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Commit Graph
1591 Commits
Author SHA1 Message Date
John Chilton 2fa7b43ab5 Merge pull request #20859 from mvdbeek/multiple_true_data_collection_map_over 
Fix `multiple="true"` data collection map over for shell_command tools
 2025-09-08 10:02:49 -04:00
Nicola Soranzo 06245f4f08 Fix test in `configfile_user_defined.yml` 
Introduced in commit 0308f25b43 .
 2025-09-08 11:56:34 +01:00
mvdbeek 5ccf97752b Verify collection is correctly consumed 2025-09-04 14:48:44 +02:00
mvdbeek 0308f25b43 Implement templatable configfiles for yaml tools 2025-09-01 17:36:08 +02:00
Nicola Soranzo 1d9d93ea50 Merge branch 'release_25.0' into dev 2025-08-07 15:54:38 +01:00
Nicola Soranzo 7f89e0eab9 Code cleanups from pyupgrade 
Found by running:

```
make pyupgrade
ruff check --fix .
ruff check --preview --unsafe-fixes --select=F401 --fix .
make format
make update-client-api-schema
```

The bulk of the changes are replacements of typing deprecated aliases
such as `Dict` and `List` with the standard library classes. These
aliases became redundant in Python 3.9 when the corresponding
pre-existing classes were enhanced to support `[]`, see
https://docs.python.org/3/library/typing.html#deprecated-aliases

Also:
- Update the `pyupgrade` Makefile target to use `--py38-plus` for the
  packages needed by Pulsar, including the new galaxy-tool-util-models
  package.
 2025-07-31 11:17:22 +01:00
Nicola Soranzo e2777065eb Merge branch 'release_25.0' into dev 2025-07-30 17:45:20 +01:00
John Chilton a2af62966d Fix parameter models for optional color params. 2025-07-30 11:37:12 -04:00
John Chilton d26605517e Implement sample sheets. 2025-07-25 11:46:59 -04:00
Patrik Smeds 64907f7937 datatype added for lexicmap index 2025-07-14 10:43:36 -04:00
Nate Coraor 96523d4570 Merge remote-tracking branch 'upstream/release_25.0' into dev 2025-06-20 16:18:47 -04:00
Nicola Soranzo cc26ab7834 Merge branch 'release_24.2' into release_25.0 2025-06-20 13:00:45 +01:00
Nicola Soranzo 36ef67be1f Merge branch 'release_24.1' into release_24.2 2025-06-20 13:00:05 +01:00
Nicola Soranzo c96792693c Merge branch 'release_24.0' into release_24.1 2025-06-20 12:55:50 +01:00
mvdbeek 2bfd283f94 Fix single data element identifier to be a regular string 
These must adhere to the input parameter they belong to.
 2025-06-11 20:02:54 +02:00
Nicola Soranzo 7160c5befd Add test 2025-05-21 17:09:06 +01:00
Nicola Soranzo 74a17ec6ff Use `printf` 
`echo` doesn't interpret backslash escapes by default, and its `-e` option is not POSIX.
 2025-05-21 17:08:23 +01:00
mvdbeek 1cbec1b8ef Fix memory and slots test 2025-05-19 19:16:43 +02:00
mvdbeek b2df0e08d7 Add missing galayx slots and memory tool 
Fixes https://github.com/galaxyproject/galaxy/issues/13212
 2025-05-16 15:59:25 +02:00
mvdbeek d2597738cb Make to_cwl compatible with pulsar 2025-05-12 10:54:56 +02:00
mvdbeek eb38fd8ec9 Merge branch 'release_24.2' into dev 2025-05-12 09:05:28 +02:00
John Chilton 219796f049 Implement paired_or_unpaired collections, list wizards. 2025-05-09 17:39:38 -04:00
John Chilton 518fa136d9 [WIP] Implement records - heterogenous dataset collections. 
Existing dataset colleciton types are meant to be homogenous - all datasets of the same time. This introduces CWL-style record dataset collections.
 2025-05-09 16:38:19 -04:00
Ahmed Hamid Awan d7fa1d19ce Merge pull request #19054 from jmchilton/tool_markdown 
Implement tool markdown reports.
 2025-05-06 20:49:30 +05:00
Marius van den Beek 79638b883a Merge pull request #19753 from bernt-matthias/env-fix-24.1 
Fix setting env and tags on resubmission
 2025-05-06 17:23:45 +02:00
mvdbeek b99112c337 Fix DataCollectionParameterModel factory 2025-05-06 14:23:23 +02:00
Marius van den Beek 507719beb5 Merge pull request #20162 from mvdbeek/yaml_parser_fixes_part2 
Yaml parser fixes part2
 2025-05-06 09:13:11 +02:00
John Chilton 4e4017c1be Merge pull request #20152 from jmchilton/collection_cleanup_2 
Fix certain cases of collection parameter handling during workflow execution.
 2025-05-05 15:45:36 -04:00
mvdbeek 7ed247059a Fix conditional parsing 2025-05-05 20:37:17 +02:00
mvdbeek fa3c19c2a4 Merge branch 'release_24.2' into dev 2025-05-05 16:52:31 +02:00
mvdbeek a53b4125aa Skip `param_value` filter if ref value is runtime value 
Fixes https://github.com/galaxyproject/galaxy/issues/20136
 2025-05-04 16:48:33 +02:00
John Chilton 9b0fb38a76 More workflow mapping test cases. 2025-05-03 10:21:17 -04:00
John Chilton f9e1022360 Test case for bug where workflow collection mapping interprets collection at wrong rank. 2025-05-03 10:21:17 -04:00
John Chilton 1f95f421c9 Tool markdown reports. 2025-05-02 11:25:21 -04:00
Marius van den Beek 01e36311a4 Merge pull request #19954 from bernt-matthias/ext-lower 
Use lower case extension for setting datatype in data discovery
 2025-04-16 12:52:23 +02:00
mvdbeek 29d3c23cf2 Merge branch 'release_24.2' into dev 2025-04-15 17:53:08 +02:00
Marius van den Beek a8cf438ec5 Merge pull request #19763 from jmchilton/missing_functional_tool 
Add missing test file.
 2025-04-15 15:09:42 +02:00
Marius van den BeekandM Bernt e2647616c5 Fix typo 
Co-authored-by: M Bernt <m.bernt@ufz.de>
 2025-04-15 15:09:32 +02:00
Marius van den Beek 7a1ea09e9c Merge pull request #19949 from jmchilton/parameter_model_fixes_0 
[24.2] Fix various parameter validation issues.
 2025-04-15 15:08:28 +02:00
mvdbeek 6edab86870 Merge branch 'release_24.2' into dev 2025-04-10 18:54:17 +02:00
mvdbeek 4f9180604f Make dbkey_filter_input more realistic, regression test for https://github.com/galaxyproject/galaxy/issues/19975 2025-04-10 16:59:09 +02:00
Matthias Bernt e612db1680 extend tests 2025-04-03 10:32:50 +02:00
John Chilton f37075c1a5 Fix various parameter validation issues. 
I previously failed to include a bunch of validation checks I assumed had been covered so fixed that first and got a bunch of new issues detected. Also added a parameter specification test case for https://github.com/galaxyproject/galaxy/issues/19908 and fixed that.
 2025-04-02 12:49:09 -04:00
Matthias Bernt 0c186b227e fix test 2025-03-26 18:07:57 +01:00
Matthias Bernt ef72ecbb66 remove tool test assertions 2025-03-26 17:37:17 +01:00
Matthias Bernt 5b017b240f fix test 
tool fails with no env var set
failing tool tests allow no output
 2025-03-26 13:52:29 +01:00
Matthias Bernt 0247be1866 fix test tool test 2025-03-26 13:52:22 +01:00
Matthias Bernt 70bfcc44dc fix resubmission integration test 
the test `test/integration/test_job_resubmission.py::TestJobResubmissionToolDetectedErrorResubmitsIntegration`
resubmits with:

```
        <destination id="local_resubmit" runner="local">
            <env id="GX_TARGET_EXIT_CODE">4</env>
            <resubmit condition="tool_detected_failure" destination="local_good" />
        </destination>

        <destination id="local_good" runner="local">
            <env id="GX_TARGET_EXIT_CODE">0</env>
        </destination>
```

since env variables are lost on resubmission the current test
was still evaluated successful (because `${GX_TARGET_EXIT_CODE:-0}`).
Now the test fails if `GX_TARGET_EXIT_CODE` is not set.
 2025-03-26 13:52:08 +01:00
mvdbeek 3c6b6c5971 Merge branch 'release_24.2' into dev 2025-03-26 09:51:08 +01:00
mvdbeek 3c12acb270 Assert column_types 2025-03-25 10:29:01 +01:00