Nicola Soranzo
95c0950ba6
Add type annotations to `JobRunnerMapper` and related code
2024-11-07 15:19:32 +00:00
Marius van den Beek
8a0fbf638b
Merge pull request #19113 from mvdbeek/stage_hashes
...
Enable specifying dataset hash in test jobs
2024-11-07 14:16:58 +01:00
mvdbeek
feb3747698
Enable specifying dataset hash in test jobs
2024-11-07 11:50:08 +01:00
Björn Grüning
3efa4c1bc1
Merge pull request #19111 from nsoranzo/uv_lock_py3.9
...
Run ``uv lock`` under Python 3.9
2024-11-06 23:18:30 +01:00
Björn Grüning
206b729337
Merge pull request #19048 from mvdbeek/invocation_metrics_api
...
Add job metrics per invocation
2024-11-06 20:02:39 +01:00
Laila Los
946d2ffa31
split vega related components into lazy loaded bundle
2024-11-06 17:26:01 +01:00
Marius van den Beek
4251715943
Merge pull request #19047 from jmchilton/toolshed_fixes
...
Better search stuff in Tool Shed 2.0.
2024-11-06 17:08:13 +01:00
Marius van den Beek
d07b528fbe
Merge pull request #19108 from mvdbeek/access_public_history_in_job_cache
...
Access public history in job cache / job search
2024-11-06 14:10:01 +01:00
Marius van den Beek
360b72a82a
Improve user_id description, set email where needed
2024-11-06 11:42:18 +01:00
mvdbeek
3a6fdf24fb
Allow searching jobs in public histories for job cache
2024-11-06 11:42:18 +01:00
mvdbeek
ec6831e14b
Merge branch 'release_24.1' into dev
2024-11-06 11:33:46 +01:00
Nicola Soranzo
84742ee141
Run `uv lock` under Python 3.9
...
Fix:
```
Using CPython 3.8.18 interpreter at: /opt/hostedtoolcache/Python/3.8.18/x64/bin/python
× No solution found when resolving dependencies for split
│ (python_full_version == '3.9.*'):
╰─▶ Because only the following versions of rucio-clients{python_full_version >= '3.9'} are available:
rucio-clients{python_full_version >= '3.9'}<=33.6.1
rucio-clients{python_full_version >= '3.9'}>=34.0.0,<=34.6.0
rucio-clients{python_full_version >= '3.9'}>=35.0.0
and all of:
rucio-clients{python_full_version >= '3.9'}>=33.6.0,<=33.6.1
rucio-clients{python_full_version >= '3.9'}>=34.0.0,<=34.6.0
rucio-clients{python_full_version >= '3.9'}>=35.0.0
require Python >=3.9, <4, we can conclude that all of:
rucio-clients{python_full_version >= '3.9'}>=33.6.0,<33.6.1
...
rucio-clients{python_full_version >= '3.9'}>35.4.1,<35.5.0
rucio-clients{python_full_version >= '3.9'}>35.5.0
are incompatible.
And because galaxy:dev depends on rucio-clients{python_full_version >=
'3.9'}>=33.6.0 and your project depends on galaxy:dev, we can conclude
that your project's requirements are unsatisfiable.
hint: The source distribution for rucio-clients{python_full_version >=
'3.9'}==35.5.0 does not include static metadata. Generating metadata for
this package requires Python >=3.9, <4, but Python 3.8.18 is installed.
```
See https://github.com/galaxyproject/galaxy/actions/runs/11684632042/job/32536277008
2024-11-05 23:45:33 +00:00
Nicola Soranzo
6004c814b3
Merge branch 'release_24.0' into release_24.1
2024-11-05 23:02:11 +00:00
John Davis
e5635dc2b7
Merge pull request #19073 from jmchilton/pydantic_model_linting
...
Integrate Tool Parameter Modeling into Linting (for Planemo)
2024-11-05 17:52:10 -05:00
Nicola Soranzo
242c533b59
Merge pull request #19109 from nsoranzo/path_upload_check_hashes
...
Test hash validation also for upload by path
2024-11-05 22:36:25 +00:00
John Davis
9834ecd4b9
Merge pull request #18986 from arash77/fix-none-alphanumeric-characters-in-slug
...
Fix issue with generating slug for sharing
2024-11-05 16:27:54 -05:00
mvdbeek
b1691c56f8
Rerender on resize
2024-11-05 17:19:55 +01:00
Nicola Soranzo
46c1dcdc23
Merge pull request #19106 from mvdbeek/sqlite_fix_workflow_test
...
[24.0] Optimize/fix sqlite hid update statement
2024-11-05 15:35:06 +00:00
Nicola Soranzo
1f223d0dc5
Test hash validation also for upload by path
2024-11-05 15:33:40 +00:00
Arash
3c601ffd38
Add python-slugify and types-python-slugify to dependencies and typecheck
2024-11-05 16:33:29 +01:00
Nicola Soranzo
b97ede779c
Add type annotations
2024-11-05 15:28:02 +00:00
Arash
5d9a867dbe
Move is_valid_slug function into SlugBuilder class as classmethod
2024-11-05 16:13:12 +01:00
Arash
4247a5cc44
Assert slug in response
2024-11-05 16:13:11 +01:00
Arash
0d21224657
Add python-slugify library to app/setup.cfg
2024-11-05 16:13:11 +01:00
Arash
9acb8a1fd0
order alphabetically
2024-11-05 16:13:10 +01:00
Arash
2740abe4c0
Add types-python-slugify library for mypy type check
2024-11-05 16:08:48 +01:00
Arash
49a22a62d5
remove unused import
2024-11-05 16:04:54 +01:00
Arash
29479cd00a
Refactor slug generation to use slugify library
2024-11-05 16:04:54 +01:00
Arash
35db3c33db
No escape needed for '/' in slug input
2024-11-05 16:04:53 +01:00
Arash
17c962a66e
Refactor valid slug to just exclude /:?# characters
2024-11-05 16:04:52 +01:00
Arash
6f91b0f68e
Fix python lint
2024-11-05 16:04:51 +01:00
Arash
217ee881ec
Add test for sharing non-alphanumeric history
2024-11-05 16:04:50 +01:00
Arash
15ad84636a
Fix issue with generating slug for sharing history
2024-11-05 16:04:49 +01:00
John Davis
3523f02f0e
Merge pull request #19094 from jdavcs/dev_purged_no_login
...
Prevent purged users from logging in
2024-11-05 09:46:23 -05:00
mvdbeek
71e499bb78
Optimize/fix sqlite hid update statement
...
`./run_tests.sh --skip-common-startup -api lib/galaxy_test/api -- -s -k
cache` would fail on sqlite with database locked.
Not using a separate connection means that we expire loaded attributes
in the sqlite case, but I don't think we need to be concerned about
performance if you're using sqlite.
2024-11-05 13:58:14 +01:00
Marius van den Beek
3150e23309
Merge pull request #19099 from nsoranzo/uv_workaround_for_6127
...
uv: Do not recalculate dependencies when exporting
2024-11-05 12:46:36 +01:00
Nicola Soranzo
1fadd2f658
Do not recalculate dependencies when exporting
...
Saves a few milliseconds :D
2024-11-05 09:53:16 +00:00
Aysam Guerler
1b4dd45f8d
Merge pull request #19097 from davelopez/support_deferred_datasets_in_visualizations
...
Support deferred datasets in visualizations
2024-11-05 01:21:28 +03:00
Björn Grüning
a5aaa1c1be
Merge pull request #19077 from davelopez/allow_deferred_as_uri
...
Allow deferred datasets to behave as URIs
2024-11-04 23:09:12 +01:00
mvdbeek
39a7ed2669
Decrease value parsing repetition, add peakMemory
2024-11-04 18:32:13 +01:00
mvdbeek
6b94267a88
Enable grouping by workflow step
2024-11-04 17:53:17 +01:00
mvdbeek
bcf212dab4
Add basic boxplot
2024-11-04 17:53:17 +01:00
mvdbeek
e5b300b9c1
Add job metrics per invocation
2024-11-04 17:53:17 +01:00
davelopez
2bdcec0dda
Add test for gx_allow_uri_if_protocol with deferred collections
2024-11-03 12:47:15 +01:00
davelopez
53e8a23747
Refactor deferred source URI handling in DatasetInstance and ToolEvaluator
2024-11-03 12:43:24 +01:00
davelopez
605389f1f2
Expand documentation on allow_uri_if_protocol
2024-11-03 11:06:25 +01:00
davelopez
557e7bed8d
Add is_deferred property to DatasetFilenameWrapper
...
For improved handling of deferred data
2024-11-03 10:37:33 +01:00
davelopez
688b08a15a
Add wildcard support for all protocols in visualization checks
2024-11-02 14:02:04 +01:00
davelopez
4be350b8e0
Add support for URI protocols in visualization datatype checks
2024-11-02 13:28:26 +01:00
davelopez
0eb1e12af9
Add allow_deferred attribute to test element in visualization.dtd
2024-11-01 10:36:52 +01:00
Nicola Soranzo