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32315 Commits
Author SHA1 Message Date
Aysam Guerler 39ea7d7a24 Merge pull request #14746 from jmchilton/installed_repository_manager_cleanup 
Cleanup installed_repository_manager.py and related code a bit more.
 2022-10-06 07:39:02 -04:00
John Chilton 13adeb3749 Rev pulsar-galaxy-lib to 0.14.16. 
CI caught another bug.
 2022-10-04 09:00:34 -04:00
John Chilton 72b319c442 Update pulsar-galaxy-lib to 0.14.15. 
Minted today.
 2022-10-03 16:19:28 -04:00
John Chilton 79a3ac12e1 Cleanup installed_repository_manager.py and related code a bit more. 
- Remove unused code and mako.
- Use more direct imports for better typing and static checking.
- Reuse existing abstractions a bit better.
 2022-10-03 09:04:00 -04:00
John Chilton 94c8218d48 setup service and fastapi layer for tool shed APIs... 2022-10-01 09:14:03 -04:00
John Chilton 2ed83560cb Merge pull request #14693 from jmchilton/cleanup_ts_test_3 
Migrate more tool shed functional testing to Galaxy API
 2022-09-29 14:05:52 -04:00
John Chilton 9bc6c1815b Merge pull request #14695 from natefoo/tailscale-container-monitor 
Configurable get IP method for container monitor
 2022-09-29 14:05:32 -04:00
Aysam Guerler 7bcda0ac51 Merge pull request #14716 from guerler/remove_workflow_sharing_mako 
Remove workflow export mako
 2022-09-29 10:35:11 -04:00
mvdbeek 8dc765713d Drop extra newline 2022-09-29 09:45:48 +02:00
Marius van den Beek cc8fa200bc Merge pull request #14720 from jmchilton/cleanup_job_files_1 
Cleanup hack in job files API for very old versions of Galaxy.
 2022-09-29 09:34:06 +02:00
Marius van den Beek 687385a68d Merge pull request #14728 from nsoranzo/fix_validation_dataset_metadata_in_file_testing 
Fix ``validation_dataset_metadata_in_file`` framework test
 2022-09-29 09:26:19 +02:00
Nicola Soranzo 5abee634b0 Cleanup 2022-09-29 01:50:33 +01:00
Nicola Soranzo 4ee1a102fb Improve error messages when parsing param validators 2022-09-29 01:50:32 +01:00
Nicola Soranzo d4afe4d10b Make `metadata_name` a required attribute of certain validators 2022-09-29 01:50:13 +01:00
John Chilton 8e31df09dd Cleanup manage_repository in admin_toolshed... 2022-09-28 13:03:58 -04:00
John Chilton 9934a83cf6 Cleanup more cruft... 2022-09-28 13:03:58 -04:00
John Chilton f9812fa2ef Remove legacy tool shed stuff just around for the tests. 2022-09-28 13:03:58 -04:00
John Chilton 4d6710172a Migrate reinstallation of repos in twill tests to an API-like endpoint (no mako and simpler handshake between shed and Galaxy) 2022-09-28 13:03:58 -04:00
John Chilton 3b29fc7f58 Improved testing for check updates... 2022-09-28 13:03:58 -04:00
John Chilton 82c1aefdb4 Notes about divergence between old and new install paths. 2022-09-28 13:03:58 -04:00
John Chilton 46eb887a66 Rework tool shed functional tests to use Galaxy APIs for installation instead of old controller. 2022-09-28 13:03:57 -04:00
John Chilton 459dfb882c We don't write version file there anymore! 2022-09-28 12:30:25 -04:00
guerler bda95f9737 Remove unused controllers, show error message when svg fails 2022-09-28 11:52:47 -04:00
Nicola Soranzo efb068e55f Add TODO for injected attributes 2022-09-28 15:01:23 +01:00
Nicola SoranzoandMarius van den Beek d86bb3edc9 Use `log_str()` method 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-09-28 14:37:11 +01:00
Nicola Soranzo 10271cf961 Add some type annotations to workflow-related code 2022-09-28 11:45:47 +01:00
guerler c2c7d4f05a Adjust workflow export selenium test, add login link to error message 2022-09-27 20:45:35 -04:00
guerler cc2e34b2f4 Remove unused attributes 2022-09-27 18:16:46 -04:00
guerler c4e518f8c2 Remove legacy individual sharing mako and controller 2022-09-27 16:04:29 -04:00
guerler ae9a25b45e Remove sharing/export makos for workflow 2022-09-27 15:56:11 -04:00
guerler f7d8a0af76 Add slug to workflow instance export, migrate features from export mako to vue component 2022-09-27 15:39:45 -04:00
guerler d452ba2307 Prep workflow export as vue component 2022-09-27 14:04:57 -04:00
John Chilton beda9e04a5 typing & linting fixes 2022-09-27 09:49:52 -04:00
John Chilton 061e3555a7 Merge pull request #14711 from nsoranzo/test_fixes 
Small test fixes
 2022-09-27 09:37:26 -04:00
John Chilton 99449db440 Merge pull request #14654 from jmchilton/invocation_jobs_test_fix 
Bug fix related to collecting invocation jobs.
 2022-09-27 09:36:37 -04:00
Dannon 0298ee36f3 Merge pull request #14679 from nsoranzo/replace_unittest.TestCase 
Replace ``unittest.TestCase`` with pytest-based partial re-implementation
 2022-09-27 09:10:59 -04:00
John Chilton 6469af4935 Merge pull request #14672 from jmchilton/cleanup_ts_test_2 
More cleanup of tool shed tests.
 2022-09-27 08:58:14 -04:00
Dannon 0627daa7ff Merge pull request #14686 from guerler/remove_beta_test 
Remove is_beta_history flag from selenium tests
 2022-09-27 08:19:00 -04:00
Nicola Soranzo 351de50bdd Update to latest mypy 0.981 and typing stubs 
Fix the following spurious error in package tests when using Python 3.10.7:

```
/tmp/gxpkgtestenv9iWFSL/lib/python3.10/site-packages/numpy/__init__.pyi:636: error:
Positional-only parameters are only supported in Python 3.8 and greater
[syntax]
        def seek(self, offset: int, whence: int, /) -> object: ...
                                                   ^
Found 1 error in 1 file (errors prevented further checking)
make: *** [Makefile:96: mypy] Error 2
```

xref. https://github.com/python/mypy/issues/13627

Also:
- Fix one newly reported incorrect typing annotation.
 2022-09-27 12:06:02 +01:00
Nicola Soranzo c35d8f2a06 Replace `unittest.TestCase` with pytest-based partial re-implementation 
Also:
- Rename `FooBarTestCase` test classes as `TestFooBar`. These were collected
  by pytest only because they were `unittest.TestCase` derived, but normally
  pytest collects only test classes whose name starts with `Test`, see
  https://docs.pytest.org/en/7.1.x/reference/reference.html#confval-python_classes
 2022-09-27 03:34:58 +01:00
Nicola Soranzo 3091737ab9 Misc test fixes 2022-09-27 03:34:55 +01:00
Nicola Soranzo 49f714f245 Drop broken way to run doctests 
We already run them with: `pytest --doctest-modules` .
 2022-09-27 03:34:55 +01:00
Björn Grüning ae02ee882f Merge branch 'dev' into invocation_jobs_test_fix 2022-09-26 22:28:06 +02:00
Marius van den Beek 955815ca11 Merge pull request #14688 from mvdbeek/dev 
Merge 22.05 into dev
 2022-09-26 15:19:53 +02:00
mvdbeek cbd38554f1 Merge branch 'release_22.05' into dev 2022-09-26 15:15:19 +02:00
guerler 9c3b03bc7a Remove legacy selenium test helpers 2022-09-24 12:18:50 -04:00
John Chilton 808eca05bd Use API repository object instead of database object in dozens of spots in tool shed functional tests. 2022-09-24 08:42:23 -04:00
John Chilton 32f34fa917 Another fix for running tool shed tests standalone. 2022-09-24 08:41:44 -04:00
John Chilton fb4708f773 Toolshed fix for lxml (only happens when run test in isolation). 2022-09-24 08:41:44 -04:00
John Chilton fabd33ee19 Add more repository index pydantic typing. 2022-09-24 08:41:43 -04:00