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Commit Graph
1893 Commits
Author SHA1 Message Date
mvdbeek 093dcc8d3d Merge branch 'release_24.0' into release_24.1 2024-05-28 14:34:20 +02:00
Nicola Soranzo 8cdca0f343 Revert some requests import changes 
introduced in https://github.com/galaxyproject/galaxy/pull/18003 .
In particular, when using requests in the tests to connect to Galaxy
or the ToolShed it's not needed to use the modified headers.

Also:
- Move some imports after conditional imports.
- Fix type annotations in `lib/tool_shed/test/base/populators.py`
- Fix typo bug in `test/unit/util/test_get_url.py`
 2024-05-23 15:55:56 +01:00
John Davis 04e77ef134 Remove legacy ref to sqlalchemy migrate 2024-05-22 14:57:53 -04:00
John Chilton 2f43c32fd9 Merge pull request #18003 from mvdbeek/add_galaxy_to_user_agent 
Add galaxy to user agent
 2024-05-20 12:14:13 -04:00
Nicola Soranzo 534010a8cb Enable flake8-implicit-str-concat ruff rules 
See https://docs.astral.sh/ruff/rules/#flake8-implicit-str-concat-isc
 2024-04-29 13:37:54 +01:00
Nicola Soranzo 0629908541 Fix new UP031 errors from ruff 0.4.2 2024-04-29 00:09:38 +01:00
mvdbeek e8a3b8c0cd Create wrapper for requests with default user agent 2024-04-16 17:54:29 +02:00
John Davis bf62b25eee Merge pull request #17922 from jdavcs/dev_model_edits1 
Model edits and bug fixes
 2024-04-11 20:30:25 -04:00
mvdbeek 9ff846aba6 Merge branch 'release_24.0' into dev 2024-04-06 16:50:48 +02:00
John Davis 09fee6aaad Remove future, autocommit args from session and engine creation 2024-04-05 13:54:39 -04:00
Nicola Soranzo ad6fbe5b82 Merge branch 'release_23.2' into release_24.0 2024-04-05 14:52:29 +01:00
mvdbeek bd846d9b2e Adjust update_cwl_conformance_tests.sh for removed branch 2024-04-05 13:49:31 +02:00
John Davis 0e61d61f47 Fix SA2.0 error: joinedload does not take str args 2024-04-02 10:08:53 -04:00
Nicola Soranzo a2018a5e60 Enable flake8-comprehensions ruff rules 
but allow `dict()` calls that make use of keyword arguments (e.g.,
`dict(a=1, b=2)`).
 2024-03-09 19:11:20 +00:00
mvdbeek f20c499154 Maybe change the initial 1.dev0 version to 0.dev0 ? 2024-02-13 17:06:21 +01:00
Nicola Soranzo e975ca3754 Update to black 2024 stable style 2024-01-30 18:09:51 +00:00
John Davis e134e8b633 Merge branch 'release_23.2' into 'release_23.3' 2024-01-29 13:27:15 -05:00
Nate Coraor 90a0df5d48 Fix the purge historyless HDAs pgcleanup action 2024-01-29 11:25:30 -05:00
mvdbeek 1188f8bdda Drop unused code from dump_openapi_schema.py 2024-01-10 17:43:30 +01:00
mvdbeek 23ff26bbc8 TEMP: schema dumpt fix 2024-01-08 11:33:29 +01:00
Nate Coraor a973e0518b Accept any number of arguments to the secret decoder ring 2023-12-14 13:07:37 -05:00
John Davis 475f7227c4 Add future=True flag to SA engine 2023-12-12 09:54:08 -05:00
Nicola Soranzo 9339fb3a2f Fix B018 errors reported by flake8-bugbear 23.12.2 2023-12-11 21:00:54 +00:00
John Davis fc0a266bdb Merge pull request #16932 from jdavcs/dev_sa20_fix21 
SQLAlchemy 2.0 upgrades (part 5)
 2023-11-29 09:55:24 -05:00
John Davis fa5adb0f52 SA2.0: Do not bind MetaData: must use engine explicitly 2023-11-27 18:30:16 -05:00
Michael R. Crusoe df807e6d17 Use the walrus := operator! 
Fixed by running:

```
ack --type=python -f | grep -v '^lib/galaxy/schema/bco/\|^lib/galaxy/schema/drs/\|^tools/\|^.venv/\|^.tox/' | grep -v '^lib/galaxy/files/sources/\|^lib/galaxy/job_metrics/\|^lib/galaxy/objectstore/\|^lib/galaxy/tool_util/\|^lib/galaxy/util/' | xargs auto-walrus
make format
```

Note that the directories for the packages listed in
`packages/packages_for_pulsar_by_dep_dag.txt`
were explictly excluded.
 2023-11-26 18:34:10 +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
John Davis f91693dc6e Merge pull request #16783 from SergeyYakubov/get-rid-of-filename-property 
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 
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. 
... 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 
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 
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 
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 
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 
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 
- 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