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9005 Commits
Author SHA1 Message Date
marius-mather 3e81fc1663 mypy fixes 2025-07-04 13:27:31 +10:00
marius-mather 5b2b4c9036 Lint fixes 2025-07-04 13:00:04 +10:00
marius-mather cc44513482 Lint fixes 2025-07-04 12:53:24 +10:00
marius-mather 2ed1783f8b Update tests of OIDC config 2025-07-04 12:50:17 +10:00
marius-mather e067b75837 Style/lint fixes 2025-07-04 11:51:03 +10:00
marius-mather 1a0844b8dc Add unit tests of OIDC config 2025-07-04 11:44:54 +10:00
marius-mather 22a646feaa Linting fixes 2025-06-27 11:48:32 +10:00
marius-mather ee17c93dee Add integration test of PSA-based OIDC, decoding access token 2025-06-27 11:11:48 +10:00
marius-mather 884e59d485 Update existing OIDC integration tests to be more reusable 2025-06-27 11:10:12 +10:00
marius-mather 6fe8c6fcf8 Test handling of opaque access token 2025-06-25 10:49:38 +10:00
marius-mather 83901969fa Merge remote-tracking branch 'upstream/dev' into psa-access-token 2025-06-24 10:38:15 +10:00
Nicola Soranzo 99e352a3d0 Merge branch 'release_25.0' into dev 2025-06-22 15:26:46 +01:00
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
Nate Coraor 96523d4570 Merge remote-tracking branch 'upstream/release_25.0' into dev 2025-06-20 16:18:47 -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
John Chilton 85d634ae9f Implement fetch workbooks. 2025-06-19 22:54:56 -04:00
mvdbeek cafd0c8c62 Merge branch 'release_25.0' into dev 2025-06-19 10:18:46 +02:00
mvdbeek 43feb0efb3 Merge branch 'release_24.2' into release_25.0 2025-06-19 10:17:22 +02:00
mvdbeek fdafb0655d Relax validation of XML test assertion parsing 
when tool source is XML. We can't really encode these attributes as JSON
in XML, and while we could make it work it doesn't feel great to force
tool authors to use such a hypothetical syntax.

I think we still keep all the nice validation here, it's just a little
more lenient.
 2025-06-18 18:55:10 +02:00
David López 22b7f14f1a Merge pull request #20372 from guerler/remove_common_templates 
Install visualizations directly to static path, avoid duplication
 2025-06-18 09:42:19 +02:00
marius-mather 336760f3cd Tests of access token decoding 2025-06-18 15:52:37 +10:00
davelopez 58a7a9adef Merge branch 'release_25.0' into dev 2025-06-16 20:14:12 +02:00
mvdbeek 03fb43a00d Merge branch 'release_24.2' into release_25.0 2025-06-16 19:34:41 +02:00
mvdbeek 6d0a0b53aa Link workflow invocation outputs upon importing invocation 2025-06-16 15:02:47 +02:00
mvdbeek 6231f4feb0 Remove `num_unique_values` tiff metadata element 
This was added in https://github.com/galaxyproject/galaxy/pull/18951 but
it's memory consumption scales with input size. On a 5.5GB TIFF file
this consumed a peak of 18GB of memory.

@kostrykin added a workaround for the memory consumption in
https://github.com/galaxyproject/galaxy/pull/19830, but this now very
slow.

Besides improving the efficient, Perhaps there is a more gentle way to approach

> Many tools assume that images are binary, or label maps, for example, and it makes no sense to run those tools on other images.

?

Could those tools just error out, and/or consume a different datatype ?
Do we need the full unique values, or is it ok to just check if it's
more than `n` unique values ?
 2025-06-15 11:44:10 +02:00
guerler d6fc3b68b9 Use galaxy directory helper to determine template path 2025-06-14 06:06:37 -04:00
guerler 3e62ada965 Add path from config 2025-06-12 14:36:53 -04:00
John Chilton b18f0708f7 Implement DatasetSource.requested_transform. 
Should be distinct from transforms apply.
 2025-06-12 18:01:30 +02:00
mvdbeek 2bfd283f94 Fix single data element identifier to be a regular string 
These must adhere to the input parameter they belong to.
 2025-06-11 20:02:54 +02:00
John Davis 16d8bf950a Merge pull request #20229 from jmchilton/sample_sheet_prereqs_1 
Small tweaks and cleanup from sample sheets branch
 2025-06-11 10:45:39 -04:00
Nicola Soranzo 3bff113bfd Build `DependencyManager only if tool_dependency_dir` is set 
as specified by the config file documentation. In fact,
`DependencyManager.__init__()` would crash otherwise.

Also:
- Improve type annotation
 2025-06-10 02:30:46 +01:00
Nicola Soranzo 010bbdd0ae Move `get_param_values() method from Job to Tool` class 
because the ``Job`` model class shouldn't have to deal with ``app``.

Also:
- Remove ``app`` parameter from ``Tool.params_from_strings()``
- Improve type annotations
- Clean up unused code
 2025-06-10 02:30:44 +01:00
Nicola Soranzo 9bd2a328f1 Type annotation fixes for mypy 1.16.0 2025-06-10 02:22:18 +01:00
Aysam Guerler 2fc1b48c36 Merge pull request #20303 from guerler/switch_default_visualization 
Switch Default Visualization Endpoint to script, migrate to YAML
 2025-06-09 14:56:44 -04:00
Nicola Soranzo e1d2815499 Merge branch 'release_25.0' into dev 2025-06-08 23:15:04 +01:00
Nicola Soranzo 90fad91813 Merge branch 'release_24.2' into release_25.0 2025-06-08 21:47:42 +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 11e53a9a3e Merge branch 'release_25.0' into dev 2025-06-07 18:14:14 +01:00
Nicola Soranzo 2c41fefdce Merge branch 'release_24.2' into release_25.0 2025-06-07 18:00:47 +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
guerler f8175b68bd Adjust unit test 2025-05-29 09:56:39 -04:00
Nicola Soranzo c929ab5034 Drop `uuid and allow_load from DynamicToolPayload` 
Passing a UUID is unused and unnecessarily complicates the code.

Also:
- Add unit tests for `DynamicToolManager` .
 2025-05-29 02:22:38 +01:00
guerler 3ea12c90c3 Adjust selenium test, switch to new visualizations 2025-05-26 09:30:01 -04:00
guerler 9aa3f41c08 Update registry tests with focus on new framework 2025-05-26 09:30:01 -04:00
Nicola Soranzo 7160c5befd Add test 2025-05-21 17:09:06 +01:00
Nicola Soranzo 74a17ec6ff Use `printf` 
`echo` doesn't interpret backslash escapes by default, and its `-e` option is not POSIX.
 2025-05-21 17:08:23 +01:00
mvdbeek 1cbec1b8ef Fix memory and slots test 2025-05-19 19:16:43 +02:00
mvdbeek a6f402803c Only test slots and memory 
Looks like kubectl hangs in this test setup.
 2025-05-19 16:05:43 +02:00