mvdbeek
bd846d9b2e
Adjust update_cwl_conformance_tests.sh for removed branch
2024-04-05 13:49:31 +02:00
Nate Coraor
90a0df5d48
Fix the purge historyless HDAs pgcleanup action
2024-01-29 11:25:30 -05:00
John Davis
f91693dc6e
Merge pull request #16783 from SergeyYakubov/get-rid-of-filename-property
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Replace file_name property with get_file_name function
2023-11-08 17:19:40 -05:00
Yakubov, Sergey
c30a4c06c2
Replace file_name property with get_file_name function
2023-11-08 17:17:14 -05:00
John Chilton
d3d812c57b
Merge pull request #16340 from jmchilton/per_object_store_admin
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Augment pgcleanup to allow periodically deleting old datasets.
2023-11-02 13:03:52 -04:00
Nicola Soranzo
45fb60c530
Ignore UP036 ruff check in check_python.py
2023-10-28 17:35:12 +01:00
John Chilton
ec6d8fd03b
Fixes...
2023-09-27 14:30:42 -04:00
John Chilton
7dc0b1378b
WIP: modern tool shed frontend
2023-09-27 14:30:42 -04:00
John Chilton
24b3abeb3e
Script for bootstrapping the tool shed.
2023-09-26 13:46:59 -04:00
John Chilton
d1d629074b
ToolShed API 2.0
2023-09-26 13:46:58 -04:00
John Chilton
360b327de6
Augment pgcleanup to allow periodically deleting old datasets.
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... and restricting operations to specific object store ids.
2023-09-25 15:10:13 -04:00
John Chilton
da8ce00d88
Cleanup docs in admin_cleanup_datasets.py.
2023-09-25 14:49:45 -04:00
Nicola Soranzo
d258e5791e
Fix new E721 errors from ruff 0.0.290
2023-09-20 01:43:40 +01:00
Michael R. Crusoe
201bc19575
cwl conformance tests: use id field, not label
2023-09-07 13:14:03 +02:00
Michael R. Crusoe
6cd71508e1
cwl testing: use the proposed 1.2.1 CWL conformance tests.
2023-09-07 12:39:22 +02:00
mvdbeek
130d2b078e
Update and apply ruff refactorings
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ruff 0.280.0 has a bug that would turn the imports guarded by `if
TYPE_CHECKING` into their non-string variant, which would break the
runtime. So we can't merge 23.1 into dev without this.
2023-08-09 17:14:07 +02:00
Nicola Soranzo
45e020e760
Merge branch 'release_23.1' into dev
2023-07-24 17:04:54 +01:00
Nicola Soranzo
0a73e1c512
Merge branch 'release_23.0' into release_23.1
2023-07-24 15:16:11 +01:00
Marius van den Beek
013c1741f9
Merge pull request #16425 from jdavcs/dev_sa20_fix12
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Fix SA2.0 syntax in scripts/helper.py, fix ancient bug
2023-07-21 09:45:30 +02:00
John Davis
25cc282c8e
Fix SA2.0 syntax, fix bug
2023-07-21 00:12:34 -04:00
Nicola Soranzo
c7db0bbeca
Do not install npm/yarn via conda if they already available at the correct version
2023-07-21 00:58:36 +01:00
Nicola Soranzo
a9b2a4f7b0
Code refactoring
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Simplification allowed by commit 39c0000c1b
2023-07-21 00:58:36 +01:00
Matthias Bernt
1b2ac2a212
also set galaxy config file variable in common startup
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otherwise GALAXY_CONDITIONAL_DEPENDENCIES can not be determined.
in run.sh set_galaxy_config_file_var is called only after common_startup
is called.
2023-07-21 00:58:35 +01:00
Matthias Bernt
bb90e3b5dc
activate the conda env before the python venv
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and install node and yarn via conda if a conda env is used
2023-07-21 00:58:35 +01:00
Nicola Soranzo
387aa1dd48
Test first startup on macOS also with Python 3.11
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- Allow passing GALAXY_CONDA_PYTHON_VERSION environment variable to
the startup script to specify the Python version to use when
creating the `_galaxy_` conda environment.
- Some Shellcheck fixes.
2023-07-21 00:58:33 +01:00
Matthias Bernt
92806a97a5
Improve log message wording
2023-07-20 18:32:00 +01:00
John Davis
09fe7b9a54
Fix select stmts in scripts
2023-07-19 11:05:55 -04:00
mvdbeek
8a1b75bbb0
Disable verbose parso logging in db_shell.py
2023-07-16 09:21:22 +10:00
Nicola Soranzo
36ed2d5ae2
Merge branch 'release_23.0' into release_23.1
2023-07-13 10:25:48 +01:00
Nicola Soranzo
62497462e0
Don't always install node in the virtualenv
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if it's already installed system-wide at the correct version.
Prevent node installation issues during CI builds where we install
node with the setup-node action but it was ignored because it was
not inside the virtualenv, e.g.:
https://github.com/galaxyproject/galaxy/actions/runs/5530959878/jobs/10091018774
2023-07-12 19:26:02 +01:00
mvdbeek
bb969c7505
Replace bootstrap_history.py with galaxy-release-util
2023-06-13 20:42:35 +02:00
mvdbeek
67c7181a6a
Merge branch 'release_23.0' into dev
2023-06-13 17:30:22 +02:00
mvdbeek
787b8040c8
Use galaxy-release-util to upload python packages
2023-06-13 15:49:37 +02:00
mvdbeek
aca993125b
Merge branch 'release_23.0' into dev
2023-06-13 15:35:05 +02:00
mvdbeek
48573d3a1f
Fix next version number
2023-06-10 11:22:42 +02:00
John Davis
fe3c2e2711
Wrap session.flush in pages_identifier_conversion scripts
2023-06-09 13:05:26 -04:00
John Davis
2ed822afd0
Wrap session.flush in set_dataset_sizes script
2023-06-09 13:05:26 -04:00
John Davis
9ddaaf8d06
Wrap session.flush in tool_shed/* scripts
2023-06-09 13:05:26 -04:00
John Davis
07867fa8c7
Wrap session.flush in update_shed_config_path script
2023-06-09 13:05:26 -04:00
John Davis
0c895d1409
Wrap session.flush in admin_cleanup_datasets script
2023-06-09 13:05:26 -04:00
John Davis
e7408dcd98
Wrap session.flush in populate_uuid script
2023-06-09 13:05:26 -04:00
John Davis
96e534122d
Wrap session.flush in cleanup_datasets script
2023-06-09 13:05:26 -04:00
mvdbeek
01a1755027
Merge branch 'release_23.0' into dev
2023-06-08 18:36:41 +02:00
mvdbeek
06c8fc073d
Add --skip-existing flag to twine upload
2023-06-08 16:53:38 +02:00
mvdbeek
e2169c6597
Drop workaround for old docutils
2023-06-06 17:26:27 +02:00
mvdbeek
368dfb3119
Merge branch 'release_23.0' into dev
2023-06-06 15:55:12 +02:00
Marius van den Beek
5c2460608b
Merge pull request #16195 from mvdbeek/quit_if_branches_not_updated
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[23.0] Assert that local branches are up to date in release point script
2023-06-06 15:53:54 +02:00
mvdbeek
7056942682
Fail if local branch doesn't match remote branch
2023-06-06 15:04:43 +02:00
mvdbeek
e2e7cbc3f4
Make point release script compatible with docutils 0.16
2023-06-05 16:02:17 +02:00
mvdbeek
73413b1627
Merge branch 'release_23.0' into dev
2023-06-01 15:19:47 +02:00
mvdbeek