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Commit Graph
186 Commits
Author SHA1 Message Date
Dannon Baker 9133f711fe Update docs from Jest to Vitest 
Changed all testing documentation to reference Vitest instead of Jest,
including test commands, mock examples, and VSCode debug config.
 2025-11-24 11:09:20 -05:00
John Chilton f701de8817 Update tool state docs for relaxed requests. 2025-10-29 16:33:27 -04:00
John Chilton a685889a32 Cleanup tool request hacks for legacy using new relaxed request tool state. 
A strict vs relaxed state for incoming requests lets us preserve some older behavior if it is needed for tests and such while also allowing us to default to "the correct thing".
 2025-10-29 16:33:27 -04:00
John Chilton e929bc648b Expand coverage for tool state docs. 2025-10-29 16:33:27 -04:00
Nicola Soranzo a802727c33 Update docs on debugging tests within GitHub actions 
Subsets were replaced with shards in commit 992edaa8b4 .
 2025-08-27 16:33:43 +01:00
John ChiltonandNicola Soranzo 0b7478b1a4 Apply suggestions from code review 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2025-08-13 14:43:31 -04:00
John Chilton d771436dae Datatype checklist. 2025-08-13 10:59:55 -04:00
John Chilton 219796f049 Implement paired_or_unpaired collections, list wizards. 2025-05-09 17:39:38 -04:00
Enis Afgan 8a5198f76a Update descriptions to indicate these are UI-options only 2025-03-07 11:11:00 -05:00
Enis Afgan bd847412a0 Add config options for tool dependency installs 2025-02-06 15:32:52 -05:00
Matthias Bernt be3c547161 document format of extension 2024-10-22 09:28:31 +02:00
John Chilton ad73e9e838 Tool Request models. 2024-09-30 13:25:02 -04:00
Polina Polunina ed48f84aa7 add data source doc to the list in index 2024-08-27 12:28:00 +02:00
John Chilton da220efd23 First pass at workflow step models - linked and unlinked. 
Work scoped out in 18536.
 2024-08-23 09:46:44 -04:00
John Chilton aca192eeaf SVG generation for tool state docs... 2024-07-15 09:46:13 -04:00
John Chilton 5359f8ba74 Input parameter schema. 2024-07-15 09:46:13 -04:00
John Davis 7721bf377f Update doc/source/dev/create_release.rst 2024-06-28 11:42:01 +02:00
M BerntandMartin Cech df044c4fff Update doc/source/dev/create_release.rst 
Co-authored-by: Martin Cech <marten@bx.psu.edu>
 2024-06-28 11:33:49 +02:00
M Bernt d006411178 Minor additions to release process 2024-06-28 10:28:19 +02:00
John Davis 396797d18f Fix typos in release documentation 2024-05-20 14:57:49 -04:00
Marius van den BeekandJohn Davis 799d27f0e5 Fix rst list syntax 
Co-authored-by: John Davis <jdavcs@gmail.com>
 2024-02-13 19:19:23 +01:00
Marius van den BeekandJohn Davis ee9396971d Simplify explanations 
Co-authored-by: John Davis <jdavcs@gmail.com>
 2024-02-13 17:58:47 +01:00
mvdbeek 13b6ed44d8 Update release process documentation 2024-02-13 16:38:09 +01:00
Björn Grüning 7e394f7aed Merge pull request #17327 from PlushZ/doc-data-source 
add documentation for data source tool
 2024-01-19 19:34:36 +01:00
PlushZ a2ed0c08e5 add doc for data source 2024-01-18 18:36:14 +01:00
John Davis 9f4254f66b Merge pull request #17322 from mvdbeek/session_docs 
Document SQLAlchemy session lifespan
 2024-01-18 12:35:27 -05:00
Marius van den Beek 0744959008 Fix typo 2024-01-18 16:31:26 +01:00
Marius van den Beek 0e4f6fed84 Drop extra newline 2024-01-18 16:30:20 +01:00
Marius van den Beek b367c09ae1 Don't explain why handling state at the outermost layer is a good idea 2024-01-18 16:30:02 +01:00
mvdbeek 7f2b8a714f Tweak the WSGI, ASGI, Celery section 2024-01-18 16:28:37 +01:00
John Davis 2e9c2241d0 Apply edits to session docs 2024-01-18 16:23:53 +01:00
mvdbeek ed98d7d21a Document SQLAlchemy session lifespan 2024-01-18 12:21:56 +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
Yakubov, Sergey c30a4c06c2 Replace file_name property with get_file_name function 2023-11-08 17:17:14 -05:00
John Davis 84b9fa3737 Update doc/source/dev/build_a_job_runner.rst 2023-09-25 16:41:24 -04:00
Maiken Pedersen 4423a0cc56 Update build_a_job_runner.rst 
The ajs job_id is supposed to be the external job runner id, not the galaxy id. job_wrapper.job_id is the galaxy id.
 2023-09-11 15:34:31 +02:00
John Davis 0ab66ae045 Provide better guidance on what to override 2023-09-08 14:02:12 -04:00
John Davis c014ae1e8b Misc. edits to text; formatting of lists, section titles 2023-09-08 13:50:14 -04:00
John Davis 082a5edc02 Clarify instructions: override logic only if needed 2023-09-07 15:12:15 -04:00
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 01a1755027 Merge branch 'release_23.0' into dev 2023-06-08 18:36:41 +02:00
mvdbeek 9cb86a9a11 More documentation for point release process 2023-06-08 16:53:01 +02:00
Nicola Soranzo 0f70c68fd9 Migrate to MyST-Parser for Markdown docs 
replacing deprecated recommonmark.

Fix https://github.com/galaxyproject/galaxy/issues/13005 .

Also:
- Drop not very useful ``doc/source/dev/file_upload.md`` .
- Small doc and link fixes.
 2023-03-27 15:01:27 +01:00
Dannon Baker 2c69c96dfd Update run_tests_help w/ client targets 2023-01-25 09:13:35 -05:00
Dannon Baker d04fb67396 Rename samples_tool_conf to sample_tool_conf to match datatypes/data_manager naming convention 2023-01-10 10:03:23 -05:00
Simon Bray 91674ac9de small change to job runner docs 
to state more explicitly what `check_watched_item()` should return
 2022-11-08 11:47:09 +01:00
Nicola Soranzo 581d001828 Remove unused `require_new and GALAXY_TEST_HISTORY_ID` 2022-11-07 15:44:02 +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
mvdbeek eec177839f Drop scripts/function_tests.py 2022-11-01 18:45:08 +00:00