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284 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 681372e916 Add directory for `area/database` label 2022-09-09 17:20:21 +01:00
Nicola Soranzo f4ed3ed7a4 Merge pull request #14540 from nsoranzo/MIT_license_20210407_onwards 
[PROCEDURES] Re-license under MIT all work from 2021-04-07 onwards
 2022-09-08 10:03:19 +01:00
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 39e03a8255 Re-license under MIT all work from 2021-04-07 onwards 
This is allowed because since 2021-04-06 (when PR
https://github.com/galaxyproject/galaxy/pull/11777 was merged), our pull
request template contains a checkbox asking the contributor to allow the
Galaxy committers to license all their contributions to the core galaxy
codebase under the MIT license.

Explicit approval to this change will be sought from the few persons who:
- opened a PR before 2021-04-07 which was merged after this date, and
- haven't already agreed to the re-licensing in a later PR.
 2022-08-30 19:12:19 +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
Nicola Soranzo 3c805558e0 Add directories for auth label 2022-05-04 23:05:11 +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