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2887 Commits
Author SHA1 Message Date
Gulsum Gudukbay 75d14cb636 adding test extensions for GPU 2022-12-14 11:03:34 +01:00
Nicola Soranzo 85a92be30a Merge pull request #15177 from jmchilton/fixup_refactoring_types 
Fixup types surrounding workflow refactoring testing.
 2022-12-13 10:48:41 +00:00
John ChiltonandNicola Soranzo 3cc3938ebb Update test/unit/workflows/test_refactor_models.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-12-12 19:34:57 -05:00
John Chilton ca8fc29436 Small tweaks to test_refactor_models. 2022-12-12 18:22:06 -05:00
John Chilton c90e1e3351 Merge pull request #15185 from jmchilton/typathon_types_1 
Small mypy improvements.
 2022-12-12 17:19:52 -05:00
John Chilton 2f46f05d48 Typing galaxy.security. 2022-12-12 14:18:28 -05:00
John Chilton 0180bf67a1 Fixup types surrounding workflow refactoring testing. 2022-12-12 10:18:20 -05:00
Marius van den Beek a85bd6d12a Merge pull request #15069 from jmchilton/mypy_unchecked_1 
Address some of the new mypy notes about unchecked annotations.
 2022-12-12 16:02:05 +01:00
mvdbeek 792617d242 Drop unused contents_near api endpoint 
It was added for the beta version of the new history, but it's unused
now.
 2022-12-12 10:02:11 +01:00
John Chilton 1efec9f8ba Address some of the new mypy notes about unchecked annotations. 2022-12-11 23:28:12 -05:00
John Davis d18e035b0f Fix mypy in tests 2022-12-09 16:35:45 -05:00
John Davis 0c1f21591b Add type hints to datatypes/*validate(), DatatypeValidation 2022-12-09 16:35:45 -05:00
Marius van den Beek 9ea96aaf35 Merge pull request #15157 from mvdbeek/fix_test_attribute 
Fix tests.lint_tsts attribute
 2022-12-08 20:02:04 +01:00
mvdbeek 793f1b2caa Fix tests.lint_tsts attribute 2022-12-08 19:57:58 +01:00
Björn Grüning 2f7f3e0ac0 Merge pull request #14770 from johanneskoester/feat/mulled-mamba-support 
feat: mamba support for mulled-build
 2022-12-08 18:35:29 +01:00
John Chilton 542908a49c Merge pull request #12975 from bernt-matthias/topic/lint-expect-num-outputs 
linter: warn if expect_num_outputs is missing
 2022-12-08 18:04:25 +01:00
Marius van den BeekandMarcel Bargull 32c330809e Fix parametrized test 
Co-authored-by: Marcel Bargull <mbargull@users.noreply.github.com>
 2022-12-08 16:40:35 +01:00
Johannes Köster e2723be5a1 extend test case 2022-12-08 16:40:34 +01:00
Björn Grüning 6a5608bcd6 Merge pull request #15031 from jmchilton/structured_test_decorators 
Infrastructure for indicating Galaxy features being used by tests.
 2022-12-03 10:34:49 +01:00
davelopez efcf76e3b5 Return 404 when target expires or doesn't exists 2022-12-02 09:57:29 +01:00
John Davis 0aa0feb610 Merge pull request #15004 from jdavcs/dev_mypy_workflow 
Run mypy on a fully loaded galaxy venv for stricter type checking
 2022-11-30 22:30:37 -05:00
Martin Cech e4becc21a0 Merge pull request #14959 from bernt-matthias/topic/lint-expect_failure_num_outputs 
lint for coexisting expect_num_outputs and expect_failure
 2022-11-30 20:06:29 +01:00
John DavisandNicola Soranzo 02ea4f531e Drop unused attr 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-11-30 13:39:16 -05:00
John DavisandNicola Soranzo 67c7e7d1ac Use a simple cast instead of relying on dependency injection 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-11-30 13:33:42 -05:00
Nicola Soranzo 139d14e952 Fix `object_store type in MinimalToolApp` protocol 2022-11-30 17:55:04 +00:00
Nicola Soranzo 95ccefacb8 Improve type annotations for model store 
and related files.

Follow-up on https://github.com/galaxyproject/galaxy/pull/14971 .
 2022-11-30 01:45:56 +00:00
John Davis 71769182b6 Ignore 2 type errors in tests 2022-11-29 14:59:17 -05:00
John Davis cbabba8f49 Fix typing error in unit test 2022-11-29 14:59:17 -05:00
John Davis aba2b4c52a Fix mypy error (has-type) 
Fixes this error: (the value is of type sqlalchemy.orm.Session; I don't
know what it's not inferred)

test/unit/app/authnz/test_custos_authnz.py:225: error: Cannot determine type of "sa_session"  [has-type]
                    self.session = self.sa_session
 2022-11-29 14:59:17 -05:00
Martin Cech 85058e4331 Merge pull request #15018 from natefoo/job-conf-yaml 
Replace XML job conf sample with YAML
 2022-11-29 00:52:05 +01:00
Matthias Bernt 0b4d75419e lint for coexisting expect_num_outputs and expect_failure 
which makes no sense since output assumption are not checked
if an error occurs
 2022-11-28 14:07:53 +01:00
Nicola Soranzo de5e9c0e71 Add some type annotations to `WebApplication and GalaxyWebTransaction` 2022-11-28 04:50:03 +00:00
Nicola Soranzo c5868cc717 Add overloads to `listify()` type annotations 
Also:
- Add unit tests.
 2022-11-28 04:50:03 +00:00
Nicola Soranzo 807fdfa5af Type annotation fixes 2022-11-28 04:50:01 +00:00
Michael R. Crusoe 2e69f64496 mypy 0.991 + bonus extra typing 2022-11-28 04:50:00 +00:00
John Chilton 018d066e36 Useful test decorators and runtime support for annotating how tests will be used. 2022-11-26 11:28:36 -05:00
John Davis d11eab88aa Merge pull request #15010 from jdavcs/dev_galaxy_root_func 
Use galaxy_directory() util function to check if code is running from root or from packages
 2022-11-22 10:25:38 -05:00
John Davis e0145fad50 Rename template.py >> templates.py 2022-11-21 18:12:04 -05:00
John Davis 3b488017b1 Normalize path before checking basename 2022-11-21 18:12:04 -05:00
John Davis b2d6b8d40d Skip dbscript tests if running from packages; refactor util function 2022-11-21 18:12:04 -05:00
John Davis 116682a59f Do not call split on cmd: there may be spaces in path 2022-11-21 18:12:04 -05:00
John Davis b934b27ea0 Move custom tempates unit test into app; rm jinja2 package dep from config 2022-11-21 18:12:04 -05:00
John Davis 29053fa9e4 Move test_dbscript into app 
JUSTIFICATION:
As per @jmchilton:
The package tests should pretend they don't have galaxy_directory()
available because they're meant to be installed into a Python env.
This test is fundamentally not testing anything about the Galaxy data
package - it is testing scripts placed in Galaxy root directory and that
would not be available in an installed Galaxy environment.
 2022-11-21 18:12:04 -05:00
John Davis 4e5a94a2b2 Use resource_path for test_dbscript 2022-11-21 18:12:04 -05:00
John Davis faf8efafd0 Use resource_path for test_migrations 2022-11-21 18:12:04 -05:00
John Davis 86cc0f2b69 Move custom templates into the config package 2022-11-21 18:12:04 -05:00
John Davis dd267e2d3e Refactor test, use galaxy_directory() 2022-11-21 18:12:04 -05:00
John Davis 821b60f30a Use galaxy_directory() instead of hacking the path 2022-11-21 18:12:04 -05:00
John Davis 44e7c97b6d Fix get_chunk(), add test 2022-11-18 18:24:54 -05:00
Nate Coraor 1cdb7b5bcd Replace XML job conf sample with YAML. 
Prefer loading job_conf.yml, fall back to job_conf.xml with a warning if
it exists.
 2022-11-17 19:58:24 -05:00