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Commit Graph
1738 Commits
Author SHA1 Message Date
Marius van den Beek 672ed4984f Merge pull request #14694 from sveinugu/dev 
Allow path-based interactive tools using nginx proxy
 2022-10-17 11:24:38 +02:00
Marius van den Beek 241da69672 Merge pull request #12288 from dannon/sorted-tools-in-sections 
Automatically sort tools in sections by name
 2022-10-17 10:49:17 +02:00
Marius van den Beek ce26561b33 Merge pull request #14708 from jdavcs/dev_celery_config 
Enable fine-grained celery configuration
 2022-10-17 10:37:24 +02:00
Marius van den Beek 934369aa3a Merge pull request #14792 from jdavcs/dev_sqlalchemy_engine_options 
Make connect_args for SQLAlchemy's engine configurable
 2022-10-17 10:30:44 +02:00
Nicola Soranzo 0391cd4b62 Rename FooBarTestCase test classes as TestFooBar in API, framework, performance, Selenium and ToolShed tests 
These are collected by pytest only because they are `unittest.TestCase` derived,
but normally pytest collects only test classes whose name starts with `Test`, see
https://docs.pytest.org/en/7.1.x/reference/reference.html#confval-python_classes

Also:
- Some type annotations
 2022-10-15 17:54:31 +01:00
John Davis d310635895 Celery config option result_backend is required 2022-10-14 19:28:17 -04:00
John Davis d26ad37e97 Remove celery_backend from config_schema, use celery_conf instead 2022-10-14 19:28:17 -04:00
John Davis b6b49897dc Remove celery_broker from config_schema, use celery_conf instead 2022-10-14 19:28:17 -04:00
John Davis 2de79dd7d1 Add default task routes to config schema 2022-10-14 19:28:17 -04:00
John Davis 71829ae6af Add more details to setting db engine options to config schema 2022-10-14 13:18:35 -04:00
Nicola Soranzo 6069023d86 Merge pull request #14740 from bernt-matthias/topic/doc-security-datatables 
Extend security docs
 2022-10-13 14:29:52 +01:00
M BerntandMarius van den Beek ffc26d5ddd Update doc/source/admin/security.md 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-10-13 13:53:06 +02:00
Nicola Soranzo a81d680cca Merge branch 'release_22.05' into dev 2022-10-11 21:34:31 +01:00
Dannon Baker c8659d1d4a Add toolbox_auto_sort config option, expose in config manager. 2022-10-06 22:20:06 -04:00
M BerntandNicola Soranzo e8adc13324 Apply suggestions from code review 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-09-30 22:38:49 +02:00
M Bernt 37594348f9 Update doc/source/admin/security.md 2022-09-30 19:00:54 +02:00
John Davis 06744d4d0f Document use of release tags in manage_db.sh 2022-09-30 10:42:01 -04:00
Matthias Bernt eddd8e89a6 extend security docs 
by adding data referred by data tables
 2022-09-30 14:33:40 +02:00
John Davis 8538ab7fcb Fix same error in sample code in the rst doc file 2022-09-29 12:23:28 -04:00
John Davis 84f22bac77 Add db migration documentation to docs 2022-09-27 15:03:12 -04:00
John Davis 5a748bb867 Display 'Config Options' as subheading of 'Galaxy Configuration' 
This corrects a (supposedly) typo that prevented this to be displayed as
a subheading on this page: https://docs.galaxyproject.org/en/master/admin/index.html
 2022-09-27 15:03:03 -04:00
Nicola Soranzo 7f03d51c17 Document how to profile memory use in tests 2022-09-27 03:34:55 +01:00
Sveinung Gundersen 4ec8c4654e Added info on galaxy.yml config 2022-09-23 17:54:01 +02:00
Sveinung Gundersen 89bf7b1e52 Adding documentation and example nginx config to allow path-based interactive tools 2022-09-23 17:19:31 +02:00
Nicola Soranzo 331d0d2465 Merge pull request #14580 from nsoranzo/recommend_draft_instead_of_WIP 
[PROCEDURES] Recommend to use PR draft state instead of WIP title/label
 2022-09-15 19:05:40 +01:00
Nicola Soranzo e08deef224 Merge pull request #14592 from nsoranzo/misc_fixes_202209 
Misc fixes 202209
 2022-09-09 21:34:38 +01:00
Nicola Soranzo 157d9647ea Update docs on adding Python dependencies 
to use Wheelforge instead of Starforge.
 2022-09-09 17:26:30 +01:00
Nicola Soranzo 404da60afa Fix Tool Shed link 2022-09-09 17:20:24 +01:00
Nicola Soranzo 08bcea5370 Fix Makefile rule and update `run_tests_help.txt` 2022-09-09 17:20:23 +01:00
Nicola Soranzo cb012c7fb2 Merge branch 'release_22.05' into dev 2022-09-09 17:14:20 +01:00
Nicola Soranzo d8986239a1 Merge branch 'release_22.01' into release_22.05 2022-09-09 17:12:29 +01:00
Marius van den BeekandNicola Soranzo b05462a188 Add sbin to PATH 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-09-09 13:06:35 +02:00
mvdbeek 0256b34b34 Include /bin in sample systemd unit path 2022-09-09 12:52:05 +02:00
Nicola Soranzo 5b3cef62b1 Recommend to use PR draft state instead of WIP title/label 
Also:
- Drop/rename ``status`` labels to sync with what we are using
  in the repository.
- Fix links.
 2022-09-07 17:29:44 +01:00
Nate Coraor 7c5f1c9319 Merge pull request #14503 from mvdbeek/place_security_document_in_canonical_location 
Place security policy in canonical location
 2022-09-07 11:44:29 -04:00
Dannon c7a275b13c Merge pull request #14570 from guerler/logout_url 
Add config option for post logout redirect url
 2022-09-07 08:00:33 -04:00
guerler 8350ff212e Add post logout url to configuration 2022-09-05 14:12:50 -04:00
Nicola Soranzo 0df5c9a5fb Updates for Poetry 1.2.0 
Also:
- Export only dev requirements to `lib/galaxy/dependencies/dev-requirements.txt` .
- Packages don't have a `requirements.txt` file.
 2022-09-05 17:23:18 +01:00
John Chilton 52d982bf74 Merge pull request #14558 from jdavcs/dev_schema_rename_option_ref 
Fix reference to config option in schema
 2022-09-02 14:39:42 -04:00
Nicola Soranzo e7d7c62de6 Merge branch 'release_22.05' into dev 2022-09-02 19:28:55 +01:00
Nate Coraor 86e42b5483 Update Gravity to 0.13.4 and document setting env vars on dynamic 
handlers.
 2022-09-01 10:40:54 -04:00
John Davis 241647c1f1 Run make config-rebuild 2022-08-31 18:08:26 -04:00
mvdbeek b43dfa2613 Merge branch 'release_22.05' into dev 2022-08-30 20:37:56 +02:00
Nicola Soranzo 61b6eb1ee9 Fix more `discovered_datasets` typos 2022-08-30 09:57:26 +01:00
Dannon Baker 7364dc02ad Update 17.09 announce security link (since it does point to dev) 2022-08-24 21:48:03 -04:00
mvdbeek 989fc135e1 Place security policy in canonical location 2022-08-24 17:29:18 +02:00
mvdbeek f208df3edc Merge branch 'release_22.05' into dev 2022-08-22 22:00:03 +02:00
mvdbeek a8ff8c62b1 Add missing image 2022-08-22 21:05:59 +02:00
mvdbeek 2e22b9e1f8 Merge branch 'release_22.05' into dev 2022-08-22 19:17:35 +02:00
Marius van den Beek c5a2d38c26 Merge pull request #14211 from mvdbeek/22.05_release_notes 
[22.05] 22.05 release notes
 2022-08-22 18:42:24 +02:00