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29 Commits
Author SHA1 Message Date
Marius van den BeekandNicola Soranzo d52c0c2b19 Drop read node.js version step 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2025-09-29 17:11:28 +02:00
mvdbeek 38a7d23fbc Drop setup-node action where possible 
Where we still use the action we don't install python dependencies.
 2025-09-28 10:05:41 +02:00
dependabot[bot] 4f491d6628 Bump actions/setup-python from 5 to 6 
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5 to 6.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5...v6)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2025-09-23 21:22:20 +00:00
dependabot[bot] 46d3e6956c Bump actions/checkout from 4 to 5 
Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 5.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v4...v5)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '5'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2025-09-22 17:29:24 +00:00
dependabot[bot] 5b7d52a9d1 Bump actions/setup-node from 4 to 5 
Bumps [actions/setup-node](https://github.com/actions/setup-node) from 4 to 5.
- [Release notes](https://github.com/actions/setup-node/releases)
- [Commits](https://github.com/actions/setup-node/compare/v4...v5)

---
updated-dependencies:
- dependency-name: actions/setup-node
  dependency-version: '5'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2025-09-18 18:46:51 +00:00
Arash 0ab38db4d8 Set persist-credentials to false in GitHub workflows 2025-05-06 16:51:29 +02:00
Dannon Baker 867dba2d66 Single point of control for node version handling; read it from the .node_version file on disk in relevant actions. 2025-04-25 10:22:09 -04:00
Dannon Baker 023412ffa2 Bump github action node to 22.15.0 2025-04-25 10:02:45 -04:00
Dannon Baker f611918142 Test w/ node version 20 in advance of updating default Galaxy pinned nodejs 2025-04-22 09:10:24 -04:00
mvdbeek 3c6b6c5971 Merge branch 'release_24.2' into dev 2025-03-26 09:51:08 +01:00
mvdbeek 648239a31f Merge branch 'release_24.1' into release_24.2 2025-03-26 09:48:18 +01:00
Nicola Soranzo 302acfbc93 Ignore changes to `packages/` in most CI workflows 2025-03-25 15:28:33 +00:00
Nicola Soranzo edd8bccf4f Drop support for Python 3.8 2025-02-25 19:20:46 +00:00
Nicola Soranzo 695e86eaa7 Test under Python 3.13 2024-10-31 12:09:21 +00:00
Nicola Soranzo 30d2443a2b Cache pip directory as part of setup-python action 2024-09-08 19:37:04 +01:00
Nicola Soranzo de2d36afe2 Update versions of GitHub actions 2024-05-23 16:06:43 +01:00
Nicola Soranzo 94de628e43 Update versions of GitHub actions 2024-05-21 12:45:57 +01:00
Ubuntu 6860c9a0fb Add support for Python 3.12 2024-01-21 11:57:59 +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
mvdbeek 3a2e936401 Install node from setup-node action in more tests 
Should help with nodeenv failing in CI tests, e.g.
```
Installing node into /home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage with nodeenv.
 * Install prebuilt node (18.12.1) .Incomplete read while readingfrom https://nodejs.org/download/release/v18.12.1/node-v18.12.1-linux-x64.tar.gz
.
Traceback (most recent call last):
  File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/bin/nodeenv", line 10, in <module>
    sys.exit(main())
  File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 1104, in main
    create_environment(env_dir, args)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 980, in create_environment
    install_node(env_dir, src_dir, args)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 739, in install_node
    install_node_wrapped(env_dir, src_dir, args)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 762, in install_node_wrapped
    download_node_src(node_url, src_dir, args)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 602, in download_node_src
    with ctx as archive:
  File "/opt/hostedtoolcache/Python/3.7.16/x64/lib/python3.7/contextlib.py", line 112, in __enter__
    return next(self.gen)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 573, in tarfile_open
    tf = tarfile.open(*args, **kwargs)
  File "/opt/hostedtoolcache/Python/3.7.16/x64/lib/python3.7/tarfile.py", line 1573, in open
    saved_pos = fileobj.tell()
AttributeError: 'bytes' object has no attribute 'tell'
```
from https://github.com/galaxyproject/galaxy/actions/runs/4883207488/jobs/8714237674?pr=16036
 2023-05-04 17:35:06 +02:00
mvdbeek e84124cb82 Switch to official setup-node action for cache 2023-02-10 09:32:04 +01:00
Nicola Soranzo 4ca163b9ca Add support for Python 3.11 
- Update Python dependencies that didn't have a cp311 wheel: h5py and
  psycopg2-binary.
- For packages for which there is no recent version that works on all
  Python versions supported by Galaxy (numpy and scipy), replace old
  requirement with multiple Python-version-specific requirements.
 2023-02-02 01:18:25 +00:00
Nicola Soranzo c1e839c570 Replace `set-output commands with $GITHUB_OUTPUT` environment file 
See https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
 2022-10-17 02:26:39 +01:00
Nicola Soranzo 5fab7ee8bd Use indentation for YAML nested sequences for consistency 2022-10-17 02:17:11 +01:00
Nicola Soranzo 2988127158 Update GitHub action versions 2022-10-17 01:21:12 +01:00
Nicola Soranzo 02da77abcb Use `${{ github.workflow }}` in concurrency group name 2022-05-17 15:09:14 +02:00
Nicola Soranzo 1155b01784 Update GitHub action versions 2022-05-04 23:05:12 +01:00
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 72874b74a5 Add tox environment and GitHub workflow for reports startup test 
Also:
- Fix tox envlist still using py36
- Partially fix running reports with `APP_WEBSERVER=dev`
 2021-12-18 15:56:46 +00:00