opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-11-03 21:34:30 +08:00
Code Issues Packages Projects Releases Wiki Activity
80,498 Commits 63 Branches 246 Tags
v24.2.4
Commit Graph
80498 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
Nate Coraor 7b1e4465bf Create version 24.2.4 v24.2.4 2025-06-17 12:17:16 -04:00
John Chilton e6a3dea50a Merge pull request #20492 from natefoo/optional-edam 
[24.2] Make optional edam-ontology in datatypes registry optional
 2025-06-17 09:03:24 -04:00
Marius van den Beek 957ccca59d Fall back to empty edam dict 2025-06-17 10:58:21 +02:00
Nate Coraor 8838912356 Make optional edam-ontology in datatypes registry optional 2025-06-16 16:48:10 -04:00
Marius van den Beek 539441ddd6 Merge pull request #20485 from mvdbeek/fix_workflow_invocation_import_link_outputs 
[24.2] Link workflow invocation outputs upon importing invocation
 2025-06-16 19:33:40 +02:00
mvdbeek 6d0a0b53aa Link workflow invocation outputs upon importing invocation 2025-06-16 15:02:47 +02:00
Marius van den Beek 876fdf0b24 Merge pull request #20475 from mvdbeek/header_string 
[24.2] Make response header values strings
 2025-06-16 13:41:47 +02:00
Marius van den Beek c7acfe7bea Merge pull request #20477 from mvdbeek/fix_legacy_metadata_get_file 
[24.2] Fix legacy get_metadata_file controller route
 2025-06-16 13:41:35 +02:00
Marius van den Beek 446c8deb68 Merge pull request #20479 from mvdbeek/prevent_launching_autodetect_on_purged_dataset 
[24.2] Prevent running datatype autodetect on purged datasets
 2025-06-16 13:41:00 +02:00
mvdbeek a7eaf5f74a Prevent running datatype autodetect on purged datasets 
Fixes https://github.com/galaxyproject/galaxy/issues/20478
 2025-06-16 11:16:09 +02:00
mvdbeek 4620f0716e Fix legacy get_metadata_file controller route 
Fixes https://github.com/galaxyproject/galaxy/issues/20476
 2025-06-16 11:09:25 +02:00
mvdbeek f508330d03 Make response header values strings 2025-06-16 11:02:46 +02:00
Ahmed Hamid Awan 6176b007ab Merge pull request #20107 from natefoo/fix-mulled-search-quay 
[24.2] Fix `mulled-search --destination quay`, add index reuse
 2025-06-13 12:41:49 -05:00
Nate CoraorandNicola Soranzo f66a9419a7 Update lib/galaxy/tool_util/deps/mulled/mulled_search.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2025-06-13 11:45:38 -04:00
John Davis 09e30616f8 Fix linting 2025-06-11 11:08:56 -04:00
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
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 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 968ef13132 Merge pull request #20394 from jdavcs/24.2_role_name_bug 
[24.2] Fix searching roles in admin UI
 2025-06-03 19:41:52 +02:00
John Davis 75ab368118 Use Role.name 
Fixes bug: the `name` hybrid property has been removed and the field has
been renamed back to `_name`

Ref:
https://github.com/galaxyproject/galaxy/pull/19679/commits/3d2eb9fd8e6281d665ead0e18eb2f3ebde866196
https://github.com/galaxyproject/galaxy/pull/18966/commits/3e6191fbe3b5b1f18c6de2dfd413e9c2a6e34b19
https://github.com/galaxyproject/galaxy/pull/18966/commits/62a8b90f8aab45441b5f6922351b8a5a20cc0848
 2025-06-03 11:57:21 -04:00
David López e3e767d24a Merge pull request #20305 from davelopez/24.2_fix_wfrun_rocrate_logo_width 
[24.2] Fix WF Run RO-Crate logo width in Firefox
 2025-05-20 15:05:06 +02:00
davelopez 2bf1b96bb0 Fix WF Run RO-Crate logo width in Firefox 2025-05-20 14:03:05 +02:00
mvdbeek 957f6f5475 Merge branch 'release_24.1' into release_24.2 2025-05-19 16:54:19 +02:00
Marius van den Beek c4605dad00 Merge pull request #20239 from natefoo/fix-ucsc-display-as 
[24.1] Refactor display_as URL generation for UCSC links and fix to remove double slashes in URL
 2025-05-19 16:52:44 +02:00
Martin Cech 1f7f2e7845 Merge branch 'release_24.1' into release_24.2 2025-05-19 12:44:19 +02:00
Martin Cech 4e1acd06ce Merge branch 'release_24.0' into release_24.1 2025-05-19 12:43:58 +02:00
Martin Cech faa7442ee7 Merge branch 'release_23.2' into release_24.0 2025-05-19 12:43:20 +02:00
Martin Cech 7d4b3de58f Merge branch 'release_23.1' into release_23.2 2025-05-19 12:32:42 +02:00
mvdbeek 2156e2d98e Merge branch 'release_24.1' into release_24.2 2025-05-16 16:23:56 +02:00
mvdbeek 9a0d482f1a Merge branch 'release_24.0' into release_24.1 2025-05-16 16:23:36 +02:00
Marius van den Beek 400a9f605b Merge pull request #20258 from mvdbeek/fix_job_summary 
[24.0] Fall back to name in job summary if no input label given
 2025-05-16 16:22:52 +02:00
mvdbeek 65df554439 Fall back to name in job summary if no input label given 2025-05-16 11:07:41 +02:00
Nate Coraor 94721e3ec5 Refactor display_as URL generation for UCSC links and fix to remove double slashes in URL 2025-05-15 12:24:49 -04:00
John Chilton 9ff304caf5 Merge pull request #20209 from natefoo/job-execution-package-config-dep 
[24.2]  Conditionally import from `galaxy.config` in `galaxy.model.mapping` if `TYPE_CHECKING`
 2025-05-13 13:35:29 -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
Nate CoraorandJohn Chilton ebf629cd47 Update lib/galaxy/model/mapping.py 
Co-authored-by: John Chilton <jmchilton@gmail.com>
 2025-05-12 16:39:41 -04:00
Nate Coraor 9ae46c2f30 Conditionally import from galaxy.config in galaxy.model.mapping if TYPE_CHECKING 2025-05-12 15:43:47 -04:00
mvdbeek 65d265fd51 Merge branch 'release_24.1' into release_24.2 2025-05-12 09:02:07 +02:00
mvdbeek c5c0599a2d Merge branch 'release_24.0' into release_24.1 2025-05-12 09:01:27 +02:00
Marius van den Beek 67d44e4503 Merge pull request #20200 from mvdbeek/fix_invocation_failure_dataset_reference 
[24.0] Fix invocation failure dataset reference
 2025-05-12 09:00:57 +02:00
mvdbeek 4fb1388e50 Fix invocation failure dataset reference 
Fixes https://github.com/galaxyproject/galaxy/issues/20049.
Many thanks for pointing me at the real issue @jdavcs!
 2025-05-10 10:57:00 +02:00
Martin Cech 205e32f884 Merge pull request #20040 from kysrpex/psa_reject_expired_tokens 
[23.1] Renew access tokens from PSA using valid refresh tokens
 2025-05-07 14:32:22 +02:00
Marius van den Beek 940ef54661 Merge pull request #20159 from natefoo/metapackage-24.2.3 
[24.2] Update dev package version in meta package
 2025-05-06 18:51:35 +02:00
Nate Coraor 0fd00d6550 Update meta package history and version 2025-05-06 10:33:00 -04:00
John Chilton e367b716ab Merge pull request #20164 from mvdbeek/data_collection_parameter_model_factory_fix 
[24.2] Fix ``DataCollectionParameterModel`` factory
 2025-05-06 10:30:01 -04:00
mvdbeek b99112c337 Fix DataCollectionParameterModel factory 2025-05-06 14:23:23 +02:00