opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
77,490 Commits 69 Branches 243 Tags
db7395b42378fe8aec00a5d25e452e033bc19164
Commit Graph
410 Commits
Author SHA1 Message Date
Nicola Soranzo e5f0a8c4eb Merge branch 'release_24.0' into release_24.1 2024-12-10 10:51:03 +00:00
ArashandNicola Soranzo afdfa789f1 Refactor version extraction in PR title update workflow for improved accuracy 
Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
 2024-11-26 12:20:19 +01:00
Arash f3e65fa1b9 Refactor PR title update workflow to handle version extraction and title formatting more efficiently 2024-11-25 11:39:58 +01:00
Nicola Soranzo 09d86951b1 Update title of edited PRs only if base ref changed 
Also:
- Update title of reopened PRs too.
- Don't unnecessarily checkout the repo.
 2024-11-22 12:16:03 +00:00
Nicola Soranzo ed07d87cf7 Merge branch 'release_24.0' into release_24.1 2024-10-22 15:52:23 +01:00
Matthias Bernt b71b6ef22e update osx startup workflow 
to use miniforge
 2024-10-21 21:31:56 +02:00
Arash Kadkhodaei 677c90bd0b PR title update workflow 2024-10-17 10:13:43 +02:00
mvdbeek ac40e41d96 Pin ubuntu 22.04 for minikube setup action 
The `ubuntu-latest` runner label is moving to 24.04, see https://github.blog/changelog/2024-09-25-actions-new-images-and-ubuntu-latest-changes/

Fixes https://github.com/galaxyproject/galaxy/actions/runs/11260477825/job/31317049837?pr=18963:
```
No VM guests are running outdated hypervisor (qemu) binaries on this host.
/usr/bin/lsb_release --short --codename
noble
Error: Unexpected HTTP response: 404
```
 2024-10-10 12:29:05 +01:00
Nicola Soranzo dd9ca09127 Merge branch 'release_24.0' into release_24.1 2024-10-10 11:31:30 +01:00
Nicola Soranzo f6200f83dd Merge branch 'release_23.2' into release_24.0 2024-10-10 11:30:51 +01:00
mvdbeek 0df29dd5e8 Pin ubuntu 22.04 for minikube setup action 
The `ubuntu-latest` runner label is moving to 24.04, see https://github.blog/changelog/2024-09-25-actions-new-images-and-ubuntu-latest-changes/

Fixes https://github.com/galaxyproject/galaxy/actions/runs/11260477825/job/31317049837?pr=18963:
```
No VM guests are running outdated hypervisor (qemu) binaries on this host.
/usr/bin/lsb_release --short --codename
noble
Error: Unexpected HTTP response: 404
```
 2024-10-09 22:04:47 +02:00
Nicola Soranzo 70e1fad3d9 Pin Ubuntu to 22.04 for Python 3.7 workflow 
Fix the following error at the setup-python step:

```
Version 3.7 was not found in the local cache
Error: The version '3.7' with architecture 'x64' was not found for Ubuntu 24.04.
The list of all available versions can be found here: https://raw.githubusercontent.com/actions/python-versions/main/versions-manifest.json
```

See e.g. https://github.com/galaxyproject/galaxy/actions/runs/11252595341/job/31294713655
 2024-10-09 15:19:39 +01:00
Nicola Soranzo 80a99f5533 Merge branch 'release_24.0' into release_24.1 2024-10-09 10:52:40 +01:00
Nicola Soranzo 31095a0e04 Pin black version to 24.8.0 in workflow action 
black 24.10.0 has dropped support for Python 3.8 .
 2024-10-08 17:18:43 +01:00
Nicola Soranzo af6e28d01a Merge branch 'release_24.0' into release_24.1 2024-07-09 10:36:20 +01:00
Nicola Soranzo eb00875001 Label issues with `area/UI-UX` only when both criteria match 2024-07-08 19:44:46 +01:00
Nicola Soranzo 0ae7b23232 Adding the milestone to a PR requires `issues: write` permission 
in addition to ``pull-requests: write``, see
https://github.com/actions/github-script/issues/255 .
 2024-07-08 19:44:36 +01:00
Dannon Baker 6ec7521e1a Merge remote-tracking branch 'upstream/release_24.0' into release_24.1 2024-06-28 09:48:27 +02:00
Nicola Soranzo 2fd90d1d9c Install node from setup-node action 2024-06-24 10:02:10 +01:00
Dannon Baker 2fcaa7792a Set github client build to fail when a plugin fails, as discussed in WG meeting; fail fast in CI so we can catch and resolve these. 2024-06-05 18:57:58 -04:00
Nicola Soranzo 043d99c0bb Use official minikube GitHub action 
Cannot used the new default driver (`docker`) as it crashes the
PostgreSQL Docker container started via job services.
 2024-06-05 08:38:36 +02:00
mvdbeek 0eaf1dc131 Update k8s-version 2024-06-05 08:34:33 +02:00
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