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38072 Commits
Author SHA1 Message Date
galaxybot 2f741fa673 Update Python dependencies 2024-04-16 17:16:53 +01:00
Nicola Soranzo 1fef07cb24 Replace pytest-celery with `celery.contrib.pytest` plugin loading 
The new 1.0.0 version of pytest-celery will move towards a Docker-based
approach for smoke and production-like testing, bringing in a number of
dependencies that we don't currently need.
Since the pre-1.0.0 version of pytest-celery was just a shim for
``celery.contrib.pytest``, we can simply load the latter for API,
integration and Selenium tests.
 2024-04-16 17:16:52 +01:00
Nicola Soranzo 053ca5198e Enable `warn_unused_ignores` mypy option 2024-04-16 01:12:58 +01:00
Nicola Soranzo dcb6f061f6 Don't install Galaxy packages in editable mode when testing them 
When enabling the `warn_unused_ignores = True` option of mypy, this
was making the `test_galaxy_packages` tests fail with:

```
mypy .
Traceback (most recent call last):
  File "/tmp/gxpkgtestenvu3fgDr/bin/mypy", line 8, in <module>
    sys.exit(console_entry())
  File "/tmp/gxpkgtestenvu3fgDr/lib/python3.10/site-packages/mypy/__main__.py", line 15, in console_entry
    main()
  File "mypy/main.py", line 100, in main
  File "mypy/main.py", line 182, in run_build
  File "mypy/build.py", line 192, in build
  File "mypy/build.py", line 266, in _build
  File "mypy/build.py", line 2942, in dispatch
  File "mypy/build.py", line 3333, in process_graph
  File "mypy/build.py", line 3414, in process_fresh_modules
  File "mypy/build.py", line 2110, in fix_cross_refs
  File "mypy/fixup.py", line 52, in fixup_module
  File "mypy/fixup.py", line 127, in visit_symbol_table
  File "mypy/lookup.py", line 49, in lookup_fully_qualified
AssertionError: Cannot find component 'util' for 'galaxy.util'
make: *** [Makefile:96: mypy] Error 1
```

Moreover, installing packages in editable mode was hiding some issues
with how files from other packages were accessed.
 2024-04-16 01:12:57 +01:00
Nicola Soranzo c286930449 Consolidate use of `galaxy.util.resources` 2024-04-15 23:43:49 +01:00
John Davis 372b8d673a Merge pull request #17902 from jmchilton/dev_model_newbase 
Outline use of type_annotation_map to fix mypy issues
 2024-04-15 12:59:56 -04:00
Dannon 450e48af88 Merge pull request #17968 from jmchilton/error_reporting_unit_tests 
Error reporting unit tests
 2024-04-15 12:39:34 -04:00
John Chilton 873ade5aaa More explicit optionals? 2024-04-15 11:40:09 -04:00
John Chilton 7afc088ea0 Fix mypy sqla errors around Dataset.transform. 2024-04-15 11:36:31 -04:00
John Chilton 0a47a2322a Outline use of type_annotation_map to fix mypy issues? 2024-04-15 11:35:43 -04:00
John Davis 8354154204 Improve variable naming 
Following suggestions from code review
 2024-04-13 13:26:20 -04:00
John Davis 82a0ef40b7 Start removing type:ingore comments from SA2.0 PR 2024-04-12 15:33:59 -04:00
John Davis 14ec0172a4 Fix type of Job.state, remove type:ignore 2024-04-12 15:20:23 -04:00
John Davis e96b00c45e Fix mypy errors, add type 
Can't reuse variable for different types: mypy complains.
 2024-04-12 14:07:57 -04:00
John Davis 61fc66745f Fix type in JobToInputDatasetCollectionElementAssociation.name 2024-04-12 13:59:51 -04:00
John Davis ce1cc2c05e Fix type in JobToInputDatasetCollectionAssociation.name 2024-04-12 13:39:23 -04:00
John Davis 83044490ee Cast as list to fix mypy error (types are correct) 2024-04-12 13:23:54 -04:00
John Davis da55f4aca5 Misc. typing edits 2024-04-12 12:24:29 -04:00
John Davis 9e40868512 Fix type in JobToOutputDatasetAssociation.name 2024-04-12 12:15:18 -04:00
John Davis d9878d103d Fix type in JobToOutputLibraryDatasetAssociation.name 
Add type to Job.output_library_datasets
 2024-04-12 12:10:16 -04:00
John Davis d76ac54f29 Fix type in JobToInputLibraryDatasetAssociation.name 
Add type to Job.input_library_datasets
 2024-04-12 11:57:08 -04:00
John Davis 78b2da5a15 Fix type in JobToImplicitOutputDatasetCollectionAssociation.name 
Add type to Job.output_dataset_collections
 2024-04-12 11:49:20 -04:00
John Davis 41d3054864 Fix type in JobToOutputDatasetCollectionAssociation.name 
+ add type hint to Job.output_dataset_collection_instances
 2024-04-12 11:42:30 -04:00
John Davis e7873d8aae Fix type in JobToInputDatasetAssociation.name 2024-04-12 11:34:52 -04:00
John Davis 585d911e08 Fix typing bug, add type in MetadatFile.dataset 2024-04-12 11:34:52 -04:00
John Davis ddf0da17d7 Correct types in item-annotation-assoc models (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis 8f02426ec7 Correct types in cleanup-event-assoc models (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis f9f9a68eea Correct types in item-rating-assoc models (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis b75154634b Correct types in item-tag-assoc models (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis ee12720120 Correct types in VisualizationUserShareAssociation (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis 6c2026849a Add+fix types in CustosAuthnzToken.user 2024-04-12 10:51:44 -04:00
John Davis fb32618722 Correct types in PageUserShareAssociation (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis 21b24dd4e9 Correct types in StoredWorkflowUserShareAssociation (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis d29d5c2567 Correct types in LibraryDatasetDatasetAssociationPermissions (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis 3a8ae7260d Correct types in DefaultQuotaAssociation (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis 985c2f6eb7 Correct types in GroupQuotaAssociation (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis cdc7c99980 Correct types in UserQuotaAssociation (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis e32c857afb Correct types in GroupRoleAssociation (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis 48c4d1a957 Correct types in UserRoleAssociation (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis a8d8dea8a0 Correct types in HistoryUserShareAssociation (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis 54d24763b7 Correct types in UserNotificationAssociation (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis a45197966b Correct types in JobContainerAssociation (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis de054fbb26 Correct types in ImplicitCollectionJobsJobAssociation (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis 0a1d3d3df4 Correct types in JobToOutputLibraryDatasetAssociation (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis b4073e1aca Correct types in JobToInputLibraryDatasetAssociation (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis 6bd8b81961 Correct types in JobToImplicitOutputDatasetCollectionAssociation (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis cc76654cb7 Correct types in JobToInputtDatasetCollectionElementAssociation (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis 65de14a505 Correct types in JobToOutputDatasetCollectionAssociation (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis 35149a05fd Correct types in JobToInputtDatasetCollectionAssociation (optional/nullable) 2024-04-12 10:51:44 -04:00
John Davis 53654e8316 Correct types in JobToOutputDatasetAssociation (optional/nullable) 2024-04-12 10:51:44 -04:00