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361 Commits
Author SHA1 Message Date
Nicola Soranzo bbb239a76b Install node from setup-node action 2023-10-20 11:14:30 +01:00
Nicola Soranzo 60aca1657d Expand `run:` values to multiple lines 2023-10-20 11:14:27 +01:00
Nicola Soranzo 72629a4f8e Expand matrix to test all combinations on Python 3.7 and 3.11 2023-10-20 11:14:26 +01:00
Nicola Soranzo f08ab1c8b4 Fix duplicated cache key 2023-10-20 11:14:26 +01:00
Nicola Soranzo 23daf7cfb4 Don't fail-fast in lint GitHub workflow 2023-10-19 12:53:59 +01:00
John Chilton 7dc0b1378b WIP: modern tool shed frontend 2023-09-27 14:30:42 -04:00
John Chilton e2e0d44312 DEBUG lint openapi CI 2023-09-26 13:47:00 -04:00
John Chilton 06667470b6 Modernized framework to replace tool shed functional tests. 
Goals:

- Replace direct database access with pydantic typed API requests.
- Replace Twill with playwright.
- Eliminate access to the Galaxy UI in the tests - the tests should assume API access from the installing party.

pytest-playwright requires small bits of #13909.

This is a worthy project that could let us remove a bunch of deprecated stuff from the Galaxy admin controllers and a bunch of mako stuff that is unused and could be used to test PRs like #14609 (which prompted me to do this) but I'm anxious about growing emotionally attached to code I want to remove and I'm worried about losing track of which helpers are required for Planemo/Emphemeris/Galaxy and which helpers are just being used to test the tool shed.
 2023-09-26 13:46:59 -04:00
John Chilton d1d629074b ToolShed API 2.0 2023-09-26 13:46:58 -04:00
John Chilton ebf8e2b0c3 Standalone implementation of tool shed client... 2023-09-26 13:46:54 -04:00
mvdbeek 0f2ef4dc0c Merge branch 'release_23.1' into dev 2023-09-14 13:43:50 +02:00
mvdbeek ed94b91456 Use --biocontainers in converter tests 2023-09-13 12:18:25 +02:00
mvdbeek 33aab28217 Merge branch 'release_23.1' into dev 2023-09-08 14:43:01 +02:00
mvdbeek 5b4179ea97 Merge branch 'release_23.0' into release_23.1 2023-09-08 14:41:13 +02:00
mvdbeek 98da5653a5 Merge branch 'release_22.05' into release_23.0 2023-09-08 14:40:36 +02:00
mvdbeek 7c11227b1c Switch to upstream setup-chromedriver action 2023-09-08 13:45:26 +02:00
Nicola Soranzo 23185e7039 Add GitHub CI workflow to test on Python 3.7 the packages needed by Pulsar 
so we will be able to drop Python 3.7 support for the rest of the code base.

Add a new `test_galaxy_packages_for_pulsar` tox environment and modify the
`test.sh` script so that when the `--for-pulsar` argument is passed:
- only the 4 packages used by Pulsar are tested
- mypy checks are skipped
- unit tests don't skip the tests marked with
  `external_dependency_management` (i.e. those conda/container-related).

Also:
- Add missing pydantic requirement to the galaxy-objectstore package
 2023-09-06 11:07:56 +01:00
Nicola Soranzo 20022b8e04 Install also Python 3.7 for update-lint-requirements 
Follow-up on commit d604bffc5f .

Drop caching of pip directory for this workflow.
 2023-09-02 21:59:32 +01:00
Nicola Soranzo d604bffc5f Run poetry under Python 3.8 
Fix broken GitHub workflow run, see e.g.:

https://github.com/galaxyproject/galaxy/actions/runs/5982465584/job/16231580682
 2023-09-01 19:09:05 +01:00
mvdbeek 493f17a323 Merge branch 'release_23.1' into dev 2023-07-26 14:22:48 +02:00
mvdbeek 9e97643df4 Merge branch 'release_23.0' into release_23.1 2023-07-26 14:19:38 +02:00
mvdbeek ff7565dd2d Merge branch 'release_22.05' into release_23.0 2023-07-26 14:16:34 +02:00
mvdbeek b9c07a7fb9 Use reusable workflow in all selenium workflows 2023-07-26 12:29:36 +02:00
mvdbeek 989551dddd Externalize selenium setup with reusable workflow 2023-07-26 12:25:04 +02:00
mvdbeek b56d785d4e Use action 2023-07-26 12:25:00 +02:00
mvdbeek eee86327ab Use upstream command to install chrome and chromedriver 2023-07-26 11:17:24 +02:00
mvdbeek 37977ebed5 Bump version of chromedriver setup action 2023-07-25 14:11:04 +02:00
Marius van den Beek 03ad09cf49 Merge pull request #16456 from ElectronicBlueberry/labeler-fix 
Fix labeler for UI UX labels
 2023-07-25 09:49:29 +02:00
Laila Los f2e6db9fe9 use negation in list instead of all option 2023-07-25 03:12:01 +02:00
Nicola Soranzo 45e020e760 Merge branch 'release_23.1' into dev 2023-07-24 17:04:54 +01:00
Nicola Soranzo 0a73e1c512 Merge branch 'release_23.0' into release_23.1 2023-07-24 15:16:11 +01:00
Nicola Soranzo 387aa1dd48 Test first startup on macOS also with Python 3.11 
- Allow passing GALAXY_CONDA_PYTHON_VERSION environment variable to
  the startup script to specify the Python version to use when
  creating the `_galaxy_` conda environment.
- Some Shellcheck fixes.
 2023-07-21 00:58:33 +01:00
Nicola Soranzo 264747f172 Merge branch 'release_23.1' into dev 2023-07-12 14:29:56 +01:00
Nicola Soranzo 5de8eca58a Merge branch 'release_23.0' into release_23.1 2023-07-12 12:14:22 +01:00
Nicola Soranzo e7500ae7db Pin black version to 23.3.0 in workflow action 
black 23.7.0 has dropped support for Python 3.7 .
 2023-07-11 12:25:41 +01:00
Laila Los 5d9959622d exclude auto-generated schema file from labeler 2023-07-07 04:13:30 +02:00
mvdbeek 192745bc22 Bump default milestone to 23.2 2023-06-21 23:37:29 +02:00
mvdbeek 67c7181a6a Merge branch 'release_23.0' into dev 2023-06-13 17:30:22 +02:00
mvdbeek 787b8040c8 Use galaxy-release-util to upload python packages 2023-06-13 15:49:37 +02:00
Nicola Soranzo afc11e2ebc Merge branch 'release_23.0' into dev 2023-05-30 17:49:58 +01:00
mvdbeek 66ca4d5e28 Run only on galaxyproject.org owner 2023-05-28 11:16:00 +02:00
mvdbeek a4f43ca6f9 Drop package_repository argument, just use TWINE_REPOSITORY_URL 2023-05-28 11:15:59 +02:00
mvdbeek 827d9b6fc1 Fix prerelease event 2023-05-28 11:15:59 +02:00
mvdbeek d79f81905e Add publishing workflow 2023-05-28 11:15:59 +02:00
Nicola Soranzo 5889ae0ff5 Run ToolShed tests on ubuntu-latest 2023-05-25 08:28:58 +01:00
Nicola Soranzo 1d59dcb409 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.
 2023-05-23 12:17:23 +01:00
mvdbeek 0148a3f7a8 Merge branch 'release_23.0' into dev 2023-05-19 14:54:02 +02:00
John Chilton 8cc7d3c5f3 Merge pull request #16082 from nsoranzo/osx_startup_py3.11 
Fix and test startup with Python 3.11 on macOS
 2023-05-15 09:07:14 -04:00
Nicola Soranzo ab99721900 Merge branch 'release_23.0' into dev 2023-05-14 14:40:28 +01:00
Nicola Soranzo 940ff9fe36 Test first startup on macOS also with Python 3.11 
- Allow passing GALAXY_CONDA_PYTHON_VERSION environment variable to
  the startup script to specify the Python version to use when
  creating the `_galaxy_` conda environment.
- Some Shellcheck fixes.
 2023-05-12 15:45:39 +01:00