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Author SHA1 Message Date
mvdbeek fde1ec3543 Merge branch 'release_23.2' into release_24.0 2024-03-05 16:33:16 +01:00
Marius van den Beek 4752af0443 Merge pull request #17597 from mvdbeek/fix_tool_shed_tests 
[23.2] Fix tool shed webapp
 2024-03-05 16:32:36 +01:00
Marius van den Beek b7c14c6559 Merge pull request #17294 from lldelisle/filter_paused 
[24.0] Add ``__KEEP_SUCCESS_DATASETS__``
 2024-03-05 16:18:20 +01:00
Marius van den Beek c598c49f62 Raise NotImplementedError for TS get_or_create_default_history 2024-03-05 15:52:17 +01:00
mvdbeek feb38afccb Fix tool shed webapp 2024-03-05 12:50:35 +01:00
Martin Cech e9e26b95c1 Merge pull request #17591 from jdavcs/version-24.0.rc1 
[24.0] Update version to 24.0.rc1
 2024-03-05 00:01:00 +01:00
John Davis 04a8011697 Update version to 24.0.rc1 2024-03-04 13:14:33 -05:00
John Davis 075ad218d9 Merge branch 'release_23.2' into dev 2024-03-04 13:02:17 -05:00
John Davis 5ff24819fc Merge branch 'release_23.1' into release_23.2 2024-03-04 12:59:12 -05:00
John Davis fab4424ded Merge pull request #17577 from jdavcs/23.1_coalesce 
[23.1] Fix ancient bug: incorrect usage of func.coalesce in User model
 2024-03-04 12:58:03 -05:00
John Davis ac9a6b4817 Merge pull request #17584 from nsoranzo/release_23.2_fix_test_page_encoding 
[23.2] Fix ``test_page_encoding`` and ``test_collection_explicit_and_implicit`` integration tests
 2024-03-04 12:57:13 -05:00
John Davis 89db9c27a9 Merge pull request #17589 from jdavcs/dev_migration_id_24.0 
Add migrations revision identifier for 24.0
 2024-03-04 12:55:56 -05:00
John Davis ece45e3440 Add revision identifier for 24.0 2024-03-04 12:50:11 -05:00
John Davis 516ecfac41 Merge branch 'release_23.2' into dev 2024-03-04 12:36:38 -05:00
Nicola Soranzo 3f0f789b82 Merge pull request #17556 from kostrykin/files_diff_images 
Add `image_diff` comparison method for test output verification using images
 2024-03-04 17:04:44 +00:00
Dannon db98eb4efa Merge pull request #17583 from ElectronicBlueberry/theme-selector-reset-vars 
Apply default theme to theme selector
 2024-03-04 10:35:46 -06:00
John Davis d02c11a10b Merge pull request #16492 from bernt-matthias/topic/consistent-profile-check 
consistently compare profile versions
 2024-03-04 11:16:35 -05:00
Dannon 29725c48b6 Merge pull request #17580 from galaxybot/dev_auto_update_dependencies 
Update Python dependencies
 2024-03-04 10:13:37 -06:00
Nicola Soranzo 241fc3b79b Fix test_collection_explicit_and_implicit test 
which was working only because `workflow_id` and `history_id` were the
same before commit 85630e2ca9 .
 2024-03-04 15:47:34 +00:00
Nicola Soranzo de1bb854fa Merge pull request #17582 from muon-spectroscopy-computational-project/33_fix_cif_sniff_23.2 
[23.2] Account for newlines in CIF Datatype sniffer
 2024-03-04 15:35:55 +00:00
Nicola Soranzo 031a8599ae Fix `test_page_encoding` test 
Don't assume that the history has unencoded id 1.

Broken by commit 85630e2ca9 .

Fix the following error:

```
______________ TestPageJsonEncodingIntegration.test_page_encoding ______________

self = <integration.test_page_revision_json_encoding.TestPageJsonEncodingIntegration object at 0x7fe178521190>
history_id = '529fd61ab1c6cc36'

    def test_page_encoding(self, history_id: str):
        request = dict(
            slug="mypage",
            title="MY PAGE",
            content=f"""<p>Page!<div class="embedded-item" id="History-{history_id}"></div></p>""",
        )
        page_response = self._post("pages", request, json=True)
        api_asserts.assert_status_code_is_ok(page_response)
        sa_session = self._app.model.session
        page_revision = sa_session.scalars(select(model.PageRevision).filter_by(content_format="html")).all()[0]
>       assert '''id="History-1"''' in page_revision.content, page_revision.content
E       AssertionError: <p>Page!</p><div class="embedded-item history placeholder" id="History-2"><p class="title">Embedded Galaxy History - 'test_history'</p><p class="content">[Do not edit this block; Galaxy will fill it in with the annotated History when it is displayed]</p></div><p></p>
E       assert 'id="History-1"' in '<p>Page!</p><div class="embedded-item history placeholder" id="History-2"><p class="title">Embedded Galaxy History - \'test_history\'</p><p class="content">[Do not edit this block; Galaxy will fill it in with the annotated History when it is displayed]</p></div><p></p>'
E        +  where '<p>Page!</p><div class="embedded-item history placeholder" id="History-2"><p class="title">Embedded Galaxy History - \'test_history\'</p><p class="content">[Do not edit this block; Galaxy will fill it in with the annotated History when it is displayed]</p></div><p></p>' = <galaxy.model.PageRevision(1) at 0x7fe0d74d81d0>.content

test/integration/test_page_revision_json_encoding.py:33: AssertionError
```
 2024-03-04 14:40:11 +00:00
Laila Los 955d7ec5f5 apply default theme to theme selector 2024-03-04 14:15:38 +01:00
Nicola Soranzo ef251326e5 Fixes for ruff 0.3.0 2024-03-04 13:14:50 +00:00
galaxybot da3c9f837c Update Python dependencies 2024-03-04 13:14:49 +00:00
Nicola Soranzo 94c43dd75c Disallow also pydantic 2.6.3 2024-03-04 13:14:48 +00:00
Nicola Soranzo b02101ba69 Unpin Cheetah as the poetry bug was fixed 2024-03-04 13:14:48 +00:00
Nalin Gupta c095ec6b88 Added newline at end of LaMnO3.cif 2024-03-04 10:17:48 +00:00
Nalin Gupta 0b7571794a Added changes to sniff.py to test #33 changes 2024-03-04 10:17:48 +00:00
Nalin Gupta fd266e3dde Added test for issue #33 fix 2024-03-04 10:17:48 +00:00
Nalin Gupta c7f7ef73b1 Attempt at resolving issue #33 2024-03-04 10:17:48 +00:00
Nicola Soranzo 62c610c250 Move numpy and pillow requirements to new extended-assertions extra 
together pysam, which is also conditionally imported in
``lib/galaxy/tool_util/verify/__init__.py`` .
 2024-03-02 01:59:10 +00:00
Martin Cech 06eada1c2c Merge pull request #17566 from jmchilton/invocation_links 
Links to individual invocations.
 2024-03-02 02:20:22 +01:00
Martin Cech a048f2dfda Merge pull request #17573 from guerler/strip_legacy_viz_artifacts 
Remove legacy phyloviz, circster and sweepster artifacts
 2024-03-02 01:28:26 +01:00
John Davis 021cb80abd Fix bug: this is not part of a sql stmt 2024-03-01 17:22:34 -05:00
Matthias Bernt db2f548d60 fix isort 2024-03-01 21:42:03 +01:00
M Bernt b5772d8a01 Merge branch 'dev' into topic/consistent-profile-check 2024-03-01 20:41:41 +01:00
John Davis 54294f03cb Merge pull request #13918 from bernt-matthias/tabular-improvement 
Make columns types an empty list for empty tabular data
 2024-03-01 13:40:33 -05:00
John Davis 25d95278cb Make comment more detailed 2024-03-01 13:39:51 -05:00
John Davis 2c966debea Merge pull request #17482 from brsynth/feature_datatypes_sbol 
Feature SBOL datatypes
 2024-03-01 11:35:35 -05:00
John Davis b6dcf9c3d2 Merge pull request #14005 from jmchilton/tour_testing_drop_jquery 
Update tour testing selector usage.
 2024-03-01 11:28:48 -05:00
John Davis 4fdc7c6bf8 Merge pull request #17106 from tuncK/tarxz 
Add support for (fast5.tar).xz binary compressed files
 2024-03-01 11:03:36 -05:00
John Davis 477e0728da Merge pull request #17357 from bernt-matthias/topic/id_ext_inputs_configfile 
Add element_identifier and ext to inputs config file export
 2024-03-01 10:22:02 -05:00
John Davis ff66f47db1 Merge pull request #17502 from ahmedhamidawan/keyboard_select_in_history 
Add multiple drag/drop and keyboard accessible selection to `HistoryPanel` items
 2024-03-01 10:13:25 -05:00
John Chilton ba418affea Merge pull request #17569 from jmchilton/help_links 
Add help text to workflow invocation states
 2024-02-29 20:13:18 -05:00
John Chilton 730494cb41 Merge pull request #17495 from itisAliRH/workflow-import-refactor 
Refactor Workflow Import components
 2024-02-29 17:15:58 -05:00
John Chilton 7f8db0dba1 Links to invocations. 2024-02-29 16:37:24 -05:00
John ChiltonandMarius van den Beek f6572b8329 Apply suggestions from code review 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2024-02-29 15:15:47 -05:00
Marius van den Beek 0718fc52df Merge pull request #17565 from richard-burhans/shmsize 
add shm_size based on ShmSize
 2024-02-29 12:50:47 -06:00
guerler 9b07d2a000 Remove legacy phyloviz, circster and sweepster artifacts 2024-02-29 12:47:19 -06:00
Nicola Soranzo 1a3edae577 Add missing package requirements 2024-02-29 18:22:42 +00:00