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270 Commits
Author SHA1 Message Date
Nicola Soranzo 7676afbf3b Update minikube-setup-action and use more recent k8s version 
The older minikube/k8s fail to launch under Ubuntu 22.04, which
is being deployed on GitHub action workers:
 2022-12-07 03:59:45 +00:00
Nicola Soranzo 71be0f9743 Move JavaScript linting to GitHub workflows 2022-12-02 15:09:31 +00:00
John Davis f07207ad6d Use 3 requirements files in the key for pip cache 2022-11-30 21:10:04 -05:00
John DavisandNicola Soranzo 1d75a584d6 Keep cache key suffix same as workflow filename 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-11-30 11:27:41 -05:00
John Davis d797c10ae8 Update github lint workflow 2022-11-29 22:02:32 -05:00
Nicola Soranzo 6d4ef85e86 Add GitHub workflow to check for regression in test class names 2022-11-07 15:44:03 +00:00
Nicola Soranzo 94427e5dea Fix the `singularity_container_test()` function 
Fix ``test_singularity_container_test`` unit test, which failed with:

```
test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py:48:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
lib/galaxy/tool_util/deps/mulled/mulled_update_singularity_containers.py:62: in singularity_container_test
    check_output(exec_command.extend(["bash", "-c", test_command]), stderr=subprocess.STDOUT)
/usr/lib/python3.8/subprocess.py:415: in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
/usr/lib/python3.8/subprocess.py:493: in run
    with Popen(*popenargs, **kwargs) as process:
/usr/lib/python3.8/subprocess.py:858: in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,

>           args = list(args)
E           TypeError: 'NoneType' object is not iterable

/usr/lib/python3.8/subprocess.py:1569: TypeError
```

Broken in commit 1dc1e5f219 .

Also:
- Use `tmp_path` pytest fixture.
- Add type annotations.
- Code refactorings.
- Install singularity in the mulled GitHub workflow so that the 2 singularity
  unit tests are not skipped any more.
 2022-11-04 00:00:16 +00:00
Nicola Soranzo afa7b713bc Replace `GALAXY_TEST_INCLUDE_SLOW env variable with external_dependency_management` pytest marker 
Fix mulled tests missing tests in `test/unit/tool_util/test_conda_resolution.py` .

Also:
- Add `coverage` tox factor to generate coverage report.
 2022-11-03 21:43:37 +00:00
Marius van den BeekandNicola Soranzo 6663fd562b Drop explicit test-data argument 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-11-02 18:04:47 +01:00
mvdbeek 969ba982b4 Don't do biocontainers for now 2022-11-01 12:19:41 +01:00
mvdbeek c214d27185 Drop more unused stuff 2022-11-01 10:38:51 +01:00
Marius van den BeekandNicola Soranzo 09af67484c Drop converter variable 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-11-01 09:57:18 +01:00
mvdbeek 0e6b4262c9 Simplify lint and test command now that planemo supports multiple test artefact paths 2022-10-31 18:54:51 +01:00
mvdbeek 6630fce2dc Use biocontainers 2022-10-31 18:01:32 +01:00
mvdbeek 83950f0631 Explicitly set test data location for converter tests 2022-10-31 12:06:32 +01:00
Nicola Soranzo c5052c7242 Add missing `python-version` to matrix expansion 
Also:
- Simplify some steps
 2022-10-17 03:15:53 +01:00
Nicola Soranzo c1e839c570 Replace `set-output commands with $GITHUB_OUTPUT` environment file 
See https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
 2022-10-17 02:26:39 +01:00
Nicola Soranzo 5fab7ee8bd Use indentation for YAML nested sequences for consistency 2022-10-17 02:17:11 +01:00
Nicola Soranzo 2988127158 Update GitHub action versions 2022-10-17 01:21:12 +01:00
Nicola Soranzo 7aaa7056fb Run ToolShed tests on ubuntu-latest 2022-09-27 12:06:02 +01:00
John Chilton d99c6f8a73 Run linting in Github actions when mypy config is updated. 2022-09-13 18:55:44 -04:00
Nicola Soranzo 36178dcd71 Drop GitHub workflow for legacy history Selenium tests 
and `GALAXY_TEST_SELENIUM_BETA_HISTORY` environment variable.

Any way I think we were not testing the legacy history any more since
https://github.com/galaxyproject/galaxy/pull/11748 was merged, see
https://github.com/galaxyproject/galaxy/pull/11748#discussion_r850401243 .
 2022-09-04 13:29:33 +01:00
Nicola Soranzo 3378348d5e Merge branch 'release_22.05' into dev 2022-08-17 01:07:02 +01:00
Nuwan Goonasekera 9da11c6ca3 Change repository to docker hub OSS repo 2022-08-15 21:44:56 +05:30
Nicola Soranzo 149c86d281 Fail "Run tests" step for any planemo test failure 2022-06-28 18:33:05 +01:00
Nicola Soranzo 5efdad7f84 Move test_galaxy_packages to GitHub workflows 
to make use of Python package caching.
 2022-06-02 17:24:23 +01:00
mvdbeek db2a5f5ff6 Bump default milestone to 22.09 2022-05-26 12:50:35 +02:00
Nicola Soranzo 1ccfdbbb4e Don't fail-fast in API GitHub workflow 2022-05-17 15:11:54 +02:00
Nicola Soranzo 02da77abcb Use `${{ github.workflow }}` in concurrency group name 2022-05-17 15:09:14 +02:00
Nicola Soranzo 02e36473a3 Split API tests in 2 jobs 2022-05-04 23:05:13 +01:00
Nicola Soranzo 1155b01784 Update GitHub action versions 2022-05-04 23:05:12 +01:00
Nicola Soranzo d93e49d970 Add `kind/enhancement` label to Python dep update PRs 2022-05-04 23:05:12 +01:00
Aysam Guerler d78a733010 Merge pull request #11748 from dannon/new-history-default 
Allow site-specific history default, leave fallback option to legacy
 2022-04-13 17:17:52 -04:00
Dannon Baker ec8bd0e9b2 Rename option to 'use_legacy_history'; invert assertions. 2022-04-13 13:28:41 -04:00
John Chilton fa4ee7b9b9 Implement asynchronous download APIs using STS. 
- Allow serving zipped collections using STS.
- Allow serving markdown PDFs using STS.
 2022-04-13 09:53:56 -04:00
Dannon Baker 6bba220f1c Set BETA_HISTORY_DEFAULT_ON for selenium_beta test workflow 2022-04-12 22:04:54 -04:00
Nicola Soranzo f677e4b94d Run 2 GitHub workflows also when Python dependencies are updated 
or the workflow YAML files are modified.
 2022-03-26 18:52:12 +00:00
Nicola Soranzo 6524e1f344 Fix path of venv when caching 2022-03-19 03:52:23 +00:00
Nicola Soranzo ca523f56b0 Cache galaxy root/.venv instead of .tox 
Unit tests are not using tox any more since commit
c90e012fda .

Reports startup also install packages in the venv and not in `.tox` .
 2022-03-19 03:38:12 +00:00
Nicola Soranzo cc5224bcf9 Use unique group id for unit-postgres tests 
Otherwise unit tests get cancelled when unit-postgres job finishes.
 2022-03-19 03:05:55 +00:00
mvdbeek 02f94a93b4 Drop tests for WEB_APP=dev 2022-03-15 21:31:59 +01:00
mvdbeek b39e8ad9a2 First pass in dropping uwsgi specific things 2022-03-15 21:31:59 +01:00
Sergey Golitsynskiy 8dacdac421 Run tests under Python 3.7 2022-03-09 18:40:07 -05:00
Sergey Golitsynskiy 9b91040f0a Add workflow for migration tests 2022-03-09 18:40:07 -05:00
Sergey Golitsynskiy ee654c1922 Remove migrations test from first starup workflow 
This tests sqlalchemy migrate which is being replaced.
 2022-03-09 18:40:07 -05:00
David López a0ad3160b2 Merge pull request #13504 from jmchilton/export_test_sele 
Integration end-to-end test for PDF export.
 2022-03-09 18:12:07 +01:00
Nicola Soranzo 25e37dd9d5 Merge pull request #13503 from mvdbeek/metadata_strategy_extended_tests_schedule 2022-03-09 14:21:26 +00:00
Marius van den BeekandNicola Soranzo 9c056a0d87 Mention why we don't run integration tests with outputs_to_working_directory 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-03-09 10:47:23 +01:00
John Chilton db4f530a57 Integration test for PDF export. 2022-03-08 15:32:22 -05:00
mvdbeek 55aec359b0 Run extended metadata test on schedule 
Including outputs_to_working_directory, except for the integration
tests.
 2022-03-08 18:58:15 +01:00