opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
83,705 Commits 69 Branches 243 Tags
7d9155d38f5cee2afbd96a013148e10c8b69efc8
Commit Graph
179 Commits
Author SHA1 Message Date
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
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
Nicola Soranzo 7f03d51c17 Document how to profile memory use in tests 2022-09-27 03:34:55 +01:00
Nicola Soranzo 08bcea5370 Fix Makefile rule and update `run_tests_help.txt` 2022-09-09 17:20:23 +01:00
Nicola Soranzo 961472cfff Merge branch 'release_22.01' into release_22.05 2022-08-16 23:25:42 +01:00
Nicola Soranzo 69defb7a20 Doc fixes 2022-08-15 19:15:02 +01:00
mvdbeek 3818f50af5 Drop interactive environments 2022-03-23 15:43:24 +01:00
mvdbeek 7a72fe5756 Drop "starting galaxy" docs 
They're outdated and changing rapidly. Without context I don't think
they're all that helpful.
 2022-03-15 21:59:21 +01:00