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20 Commits
Author SHA1 Message Date
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 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 afa7b713bc Replace `GALAXY_TEST_INCLUDE_SLOW env variable with external_dependency_management` pytest marker 
Fix mulled tests missing tests in `test/unit/tool_util/test_conda_resolution.py` .

Also:
- Add `coverage` tox factor to generate coverage report.
 2022-11-03 21:43:37 +00:00
Nicola Soranzo c1e839c570 Replace `set-output commands with $GITHUB_OUTPUT` environment file 
See https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
 2022-10-17 02:26:39 +01:00
Nicola Soranzo 2988127158 Update GitHub action versions 2022-10-17 01:21:12 +01:00
Nicola Soranzo 02da77abcb Use `${{ 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
mvdbeek c90e012fda Upload coverage results to codecov.io 2022-02-11 17:11:08 +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
Nicola Soranzo 0bdc93a7cc Drop support for Python 3.6, add Python 3.10 2021-12-08 08:14:10 +00:00
Nicola Soranzo 31eb397850 Upload unit test results as artifact in case of failure 2021-12-06 17:32:30 +00:00
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
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
Nicola SoranzoandMarius van den Beek 4236659539 Add Python 3.9 to unit tests CI matrix 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2021-03-04 20:01:06 +00:00
Nicola Soranzo 8c444ac5c1 Move unit tests to GitHub workflows 
Also some random fixes to other GitHub workflows.
 2021-03-04 20:01:06 +00:00