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388 Commits
Author SHA1 Message Date
mvdbeek 093dcc8d3d Merge branch 'release_24.0' into release_24.1 2024-05-28 14:34:20 +02:00
Nicola Soranzo 9b70b7582d Exclude bcsl.ts test files from CodeQL code scanning 
Fix errors like:

```
lib/galaxy/datatypes/test/test_file3.bcsl.ts#L2C12:12: A parse error
occurred: `';' expected.`. Check the syntax of the file. If the file
is invalid, correct the error or
[exclude](https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/customizing-code-scanning)
the file from analysis.
```

seen in https://github.com/galaxyproject/galaxy/actions/runs/9170180020/job/25211944475 .
 2024-05-23 16:09:31 +01:00
Nicola Soranzo 028630afcb Update syntax for labeler action v5 
See https://github.com/marketplace/actions/labeler#breaking-changes-in-v5
 2024-05-23 16:09:22 +01:00
Nicola Soranzo b19136073e Use official minikube GitHub action 
Cannot used the new default driver (`docker`) as it crashes the
PostgreSQL Docker container started via job services.
 2024-05-23 16:07:25 +01:00
Nicola Soranzo de2d36afe2 Update versions of GitHub actions 2024-05-23 16:06:43 +01:00
Nicola Soranzo 4c4ed106a4 Use job permissions instead of token 2024-05-23 16:06:21 +01:00
Nicola Soranzo 1d64120a00 Merge branch 'release_24.0' into dev 2024-04-25 14:32:52 +01:00
mvdbeek ab087383c8 Update setup-miniconda@v3 action 2024-04-24 17:38:58 +02:00
mvdbeek 64be33ebc9 Update k8s-version 2024-04-24 17:11:53 +02:00
Laila Los c026a2ece4 add browser and operating system to issue template 2024-03-13 13:51:36 +01:00
John Davis 1f08249d0a Change default milestone 2024-02-26 14:24:51 -05:00
Nicola Soranzo 6250c9797c Allow manual dispatch of "Update dependencies" GH workflow 2024-02-14 00:57:48 +00:00
mvdbeek b278d8a2aa Merge branch 'release_23.2' into dev 2024-02-08 11:35:49 +01:00
Nicola Soranzo 0e499dc26f Merge branch 'release_23.1' into release_23.2 2024-02-01 12:01:34 +00:00
Nicola Soranzo 11fdad09e2 Merge branch 'release_23.0' into release_23.1 2024-02-01 12:00:50 +00:00
Nicola Soranzo e82b950aba Fix uploading of docs for release_NN.N branches 2024-01-31 17:18:10 +00:00
Nicola Soranzo e975ca3754 Update to black 2024 stable style 2024-01-30 18:09:51 +00:00
Ubuntu 6860c9a0fb Add support for Python 3.12 2024-01-21 11:57:59 +00:00
Nicola Soranzo e565c7a9b5 Install node from setup-node action 
instead of relying on the node version pre-installed in the CI worker.
 2024-01-15 18:44:28 +00:00
mvdbeek a7a48131fe Add missing re-usable commit-id output 2024-01-06 10:14:19 +01:00
mvdbeek f228a72f6c Add name attribuite to cache actions 2024-01-04 21:48:35 +01:00
mvdbeek 74970749f8 Build and cache galaxy client for selenium test 2024-01-04 14:22:55 +01:00
mvdbeek 245c268342 Bump default milestone to 24.0 2023-12-19 11:31:00 +01:00
Nicola Soranzo 472bc3f7e6 Merge branch 'release_23.2' into dev 2023-12-05 13:15:46 +00:00
Nicola Soranzo ef5581c5c1 Install dev wheels in ToolShed tests 
Fix ToolShed tests failing on release branches due to playwright
not being installed, e.g.:

https://github.com/galaxyproject/galaxy/actions/runs/7090013789

Broken in commit 06667470b6 .
 2023-12-04 18:53:06 +00:00
Michael R. Crusoe c00967cca4 Python 3.8 as new minimum version 
Fixes: https://github.com/galaxyproject/galaxy/issues/16394

Also upgrade code to Python 3.8 syntax with:

```
ack --type=python -f | grep -v '^lib/galaxy/schema/bco/\|^lib/galaxy/schema/drs/\|lib/tool_shed_client/schema/trs.*.py\|^tools/\|^.venv/\|^.tox/' | grep -v '^lib/galaxy/files/sources/\|^lib/galaxy/job_metrics/\|^lib/galaxy/objectstore/\|^lib/galaxy/tool_util/\|^lib/galaxy/util/' | xargs pyupgrade --py38-plus
```
 2023-11-26 18:34:09 +00:00
davelopez 32b3a6d83f Move client schema package into api/schema 2023-10-23 18:13:42 +02:00
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