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Commit Graph
49 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
Nicola Soranzo 51a81b3cc0 Merge pull request #20921 from galaxyproject/dependabot/github_actions/actions/setup-node-5 
Bump actions/setup-node from 4 to 5
 2025-09-19 00:16:29 +01:00
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
dependabot[bot] 1b52e4acb0 Bump codecov/codecov-action from 3 to 5 
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 5.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v3...v5)

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

Signed-off-by: dependabot[bot] <support@github.com>
 2025-09-18 18:46:35 +00:00
Nicola Soranzo 703857eb3c Update GitHub workflows to use PostgreSQL 17 image 2025-05-19 18:49:05 +01:00
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
John Chilton d3e0e28ce3 Do not skip CI tests on missing tools. 2024-10-15 16:02:27 -04:00
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
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
Nicola Soranzo c1e839c570 Replace `set-output commands with $GITHUB_OUTPUT` environment file 
See https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
 2022-10-17 02:26:39 +01:00
Nicola Soranzo 2988127158 Update GitHub action versions 2022-10-17 01:21:12 +01:00
Nicola Soranzo 1ccfdbbb4e Don't fail-fast in API GitHub workflow 2022-05-17 15:11:54 +02:00
Nicola Soranzo 02da77abcb Use `${{ github.workflow }}` in concurrency group name 2022-05-17 15:09:14 +02:00
Nicola Soranzo 02e36473a3 Split API tests in 2 jobs 2022-05-04 23:05:13 +01:00
Nicola Soranzo 1155b01784 Update GitHub action versions 2022-05-04 23:05:12 +01:00
Nicola Soranzo 6524e1f344 Fix path of venv when caching 2022-03-19 03:52:23 +00:00
Nicola Soranzo 25e37dd9d5 Merge pull request #13503 from mvdbeek/metadata_strategy_extended_tests_schedule 2022-03-09 14:21:26 +00:00
mvdbeek 55aec359b0 Run extended metadata test on schedule 
Including outputs_to_working_directory, except for the integration
tests.
 2022-03-08 18:58:15 +01:00
mvdbeek 8065893ed2 Run all relevant tests with GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY: 'extended 2022-03-08 18:29:18 +01:00
mvdbeek c90e012fda Upload coverage results to codecov.io 2022-02-11 17:11:08 +01:00
Marius van den Beek 5df80bd0b7 Merge pull request #13171 from ic4f/dev_sa20warning 
Enable setting SQLALCHEMY_WARN_20
 2022-01-24 18:47:35 +01:00
mvdbeek 64d395862e Merge branch 'release_21.09' into dev 2022-01-24 09:28:08 +01:00
mvdbeek 6c7f4b0702 Skip api tests if lib/galaxy_test/selenium is touched 
(and other unrelated test).
 2022-01-23 10:42:34 +01:00
Sergey Golitsynskiy bd02eaff6c Enable SA2.0 warning on api/selenium/integration tests 2022-01-18 22:02:13 -05:00
John Chilton ebcedbaf09 Test case for PDF generation of pages. 2021-10-29 15:10:26 -04:00
mvdbeek 198c59177d Add various include/exclude patterns for github workflows 2021-10-27 10:15:41 +02:00
mvdbeek b3a61496b2 Add various include/exclude patterns for github workflows 2021-10-27 10:11:27 +02:00
mvdbeek 0e11349685 Merge branch 'release_21.09' into dev 2021-10-20 17:24:41 +02:00
mvdbeek b4befd02b5 Raise exception for if we're saving a historyless HDA 2021-10-18 11:42:39 +02:00
Nuwan Goonasekera baf5bc6331 Made venv cache dependent on exact python and os version. 
xref: https://github.com/python-poetry/poetry/pull/1908
xref: https://github.com/actions/setup-python/issues/182
 2021-10-04 19:24:21 +05:30
Nuwan Goonasekera ef2c5a357c Added more caching for github actions using tox and venv 2021-10-04 18:57:08 +05:30
mvdbeek 5c8898ffd9 Cancel already running job with same ref 
ref is "
The branch or tag ref that triggered the workflow run. For branches this in the format refs/heads/<branch_name>, and for tags it is refs/tags/<tag_name>.
"
 2021-06-30 16:25:29 +02:00
Sergey Golitsynskiy 94cc475681 Update github workflows to use postgres 13 2021-04-05 15:08:34 -04:00
Sergey Golitsynskiy be4429e4fb Replace: s/postgres/posgresql in db URLs 
Was deprecated in SQLAlchemy 1.3, removed in SQLAlchemy 1.4
https://docs.sqlalchemy.org/en/14/changelog/changelog_14.html#change-3687655465c25a39b968b4f5f6e9170b
https://github.com/sqlalchemy/sqlalchemy/issues/4643
 2021-04-05 15:02:26 -04:00
Nicola Soranzo 313625ed47 Upload test results as artifact in case of failure 2021-01-02 03:37:43 +00:00
Nicola Soranzo be1e21bffc Migrate API tests to GitHub workflow 2020-11-10 19:29:22 +00:00