 2025-06-03 19:51:35 -05:00
Ahmed Awan 857b99999f [25.0] Prevent waiting for history item state to be ok in uploader 
Fixes https://github.com/galaxyproject/galaxy/issues/20241

We now wait for the extension to change from `auto` and prevent an item from being used if it gets a terminal state other than `ok` and `deferred`.
 2025-06-03 14:50:07 -05:00
Dannon Baker 1b1d959a8a Add explicit preventWindowManager parameter to router.push 
Replace implicit window manager control (based on title presence) with
explicit preventWindowManager parameter for clearer intent.  Leaving off
title still works, but having an explicit control is what we should push
for.
 2025-06-03 14:21:46 -04:00
Dannon Baker 9b0bc2bfbe Cleanup, formatting, comments. 2025-06-03 13:45:48 -04:00
Dannon Baker 67d86e7685 Use explicit async component wrapper/factory for CustomToolEditor code splitting 2025-06-03 13:45:48 -04:00