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8985 Commits
Author SHA1 Message Date
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
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
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
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
John Chilton fc4725925d Merge pull request #20262 from mvdbeek/slots_and_memory 
Add missing galaxy slots and memory tool
 2025-05-19 08:43:17 -04:00
mvdbeek a4bad06a06 Merge branch 'release_24.2' into dev 2025-05-16 16:24:49 +02:00
mvdbeek b2df0e08d7 Add missing galayx slots and memory tool 
Fixes https://github.com/galaxyproject/galaxy/issues/13212
 2025-05-16 15:59:25 +02:00
mvdbeek 3eaa78b745 Fix job rerun for dynamic tools 
Fixes https://github.com/galaxyproject/galaxy/issues/20255
 2025-05-16 12:17:42 +02:00
John Chilton cb2d5cc611 Implement nested collection test in test_model_discovery. 2025-05-14 12:57:29 -04:00
John Chilton 631e33f5bd Merge pull request #19716 from jmchilton/fix_citation_handling 
[24.2] Fix #19515 - invalid citation handling changed with 24.2.
 2025-05-13 13:04:22 -04:00
mvdbeek 73c72b8fc7 Fix unit test import 2025-05-12 12:29:43 +02:00
mvdbeek d2597738cb Make to_cwl compatible with pulsar 2025-05-12 10:54:56 +02:00
mvdbeek e6b0783194 Enable (Javascript) requirements on frontend/backend 2025-05-12 10:54:42 +02:00
mvdbeek 152bc2ffa5 Add runtime model to API 
Like job_internal but replaces dataset and dataset collection with file
and array / object of files.
 2025-05-12 10:54:30 +02:00
mvdbeek 90b21f7212 YamlToolSource parser fixes 2025-05-12 10:54:24 +02:00
mvdbeek a6d6477122 Bypass global toolbox for unprivileged tools 2025-05-12 10:54:23 +02:00
mvdbeek eb38fd8ec9 Merge branch 'release_24.2' into dev 2025-05-12 09:05:28 +02:00
John Chilton 219796f049 Implement paired_or_unpaired collections, list wizards. 2025-05-09 17:39:38 -04:00
John Chilton 9c7770d3aa More dataset collection unit testing... 2025-05-09 16:38:20 -04:00
John Chilton 0b3b408b50 Migrate doctests to unit tests. 2025-05-09 16:38:19 -04:00
John Chilton 518fa136d9 [WIP] Implement records - heterogenous dataset collections. 
Existing dataset colleciton types are meant to be homogenous - all datasets of the same time. This introduces CWL-style record dataset collections.
 2025-05-09 16:38:19 -04:00
John Chilton 8e3e86a706 Option for add_column_regex to be unmatched, improved testing. 
Can easily be combined concatenate and such to get conditionals on rewriting values. Used for new tests in new collection types branch that mirror I think useful, real-world examples. Also extends the test framework a bit to allow testing errors during evaluation and not just errors that can be caught statically by inspecting the rule itself.
 2025-05-09 16:38:18 -04:00
Marius van den Beek 9fb00287e4 Merge pull request #20054 from davelopez/explore_rocrate_import 
Add ZIP explorer to import individual files from local or remote ZIP archives
 2025-05-09 12:07:14 +02:00
Marius van den Beek de1e356e35 Merge pull request #18628 from rhpvorderman/singularity_settings 
Isolate singularity containers more thoroughly for better reproducibility.
 2025-05-09 11:39:50 +02:00