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7219 Commits
Author SHA1 Message Date
Nicola Soranzo a23cff23b2 Check GitHub API rate limit in `get_alternative_versions`, skip test if hit 
Fix the following mulled unit test random failure:

```
    @external_dependency_management
    def test_get_alternative_versions():
>       versions = get_alternative_versions("recipes/bioblend", "meta.yaml")

test/unit/tool_util/mulled/test_get_tests.py:79:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
lib/galaxy/tool_util/deps/mulled/get_tests.py:178: in get_alternative_versions
    r.raise_for_status()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <Response [403]>

                f"{self.status_code} Server Error: {reason} for url: {self.url}"
            )

        if http_error_msg:
>           raise HTTPError(http_error_msg, response=self)
E           requests.exceptions.HTTPError: 403 Client Error: rate limit exceeded for url: https://api.github.com/repos/bioconda/bioconda-recipes/contents/recipes/bioblend

.tox/mulled/lib/python3.7/site-packages/requests/models.py:1021: HTTPError
------------------------------ Captured log call -------------------------------
DEBUG    urllib3.connectionpool:connectionpool.py:1007 Starting new HTTPS connection (1): api.github.com:443
DEBUG    urllib3.connectionpool:connectionpool.py:465 https://api.github.com:443 "GET /repos/bioconda/bioconda-recipes/contents/recipes/bioblend HTTP/1.1" 403 277
```
 2023-01-04 10:48:34 +00:00
Nicola Soranzo 2cd3eb60ab Fix typos and wording 2023-01-04 09:40:24 +00:00
Martin Cech fc829c1694 Merge pull request #15273 from martenson/merge-15265 
Merge 22.05 to dev
 2023-01-04 02:17:25 +01:00
Martin Cech d03849df7a Merge pull request #14247 from bernt-matthias/topic/add-doc-lint-compare 
add doc and linting for test output compare attribute
 2023-01-03 23:32:13 +01:00
Martin Cech 36da2067ce Merge branch 'release_22.05' into dev 2023-01-03 13:13:53 -08:00
Martin Cech ca77e18411 Merge pull request #15265 from Lain-inrae/fix_gxit_short_token_-issue_15224 
[22.05] Fixes #15224 - tools token are created with a size of 10 chars when interactivetools_shorten_url is true
 2023-01-03 22:08:22 +01:00
Dannon e47769a1ca Merge pull request #15214 from jmchilton/auth_fastapi 
Migrate baseauth endpoint to FastAPI
 2023-01-03 10:40:51 -05:00
Dannon 86f9fa77ab Merge pull request #15254 from bernt-matthias/topic/lint-dm 
Apply all linters to data managers (which are applied to tools)
 2023-01-03 10:16:18 -05:00
Lain Pavot cdbfe6787b Fixes #15224 - tools token are created with a size of 10 chars when interactivetools_shorten_url is true 2023-01-03 09:37:18 +01:00
Nicola Soranzo a850a47419 Update pysam depedency to 0.20.0 
Fix `pysam.index()` calls which now use samtools 1.16 where
`samtools index input output` doesn't work any more if `output` is the path
of an already existing file, but `samtools index -o output input` works
fine.

Also:
- Pre-create the (empty) index file for mock test datasets as a unit test
  reproducer of the above issue.
- Fix `test_cram` unit test that wasn't checking the return value of
  `CRAM.set_index_file()`, which was in fact returning False because
  `test-data/2.cram` was not sorted (updated now).
 2023-01-01 03:37:53 +00:00
Nicola Soranzo 14ab87b6e7 Download involucro in a temporary directory in unit tests 2022-12-23 11:58:15 +00:00
Matthias Bernt 598521f496 add test 2022-12-23 10:18:12 +01:00
Marius van den Beek 69aba559a0 Merge pull request #12775 from gulsumgudukbay/dev 
Adding GPU support to Galaxy
 2022-12-20 16:24:22 +01:00
John Chilton 74491c2362 Migrate baseauth endpoint to FastAPI. 2022-12-17 10:16:27 -05:00
mvdbeek 36a632672e Linting fixes 2022-12-14 11:03:34 +01:00
Gulsum Gudukbay 75d14cb636 adding test extensions for GPU 2022-12-14 11:03:34 +01:00
John Chilton 788b231cd2 Merge remote-tracking branch 'origin/dev' into trs-url-import 2022-12-13 10:11:57 -05:00
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
Marius van den Beek aa05a21f23 Merge pull request #15192 from jmchilton/tool_test_typing_2_decompose 
Typing for tool test plumbing code.
 2022-12-13 11:47:54 +01:00
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 958d403ce8 Type+PydanticModel more tool test code. 2022-12-12 17:54:02 -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 59044511f5 Merge branch 'fixup_refactoring_types' into trs-url-import 2022-12-12 10:20:27 -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
Marius van den Beek 169705f007 Merge pull request #14839 from davelopez/history_export_tracking 
Add task-based history export tracking
 2022-12-12 09:42:44 +01:00
John Chilton 1efec9f8ba Address some of the new mypy notes about unchecked annotations. 2022-12-11 23:28:12 -05:00
davelopez e85798511c Move test_history_export selenium test 
This selenium test is for testing the previous history export UI that is based on jobs and not tasks.
Since Celery is enabled by default in the test instance it is more consistent to convert it into an integration selenium test to modify the config and disable Celery.
 2022-12-10 11:28:41 +01:00
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
Matthias Bernt 76be72a84f post rebase cleanup 2022-12-09 16:59:17 +01:00
John Chilton 13468884d8 Linting fixes. 2022-12-09 14:08:01 +01:00
Matthias Bernt ddc270e7d9 add doc and linting for test output compare attribute 2022-12-09 14:08:01 +01:00
Matthias Bernt 9558105502 add doc and linting for test output compare attribute 2022-12-09 14:07:58 +01:00
davelopez 6432a29739 Fix export record ready state + refactor test 2022-12-09 12:06:36 +01:00
davelopez b816fabaa9 Add integration selenium test for export tracking 2022-12-09 12:06:36 +01:00
davelopez 3a1ae0627b Increase test_export_tracking coverage 2022-12-09 12:06:36 +01:00
davelopez 32a08e05b5 Add API test for history export tracking 2022-12-09 12:06:36 +01:00
davelopez 67b8ba46c5 Disable celery in existing history export selenium test 
So the previous job-based export system is correctly tested
 2022-12-09 12:06:35 +01:00
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
davelopez e1804900e2 Skip this commit when merging forward 
This is just to make the test compatible with 22.05 since there is no "rocrate.zip" model store format yet.
 2022-12-08 13:33:08 +01:00
davelopez 2e81952877 Relax file source access requirements in tests 
By default the user must have the required role and groups. To simplify the setup of other tests, by default `PosixFileSourceSetup` will not require groups unless explicitly specified in the test.
This way we are always testing the default `test user` access through the role.
 2022-12-08 13:33:08 +01:00