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
...
to actually check set metadata values
2024-02-19 12:04:40 +01:00
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
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
mvdbeek
84604bd2cb
Merge branch 'release_23.2' into dev
2024-02-14 18:44:36 +01:00
Nicola Soranzo
f4229aad0a
Merge pull request #17440 from mvdbeek/fix_it_templating
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[23.2] Build param dict before creating entrypoint
2024-02-13 16:41:44 +00:00
mvdbeek
9eebb60647
Sandwich IT entry point creating after param_dict building and env var creation
2024-02-13 14:57:12 +01:00
mvdbeek
5aabab9c93
Implement request header and body templating
2024-02-13 14:51:16 +01:00
Marius van den Beek
818c147e9c
Merge pull request #17365 from mvdbeek/warn_unreachable
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Enable ``warn_unreachable`` mypy option
2024-02-12 11:04:45 +01:00
Martin Cech
cc94611a18
Merge pull request #17329 from jmchilton/device_source
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API endpoint that allows "changing" the objectstore for "safe" scenarios.
2024-02-10 01:09:30 +01:00
John Chilton
87321dcffa
Fix overlapping names in extra files for model stores.
2024-02-08 11:01:22 +01:00
John Chilton
b8cf19f0bd
Utilities for higher level composite tests in test_model_store.
2024-02-08 11:01:17 +01:00
John Chilton
cf8e72ff98
Minimal test case demonstrating model stores break on implicit conversions.
2024-02-08 11:01:13 +01:00
John Chilton
2259e1f633
More de-duplication in test_model_store.py.
2024-02-08 11:01:09 +01:00
John Chilton
570a05541a
Reduce duplication in test_model_store.
2024-02-08 11:01:02 +01:00
Marius van den Beek
5f25655096
Merge pull request #17346 from jmchilton/model_store_fixes
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Fix model store exports that include implicit conversions.
2024-02-08 10:59:36 +01:00
John Chilton
c106a87a90
Implement device source ID for object stores.
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Allow attaching a device ID on object stores that indicates they produce equivalent paths. Implement an API endpoint that allows swapping datsets between equivalent object stores if they have not been copied by new users.
2024-02-07 11:39:51 -05:00
mvdbeek
26e6f3652e
Add remaining exlcudes
2024-02-01 10:32:03 +01:00
Nicola Soranzo
e975ca3754
Update to black 2024 stable style
2024-01-30 18:09:51 +00:00
Nicola Soranzo
37116c39a0
Fix type annotation of code using XML etree
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by adding lxml-stubs to our typecheck requirements.
2024-01-26 18:41:09 +00:00
John Chilton
4157042ffa
Fix overlapping names in extra files for model stores.
2024-01-25 10:03:44 -05:00
John Chilton
69b01ac0e8
Utilities for higher level composite tests in test_model_store.
2024-01-25 10:03:44 -05:00
John Chilton
3a71150819
Minimal test case demonstrating model stores break on implicit conversions.
2024-01-25 09:32:40 -05:00
John Chilton
936a35d90d
More de-duplication in test_model_store.py.
2024-01-25 09:32:35 -05:00
John Chilton
24d215c9e7
Reduce duplication in test_model_store.
2024-01-24 11:11:16 -05:00
Nicola Soranzo
0e7b0eb83b
Extend .venv paths to ignore
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Useful when creating virtual environments for several Python versions
(e.g. `.venv38`, `.venv312`), which otherwise are linted by tools like
black, isort and flake8.
2024-01-22 20:33:47 +00:00
Nicola Soranzo
12ad482d66
Fix B038 errors reported by flake8-bugbear 24.1.17
2024-01-22 20:33:47 +00:00
Nicola Soranzo
9978004f34
Fix tests after Python 3.12 changes for comprehensions
2024-01-21 20:46:09 +00:00
mvdbeek
e02a765b7b
Merge branch 'release_23.2' into dev
2024-01-18 12:23:00 +01:00
Matthias Bernt
3a98a3a262
implement listing of linters
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using `__subclasses__`
2024-01-17 15:07:23 +01:00
mvdbeek
ef26fc4685
Use MockApp instead of celery_injected_app_container
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Sorry, I guess the idea was to not have to build a full MockApp ?
Realisitically all tasks access the database at this point.
I suppose we could make the decorators more specific if necessary ?
2024-01-17 12:45:20 +01:00
Matthias Bernt
ccced2f6e1
add function to list available linters
2024-01-16 10:08:48 +01:00
Nicola Soranzo
81a16d3e92
Skip unit tests that require node when it's not installed
2024-01-15 18:32:05 +00:00
mvdbeek
03f01da108
Merge branch 'release_23.2' into dev
2024-01-15 12:09:43 +01:00
mvdbeek
a2cb91487a
Merge branch 'release_23.1' into release_23.2
2024-01-15 12:05:09 +01:00
mvdbeek
01502917f7
Fix `to_cwl` for nested collections
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Fixes
```
TypeError
Object of type DatasetCollection is not JSON serializable
```
seen when running https://github.com/galaxyproject/iwc/pull/315
2024-01-12 12:24:59 +01:00
mvdbeek
04441e503c
Fix encoded id unit test
2024-01-08 11:33:44 +01:00
mvdbeek
a13932c71c
Fix id field unit tests
2024-01-08 11:33:34 +01:00
mvdbeek
649895eb8d
.dict() -> .model_dump()
2024-01-08 11:33:32 +01:00
mvdbeek
79f1c292b5
Drop more deprecated .dict() and .construct() calls
2024-01-08 11:33:31 +01:00
mvdbeek
ac41a2bd44
More root and model fixes
2024-01-08 11:33:30 +01:00
mvdbeek
8a3d8058f6
Remove more __root__ and construct calls
2024-01-08 11:33:30 +01:00
mvdbeek
ed1c30a8b9
Fix fetch_data schema unit tests
2024-01-08 11:33:29 +01:00
mvdbeek
1593570e33
Replace DecodedDatabaseIdField.encode with Security.security.encode_id
2024-01-08 11:33:25 +01:00
mvdbeek
7f529e63c7
Merge branch 'release_23.2' into dev
2024-01-04 16:07:26 +01:00
mvdbeek
bc5259f5d2
Merge branch 'release_23.1' into release_23.2
2024-01-04 16:02:16 +01:00
Marius van den Beek
d0a7562ad7
Merge pull request #17236 from mvdbeek/fix_schema_integrity
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[23.1] Separate collection and non-collection data element
2024-01-02 20:41:31 +02:00
Matthias Bernt