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
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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
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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
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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
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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
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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
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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 Beek and Nicola Soranzo
5a9b95179c
Clarify position of pytest arguments
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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
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Spanish Translations for remaining untranslated UI components
2021-09-15 09:19:58 -04:00
Helena and Nicola Soranzo
291c39aac8
Review and improvements of the documentation/short-tut
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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
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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
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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
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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 Chilton and Nicola Soranzo
400da5d677
Apply suggestions from code review
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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 Golitsynskiy and Nicola Soranzo
64139e9bb3
Update doc/source/dev/writing_tests.md
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2021-01-12 10:04:27 -05:00
Sergey Golitsynskiy and Nicola Soranzo
f9b38719fd
Update doc/source/dev/writing_tests.md
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2021-01-12 10:03:41 -05:00
Sergey Golitsynskiy and Nicola Soranzo
0b0ec0cada
Update doc/source/dev/writing_tests.md
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2021-01-12 00:37:06 -05:00
John Davis