mvdbeek
a42496e8ec
Disable locking when opening h5 files, add missing with
2024-10-12 09:26:54 +02:00
Matthias Bernt
c201daa7a8
remove linter for unstripped text content for tool xml leaves
...
reverts #17656
we have to many xml nodes where this is allowed (e.g. command)
and limiting the linter to a statically defined list of node types
seemed difficult to maintain
replaced this with a change in the xsd that should lead to the
automatic removal of surplus white spaces (leading/trailing are removed,
multiple whitespaces are replaced by a single space) for some of the
node types that were the original motivation for the linter
(if this proves useful this could be used for more node types).
2024-05-29 15:29:00 +02:00
Matthias Bernt
74b19f02e5
fix number of tests test
...
bad merge
2024-05-07 18:12:40 +02:00
Matthias Bernt
55c5d0847c
remove unused import
2024-05-07 17:53:26 +02:00
M Bernt
1d945bff72
Merge branch 'dev' into topic/lint-whitespace-text
2024-05-07 17:43:01 +02:00
mvdbeek
634e6c408e
Merge branch 'release_24.0' into dev
2024-05-07 15:47:26 +02:00
Matthias Bernt
07aa429ff6
linting: restore possibiity to skip old linter function names
...
until 23.2 we had linter functions lint_xyz in linter modules xyz.
with 24.0 we splited the functions linter classes.
lint contexts allow to skip linters by name (xyz for the old functions
now the class name), i.e. we can not skip by the old names anymore.
this may break planemo command lines xref
https://github.com/galaxyproject/planemo/pull/1441#discussion_r1587995463 .
here I suggest to add a check for the module name against the names
listed in the skip list. this restores the possibility to skip by old
linter names and adds the possibility to skip whole linter modules
(which might be handy anyway).
tried to add some tests that hopefully help to maintain this
functionality.
2024-05-03 13:05:15 +02:00
Nicola Soranzo
0629908541
Fix new UP031 errors from ruff 0.4.2
2024-04-29 00:09:38 +01:00
Nicola Soranzo
053ca5198e
Enable `warn_unused_ignores` mypy option
2024-04-16 01:12:58 +01:00
Leonid Kostrykin
cdfc3f0e57
Add pin_labels attribute for image_diff comparison method
2024-03-29 12:01:34 +01:00
M Bernt
4603168fbe
Merge branch 'dev' into topic/lint-whitespace-text
2024-03-28 11:57:36 +01:00
Matthias Bernt
af612e9342
add linting for valid EDAM terms
2024-03-26 09:40:15 +01:00
John Chilton
0a3e222e62
Merge pull request #17655 from bernt-matthias/topic/lint-bio.tools
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tool linter: check for valid bio.tools entries
2024-03-12 13:43:48 -04:00
John Davis
728bbeb296
Merge pull request #17654 from nsoranzo/ruff_C4_pyupgrade
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Code cleanups from ruff and pyupgrade
2024-03-11 15:21:30 -04:00
Matthias Bernt
e0e6a6e825
fix tests
2024-03-11 18:45:55 +01:00
Matthias Bernt
5a03b37f0c
black
2024-03-11 18:11:02 +01:00
Matthias Bernt
3dae54a672
make it a warning
2024-03-11 15:23:52 +01:00
Matthias Bernt
4003cb4a74
remove unused imports
2024-03-11 13:15:56 +01:00
Matthias Bernt
082d4656c8
tool linter: check for lead nodes with unstripped text content
2024-03-11 12:57:19 +01:00
mvdbeek
3dbc2c6760
Merge branch 'release_23.2' into release_24.0
2024-03-11 11:55:56 +01:00
Matthias Bernt
4e1a6d3b94
tool tinter: check for valid bio.tools entries
2024-03-11 11:47:55 +01:00
Nicola Soranzo
a2018a5e60
Enable flake8-comprehensions ruff rules
...
but allow `dict()` calls that make use of keyword arguments (e.g.,
`dict(a=1, b=2)`).
2024-03-09 19:11:20 +00:00
Matthias Bernt
5a48f66c46
use asserts also in test
2024-03-09 15:10:52 +01:00
Matthias Bernt
e76f5ff4e0
adad test to allow for Optional list
2024-03-08 13:05:42 +01:00
Matthias Bernt
2a7cce03f3
yaml parsing: fix nested assertions
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were forgotten to be implemented
2024-03-08 12:46:17 +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
...
idea came up here https://github.com/galaxyproject/tools-iuc/issues/5629#issuecomment-1807050561
2024-03-01 22:45:38 -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
mvdbeek