Matthias Bernt
3dae54a672
make it a warning
2024-03-11 15:23:52 +01:00
Matthias Bernt
4e1a6d3b94
tool tinter: check for valid bio.tools entries
2024-03-11 11:47:55 +01:00
John Davis
5e05e00656
Merge pull request #17016 from bernt-matthias/topic/stdio-regex-extend
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[24.0] Extend regex groups in stdio regex matches
2024-03-05 14:32:57 -05:00
Nicola Soranzo
3f0f789b82
Merge pull request #17556 from kostrykin/files_diff_images
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Add `image_diff` comparison method for test output verification using images
2024-03-04 17:04:44 +00:00
Matthias Bernt
a8e6e8d5d6
fix test exit code default
2024-03-01 22:45:39 -05:00
Matthias Bernt
6d99463613
fix test
2024-03-01 22:45:38 -05:00
Matthias Bernt
43bdd28bbd
formating fixes
2024-03-01 22:45:38 -05:00
Matthias Bernt
73219583f1
remove unused variable job_id_tag
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was used in the past for log messages which are now gone
2024-03-01 22:45:38 -05:00
Matthias Bernt
93b9678e0b
make regex string
2024-03-01 22:45:38 -05:00
Matthias Bernt
666696c666
extend regex groups in stdio regex matchs
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idea came up here https://github.com/galaxyproject/tools-iuc/issues/5629#issuecomment-1807050561
2024-03-01 22:45:38 -05:00
John Davis
54294f03cb
Merge pull request #13918 from bernt-matthias/tabular-improvement
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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
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Feature SBOL datatypes
2024-03-01 11:35:35 -05:00
Richard Burhans
57b4c8b239
removing quotes
2024-02-28 12:32:21 -06:00
Richard Burhans
47b1d58025
add shm_size based on ShmSize
2024-02-28 11:51:53 -06:00
Leonid Kostrykin
8567aced02
Fix linting issues
2024-02-27 22:30:21 +01:00
Leonid Kostrykin
49fe197d8b
Fix bugs
2024-02-27 21:40:20 +01:00
Leonid Kostrykin
d2a40cb955
Fix linting issues
2024-02-27 15:21:39 +01:00
Leonid Kostrykin
1937e2ba78
Fix bug
2024-02-27 15:09:38 +01:00
Leonid Kostrykin
4d800a8f36
Fix bug
2024-02-27 14:16:55 +01:00
Leonid Kostrykin
e5eb5d43be
Fix linting issues
2024-02-27 13:29:35 +01:00
Leonid Kostrykin
f22d051e8a
Fix bugs
2024-02-27 13:25:56 +01:00
Leonid Kostrykin
79967031d0
Fix bugs
2024-02-27 13:24:43 +01:00
Leonid Kostrykin
0d6077db8f
Fix bugs
2024-02-27 13:10:25 +01:00
Leonid Kostrykin
ea1c980701
Fix pillow usage
2024-02-27 12:54:48 +01:00
Leonid Kostrykin
7c447f087d
Fix pillow imports
2024-02-27 12:52:27 +01:00
Leonid Kostrykin
5bf2f3f1a5
Fix linting issues
2024-02-27 11:58:34 +01:00
Leonid Kostrykin
b73091246d
Fix linting issues
2024-02-27 11:49:55 +01:00
Leonid Kostrykin
a1b51ea3c9
Fix linting issues
2024-02-27 11:44:35 +01:00
Leonid Kostrykin
3af5443a45
Fix linting issues
2024-02-27 11:35:29 +01:00
Leonid Kostrykin
56506e49dd
Fix linting issues
2024-02-27 11:32:50 +01:00
Leonid Kostrykin
bcf78ecc28
Add tests for files_image_diff
2024-02-27 11:21:36 +01:00
guillaume-gricourt
1dc9eb9e2e
tests(datatypes): add SBOL
2024-02-27 09:56:40 +01:00
John Davis
51749bf6d3
Merge pull request #17490 from bernt-matthias/topic/has_size_size
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has_size assertion: implement size (as synonym for value)
2024-02-26 13:42:00 -05:00
Martin Cech
0d380c4f10
Merge pull request #17462 from bernt-matthias/topic/fasta-set-meta
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Faster FASTA and FASTQ metadata setting
2024-02-19 21:15:09 +01:00
Matthias Bernt
f198184350
add type ignores
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for mock
2024-02-19 16:44:31 +01:00
Matthias Bernt
d90a101331
treat empty files correctly
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as 0 column files
- refactor type_overrules_type for simplicity
- add tests
2024-02-19 12:07:37 +01:00
Matthias Bernt
b7ca5258a3
add unit test for Tabular.set_meta for empty files
2024-02-19 12:05:09 +01:00
Matthias Bernt
9f04af05cd
extend existing unit test for Tabular.set_meta
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to actually check set metadata values
2024-02-19 12:04:40 +01:00
Marius van den Beek
0d9abfee16
Merge pull request #17435 from mvdbeek/bundle_as_input
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Allow using tool data bundles as inputs to reference data select parameters
2024-02-19 10:49:22 +01:00
Matthias Bernt
433585d91f
has_size assertion: implement size (as synonym for value)
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https://github.com/galaxyproject/galaxy/issues/17189
2024-02-18 12:00:33 +01:00
John Chilton
e93ea2a665
Display workflow invocation counts.
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Performance: Workflows render fine without the data, data is fetched asynchronously from other queries, joins only happen across a couple of fields that are all indexed, avoiding serializing objects and such - the SQL is quite low-level.
2024-02-17 16:12:58 -05:00
Marius van den Beek
74a1b02fa0
Merge pull request #17081 from bernt-matthias/topic/linter-overhaul
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Split linters in separate classes
2024-02-16 17:41:44 +01:00
mvdbeek
b1aaec0435
Fix TestSelectToolParameter test cases
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Without this user is mocked, whuch breaks `user.get_user_data_tables`
2024-02-16 15:53:17 +01:00
mvdbeek
03e2b8a807
Clean up dataset passing
2024-02-16 15:53:17 +01:00
mvdbeek
fe05a35606
WIP: Experiment with allowing tool data bundles as job inputs
2024-02-16 15:36:52 +01:00
mvdbeek
35c0fd21cb
Merge branch 'release_23.2' into dev
2024-02-16 15:28:57 +01:00
mvdbeek
513ca7494d
Drop overly complicated state setter logic
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I doubt anyone instinctively know when to use `._state`, `.state`,
`.raw_set_dataset_state` or `.set_dataset_state` and I think that was
part of what led to this bug.
2024-02-15 11:28:37 +01:00
M Bernt
2428b9db97
Merge branch 'dev' into topic/linter-overhaul
2024-02-15 09:40:48 +01:00
Marius van den Beek
ddabba7c2f
Merge pull request #17087 from mvdbeek/from_url_option
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Add select parameter with options from remote resources
2024-02-14 18:47:40 +01:00
Matthias Bernt