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420 Commits
Author SHA1 Message Date
Nicola Soranzo 84742ee141 Run `uv lock` under Python 3.9 
Fix:

```
Using CPython 3.8.18 interpreter at: /opt/hostedtoolcache/Python/3.8.18/x64/bin/python
  × No solution found when resolving dependencies for split
  │ (python_full_version == '3.9.*'):
  ╰─▶ Because only the following versions of rucio-clients{python_full_version >= '3.9'} are available:
          rucio-clients{python_full_version >= '3.9'}<=33.6.1
          rucio-clients{python_full_version >= '3.9'}>=34.0.0,<=34.6.0
          rucio-clients{python_full_version >= '3.9'}>=35.0.0
      and all of:
          rucio-clients{python_full_version >= '3.9'}>=33.6.0,<=33.6.1
          rucio-clients{python_full_version >= '3.9'}>=34.0.0,<=34.6.0
          rucio-clients{python_full_version >= '3.9'}>=35.0.0
      require Python >=3.9, <4, we can conclude that all of:
          rucio-clients{python_full_version >= '3.9'}>=33.6.0,<33.6.1
          ...
          rucio-clients{python_full_version >= '3.9'}>35.4.1,<35.5.0
          rucio-clients{python_full_version >= '3.9'}>35.5.0
       are incompatible.
      And because galaxy:dev depends on rucio-clients{python_full_version >=
      '3.9'}>=33.6.0 and your project depends on galaxy:dev, we can conclude
      that your project's requirements are unsatisfiable.

      hint: The source distribution for rucio-clients{python_full_version >=
      '3.9'}==35.5.0 does not include static metadata. Generating metadata for
      this package requires Python >=3.9, <4, but Python 3.8.18 is installed.
```

See https://github.com/galaxyproject/galaxy/actions/runs/11684632042/job/32536277008
 2024-11-05 23:45:33 +00:00
Nicola Soranzo 695e86eaa7 Test under Python 3.13 2024-10-31 12:09:21 +00:00
Nicola Soranzo 93078d949a Replace poetry with uv 
for lightning-fast Python dependency updates.

To update all dependencies (as done by the GitHub action):

$ make update-dependencies

To update only one package:

./lib/galaxy/dependencies/update.sh -p <PKG>
 2024-10-31 10:22:52 +00:00
Björn Grüning d4b2b83310 Merge pull request #19002 from jmchilton/do_not_skip_ci_tests_on_missing_tools 
Do not skip CI tests on missing tools.
 2024-10-29 18:02:27 +01:00
John Chilton d3e0e28ce3 Do not skip CI tests on missing tools. 2024-10-15 16:02:27 -04:00
John Chilton 12fed2add3 Swap workflow framework tests to do a rerun. 2024-10-15 09:12:05 -04:00
Nicola Soranzo 70bea1b935 Define environment variables in `env:` section 
Fix potential command injection via PR title, see

https://securitylab.github.com/resources/github-actions-untrusted-input/
 2024-10-14 11:56:50 +01:00
Nicola Soranzo 3b4cfedaed Merge pull request #18835 from arash77/Update-PR-Title-Workflow 
Add workflow to update PR title based on target branch version
 2024-10-14 09:53:23 +01:00
ArashandNicola Soranzo 9433ecef18 Using github action contexts instead of gh CLI 
Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
 2024-10-14 10:51:13 +02:00
Arash KadkhodaeiandNicola Soranzo f4ffa9d74b More generic and shorter title 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2024-10-11 13:50:20 +02:00
Nicola Soranzo 6dc681dc01 Merge pull request #18975 from arash77/bioblend_tests 
Add BioBlend tests
 2024-10-11 07:18:14 +01:00
Arash KadkhodaeiandNicola Soranzo 17cfc6df5f virtualenv was only needed by old Galaxy versions. 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2024-10-11 01:00:43 +02:00
Arash b5d1432818 checkout first as it need to run git commands 2024-10-10 18:43:39 +02:00
Arash KadkhodaeiandNicola Soranzo 95e6d4cf73 No need to test BioBlend's interactions with the Test ToolShed. 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2024-10-10 17:51:42 +02:00
ArashandNicola Soranzo ece4b6708b Apply suggestions 
Drop galaxy_version and os from matrix and use galaxy_python_version.
Use actions/checkout instead of git clone.

Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
 2024-10-10 17:45:04 +02:00
Arash c03bb67505 Format bioblend workflow 2024-10-10 16:44:04 +02:00
Arash 93b7212e6a Update bioblend test script path 2024-10-10 16:41:06 +02:00
Arash 8c273c9d83 use bioblend repo instead of put the run test file in galaxy repo 2024-10-10 16:35:44 +02:00
Nicola Soranzo 385a5863da Merge branch 'release_24.1' into dev 2024-10-10 11:32:47 +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
Arash e3fb5bd27c add bioblend tests 2024-10-10 11:50:26 +02:00
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 01512cb159 Merge branch 'release_24.1' into dev 2024-10-09 10:55:01 +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
Arash Kadkhodaei d3c9e0354c Trigger workflow on edited PR 2024-09-17 18:29:52 +02:00
Arash e5acd13f02 use branches instead of if in the job, add permissions 2024-09-17 18:21:40 +02:00
Arash KadkhodaeiandNicola Soranzo 17a124ef43 Use pull_request_target instead of pull_request 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2024-09-17 18:02:42 +02:00
Arash 4160c31377 Add workflow to update PR title based on target branch version 2024-09-17 17:36:47 +02:00
Nuwan Goonasekera 0d4cb1091f Merge pull request #18514 from Bioconductor/dev 
Improvements for K8S deployment (especially ITs)
 2024-09-10 23:37:24 +05:30
Nicola Soranzo d3c369fc45 Drop caching the tox env when Python is installed via conda 2024-09-09 00:48:21 +01:00
Nicola Soranzo 30d2443a2b Cache pip directory as part of setup-python action 2024-09-08 19:37:04 +01:00
Matthias Bernt 9c9b52d5a6 update osx startup workflow 
to use miniforge
 2024-09-02 12:06:10 +02:00
John Chilton f6fcc95099 Setup workflow test framework. 2024-07-29 09:19:09 -04:00
Nicola Soranzo 945bd5db13 Sync cwl_conformance GitHub workflow with api one 2024-07-12 18:26:26 +01:00
Nicola Soranzo 269ec402e9 Merge branch 'release_24.1' into dev 2024-07-09 10:37:31 +01:00
Nicola Soranzo af6e28d01a Merge branch 'release_24.0' into release_24.1 2024-07-09 10:36:20 +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
Alexandru Mahmoud 7817a99c15 Add GHCR build 2024-07-05 18:10:34 -04:00
Dannon Baker fbaac02e69 Merge remote-tracking branch 'upstream/release_24.1' into dev 2024-06-28 09:55:22 +02:00
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 4c4b62b8d3 Merge remote-tracking branch 'upstream/release_24.1' into dev 2024-06-06 10:25:58 -04:00
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 32868aa798 Merge branch 'release_24.1' into dev 2024-05-28 19:26:42 +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