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72,925 Commits 69 Branches 243 Tags
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154 Commits
Author SHA1 Message Date
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
mvdbeek 4c4f10e24f Drop interactive environment build instructions form docs 2022-02-24 19:34:48 +01:00
Nicola Soranzo 98ecc39b1b Remove PhantomJS support, dropped in Selenium 4.0 2021-12-08 08:14:10 +00:00
Marius van den BeekandNicola Soranzo 5a9b95179c Clarify position of pytest arguments 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-10-14 11:40:15 +02:00
mvdbeek 0b461c7bd7 Extend debugging test instructions for GHA 2021-10-14 11:29:18 +02:00
Dannon 0b3c7aa834 Merge pull request #12427 from hexylena/es-ui 
Spanish Translations for remaining untranslated UI components
 2021-09-15 09:19:58 -04:00
HelenaandNicola Soranzo 291c39aac8 Review and improvements of the documentation/short-tut 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-09-15 13:55:21 +02:00
Helena Rasche c7a7c83fb1 Add translating rst file 2021-09-15 10:21:21 +02:00
Helena Rasche 9decfc2ba2 Document what I did 2021-09-14 19:05:55 +02:00
John Chilton cd2e6527fc Merge pull request #12255 from bernt-matthias/topic/deprecate_datamanager_version 
Deprecate data manager version
 2021-09-08 14:36:01 -04:00
Kaivan Kamali 952d947087 Removed resources section per John's comment 2021-09-03 12:49:36 -04:00
Kaivan Kamali 99880294c6 Minor revision 2021-09-03 09:27:29 -04:00
Kaivan Kamali b47374aef7 Added instructions for debuuging Galaxy using a Slurm cluster 2021-09-02 17:10:15 -04:00
Kaivan Kamali 96ef23a79b Added instructions on how to debug Galaxy backed by a Slurm cluster 2021-09-02 16:10:41 -04:00
Matthias Bernt ee4c5d0817 deprecate data manager version 
Data managers (DM) could define a version for the data manager
(`<data_manager version="0.0.1">`) and for the data manager tool (DMT).

The version attribute of the data manager was undocumented and only
used seldomly (for IUC in 24 out of 88). If no version was set for
the DM it defaults to 0.0.1. Hence in `shed_data_manager_conf.xml`
multiple versions of the (DM) with version 0.0.1 are listed.

This leads to loading only one DM (I guess the oldest) and a
warning like the following on startup:

`A data manager has been defined twice: toolshed.g2.bx.psu.edu/repos/galaxyp/data_manager_eggnog_mapper/data_manager/data_manager_eggnog/0.0.1 `

which is easily overlooked.
 2021-07-14 15:24:38 +02:00
Dannon 38f89e18b5 Merge pull request #12234 from eancelet/debug-doc-update 
Add a note to get Python extension and set interpreter
 2021-07-06 14:28:29 -04:00
Sergey Golitsynskiy 59ee7b55e7 Update doc/source/dev/debugging_tests.md 2021-07-06 14:21:21 -04:00
Estelle Ancelet beaabd1817 Add a note to get Python extension and set interpreter 2021-07-06 14:07:05 +02:00
Dannon Baker a57202da59 Consistency in referring to assumed galaxy root 2021-07-01 12:09:30 -04:00
Dannon Baker 44b7d165c6 Add a note about needing galaxy.yml (and not sample) here. 2021-07-01 12:05:55 -04:00
Dannon Baker 9058c02026 Update debug target name in example .vscode launchconfig 2021-07-01 11:58:22 -04:00
mvdbeek 5cb1b8176c Update instructions for debugging using vscode 2021-01-29 17:15:42 +01:00
John Chilton 422d48bce1 Link to some recently filled out pydocs from sphinx testing docs. 2021-01-18 17:24:28 -05:00
John ChiltonandNicola Soranzo 400da5d677 Apply suggestions from code review 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-01-13 18:19:29 -05:00
John Chilton 21f06bafef API design guidelines. 2021-01-13 18:18:39 -05:00
Sergey GolitsynskiyandNicola Soranzo 64139e9bb3 Update doc/source/dev/writing_tests.md 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-01-12 10:04:27 -05:00