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
215beecece
Replace conditional `self.fail()` method calls with asserts
2022-09-27 03:34:57 +01:00
Nicola Soranzo
7646d9eb7b
Workaround for abstract test classes
2022-09-27 03:34:56 +01:00
Nicola Soranzo
30d8d2ba66
Remove unused function
2022-09-27 03:34:56 +01:00
Nicola Soranzo
3091737ab9
Misc test fixes
2022-09-27 03:34:55 +01:00
Marius van den Beek
955815ca11
Merge pull request #14688 from mvdbeek/dev
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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
John Chilton
156977f65a
Merge pull request #14691 from jmchilton/tool_util_testing_3
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More typing and unit testing for tool test verification functions
2022-09-24 08:41:04 -04:00
Björn Grüning
e4636cead0
Merge pull request #14682 from jmchilton/galaxy_install_typing
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More typing for tool shed install and relevant utility code.
2022-09-23 21:56:06 +02:00
John Chilton
fc491434ab
Merge pull request #14673 from natefoo/container-monitor-relocate
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Packaging and configurability for the container monitor script
2022-09-23 09:17:23 -04:00
John Chilton
550d29493f
Merge pull request #14683 from mvdbeek/type_annotation_workflow_run
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Add type hints for galaxy.workflow.{run, run_request}
2022-09-23 09:14:46 -04:00
John Chilton
19aba1807e
Initial unit test for copying test data.
2022-09-23 09:11:40 -04:00
John Chilton
2684cdb908
Refactor mock tool test interactor for reuse.
2022-09-23 09:06:15 -04:00
mvdbeek
81b2f3e1e1
Add ModuleInjector, avoids test type mismatch
2022-09-23 10:19:02 +02:00
mvdbeek
48c654d1b2
Add type hint for galaxy.workflow.{run, run_request}
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Trying out https://github.com/dropbox/pyannotate here.
It's still a lot of work even with pyannotate, but I think this fixes
some minor oddities, like assigning non-mapped attributes to
WorkflowInvocation instances.
2022-09-23 09:33:47 +02:00
John Chilton
ace1e13da3
Merge pull request #14641 from mvdbeek/fix_optional_data_input_submission_expanded_tool_form
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[22.05] Fix delayed optional data input handling
2022-09-22 18:08:58 -04:00
John Chilton
357a2ee954
Improved assertion in error in failing test.
2022-09-22 18:05:33 -04:00
John Chilton
ba9df94510
Merge pull request #14674 from nsoranzo/replace_self.assert_methods
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Replace ``self.assert*()`` method calls with plain asserts
2022-09-22 11:20:29 -04:00
John Davis
06c9475683
Merge pull request #14537 from jdavcs/dev_managedb_cli
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A replacement for manage_db.sh + rewrite of migration system documentation
2022-09-22 10:06:45 -04:00
Nicola Soranzo
a5c41adb96
Remove unused `get_suite()` functions
2022-09-22 02:21:12 +01:00
Nicola Soranzo
2ec191e764
Fix typos
2022-09-21 23:50:06 +01:00
Nicola Soranzo
853c8f913a
Use `self.assertRaises*()` as a context manager
2022-09-21 23:50:06 +01:00
Nicola Soranzo
f3b04b8f26
Remove `unittest.main()` calls
2022-09-21 23:50:05 +01:00
Nicola Soranzo
b5c7e2c86a
Replace `self.assert* method calls with plain asserts in test/`
...
using https://github.com/pytest-dev/unittest2pytest with the following command:
```
unittest2pytest -f self_assert -w -n test/
```
(excluding ``self.assertRaises*`` method calls).
2022-09-21 23:50:05 +01:00
Nate Coraor
836d68df40
Update job_conf docs for container_monitor options
2022-09-21 17:49:11 -04:00
mvdbeek
64cb245ddd
Fix running subworkflows with disconnected optional/default inputs
2022-09-21 19:31:41 +02:00
John Chilton
0da47b2ccf
Merge pull request #14649 from jmchilton/review
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Remove repository review functionality from tool shed.
2022-09-19 14:50:25 -04:00
John Chilton
44d6a34178
Remove repository review functionality from tool shed.
2022-09-16 20:25:37 -04:00
John Davis
4c7d6805e7
Drop integration test for config defaults
2022-09-16 15:31:55 -04:00
John Davis
5236b66382
Improve test of assignment of default config values
2022-09-16 15:15:03 -04:00
John Davis
eb9dccef58
Drop unit tests for default config values
2022-09-16 15:05:20 -04:00
davelopez
0128e05a23
Fix export ro-crate to file source
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Write to the store the correct archive file
2022-09-16 17:19:49 +02:00
John Davis
1eb4d15f38
Split script into admin and dev
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TODO: remove duplication between db.py and db_dev.py (split into
multiple commits is intentional)
2022-09-16 00:39:44 -04:00
John Davis
b6a5286487
Rename db.sh > manage_db.sh, following code review feedback
2022-09-16 00:39:44 -04:00
John Davis
3c094790a1
Update test comments
2022-09-16 00:39:03 -04:00
John Davis
372d4af0b8
Add type hints
2022-09-16 00:39:03 -04:00
John Davis
1f5b0e6bba
Drop LegacyScripts: no longer used
2022-09-16 00:39:03 -04:00
John Davis
7e238bf591
Add --raiseerr option; hide error traceback by default
2022-09-16 00:39:03 -04:00
John Davis
959bc49e66
Add missing tests
2022-09-16 00:39:03 -04:00
John Davis
0745e2e05c
Fix mypy by asserting object before accessing its attributes
2022-09-16 00:39:03 -04:00
John Davis
89f753767b
Fix packages tests: script is one level up
2022-09-16 00:39:03 -04:00
John Davis
ac6b0ceee0
Fix linting
2022-09-16 00:39:03 -04:00
John Davis
0a798ea536
Test against 1 or 2 databases
2022-09-16 00:39:03 -04:00
John Davis
b30e4e14ae
Add inline testing documentation
2022-09-16 00:39:03 -04:00
John Davis
a69ab407a6
Add initial draft
2022-09-16 00:39:03 -04:00
John Davis
6abc9dc1c5
Refactor get_alembic_cfg: make available to other code
2022-09-16 00:39:03 -04:00
John Chilton
a887fc894d
Merge pull request #14616 from jmchilton/ts_tests_1
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More tool shed API tests (+fixes)
2022-09-15 09:08:31 -04:00
John Chilton
f8c1c11016
API tests for tool shed search APIs.
2022-09-14 09:31:27 -04:00
John Chilton
3dbe2891e7
Implement RO Crate export of Galaxy histories and invocations.
2022-09-13 19:20:48 -04:00
John Chilton
42364892ac
Merge pull request #14604 from bernt-matthias/topic/lint-duplicate-inputs
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linter: check for inputs with duplicated names
2022-09-12 15:24:01 -04:00
Nicola Soranzo