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4115 Commits
Author SHA1 Message Date
John Chilton 248ffcde05 Merge pull request #19086 from jmchilton/markdown_embedded_directives 
Allow several Galaxy Markdown directives to be embedded.
 2025-09-23 10:48:32 -04:00
mvdbeek b204902146 Discriminate user defined tools via tool_type and tool_class 2025-09-21 15:28:27 +02:00
David López e44d3f096d Merge pull request #20332 from davelopez/explore_short_term_storage_expiration_indicator 
Add short term storage expiration indicator to history items
 2025-09-17 13:13:57 +02:00
Ahmed Hamid Awan 2d513e834c Merge pull request #20911 from ahmedhamidawan/merge_25.0_into_dev_sept 
Merge 25.0 into dev
 2025-09-15 21:06:30 -05:00
Ahmed Awan f823afcc2a Merge remote-tracking branch 'upstream/release_25.0' into merge_25.0_into_dev_sept 2025-09-15 14:46:12 -05:00
marius-mather fff7a92d1c Update unit tests to use attribute access 2025-09-15 13:30:38 +10:00
marius-mather c11e7529c8 Merge remote-tracking branch 'upstream/dev' into oidc-pipeline-config 2025-09-15 11:05:44 +10:00
John Davis b10409b2dd Skip broken unit tests 
These tests require a rewrite of the entire test module, which is not a
quick fix, and so should not slow down the merging of the bug fix in
this PR.
 2025-09-11 11:35:37 -04:00
John Davis aed502d340 Merge pull request #20811 from ksuderman/20810-ipynb-sniffer 
Fix Ipynb datatype sniffer and add unit tests.
 2025-09-05 14:11:02 -04:00
John Davis 763c859530 Ignore type error: function is defined in sniff.py 2025-09-05 14:00:29 -04:00
Keith Suderman d0b4b9a1b4 Rebase with upstream changes 2025-09-05 13:22:19 -04:00
Keith Suderman 14188b8402 Run make format to fix linting errors 2025-09-05 11:27:40 -04:00
Tim Kok 7d21159a28 Fix linting + remove debug statement 2025-09-05 13:08:52 +02:00
Tim Kok 3f029fdf5e Remove debug statement 2025-09-05 12:31:24 +02:00
Tim Kok cc6da148c1 Add support for hierarchical module systems in lmod + modules dependency resolvers 2025-09-05 09:04:31 +02:00
Keith Suderman b9f3b1f552 Simplify unit tests and add test data files. 2025-09-04 19:34:42 -04:00
marius-mather da6bb6f8ba Lint fixes 2025-09-02 11:41:50 +10:00
marius-mather 9436735034 Add tests of pipeline config 2025-09-02 10:42:40 +10:00
mvdbeek eb823365bb Don't load custom tools into toolbox 2025-09-01 17:36:11 +02:00
mvdbeek 0308f25b43 Implement templatable configfiles for yaml tools 2025-09-01 17:36:08 +02:00
davelopez 1b5673b6b8 Adapt test_export_dataset_collection_paired test 2025-08-29 10:43:25 +02:00
davelopez f13a648b89 Patch serialize_object_store_ids in test_export_dataset_collection_paired test 
To handle mock datasets when serializing the collection during export
 2025-08-29 10:43:24 +02:00
davelopez 92dfd18ce2 Enhance BaseFileSource test suite 
With comprehensive entry property verification
 2025-08-25 09:48:29 +02:00
Keith Suderman 1cf079b56d Fix Ipynb datatype sniffer and add unit tests. 2025-08-22 11:23:08 -04:00
Nicola Soranzo 7a65393d4b Merge branch 'release_25.0' into dev 2025-08-21 16:25:52 +01:00
Nicola Soranzo 429366e7d0 Add unit test 2025-08-21 11:33:38 +01:00
Marius van den Beek fed092fe46 Merge pull request #20698 from davelopez/add_fsspec_support 
Add `fsspec` base implementation for File Source plugins
 2025-08-20 10:58:47 +02:00
Marius van den Beek 41a72b2ab9 Merge pull request #20592 from jmchilton/tool_landing 
Implement Data Landing Requests
 2025-08-19 14:55:55 +02:00
davelopez 552396cc7a Add test suite for MemoryFilesSource 2025-08-19 14:01:11 +02:00
davelopez 060e4735f3 Refactor TempFilesSource tests to use generic test suite 2025-08-19 14:00:48 +02:00
davelopez 4826d63a3c Add generic test suite for BaseFilesSource implementations 2025-08-19 14:00:17 +02:00
davelopez ec80e9987d Add type assertions for TempFilesSource in test fixtures 2025-08-19 10:19:36 +02:00
John Chilton 689aaf013d markdown embed 2025-08-18 12:56:08 -04:00
John Chilton a252af81b9 Tool Landing API... 2025-08-18 11:08:06 -04:00
John Chilton d394f76580 Fix unit test names. 2025-08-18 11:08:05 -04:00
John Chilton 5eba4df33d Fix aliases in fetch_data. 2025-08-18 11:08:05 -04:00
davelopez cc12cf5c42 Refactor test_config_options to use template_config and resolved config 2025-08-18 11:21:11 +02:00
davelopez 6a7bf2454b Fix file source initialization by converting root LocalPath to string 
As the TestPosixConfiguredFileSources expects a string as root argument as well as the pydantic model for PosixFilesSource
 2025-08-18 11:21:05 +02:00
davelopez 9ba75f1dd2 Fix imports for models 2025-08-18 11:20:58 +02:00
davelopez f1b24c121c Adapt tests to new models 2025-08-18 11:20:54 +02:00
davelopez 7ccac30f43 Adapt some types 2025-08-18 11:20:37 +02:00
Marius van den Beek b7008a1f2f Merge pull request #20731 from mvdbeek/hierarchical_display_collection_dataset_states 
Hierarchical display collection dataset states
 2025-08-13 12:55:14 +02:00
mvdbeek ec7929c742 Construct CTEs using sqlalchemy core 2025-08-11 17:17:15 +02:00
mvdbeek a703c9b873 Mock out serialize_to_view, test doesn't add elements to database 2025-08-11 17:17:14 +02:00
mvdbeek 1de8f5a65e Fix pytest raises assertions 2025-08-11 17:17:14 +02:00
mvdbeek 2924f29a1e Use NamedTupe for collection state summary 2025-08-11 17:17:13 +02:00
mvdbeek c2ddea2217 Implement touch collection update time CTE 2025-08-11 17:17:10 +02:00
Ahmed Hamid Awan 57e16eeebd Merge pull request #20624 from ahmedhamidawan/add_error_tab_in_invocation_view 
Add a "Debug" (email report) tab to Workflow Invocations
 2025-08-11 09:37:30 -05:00
mvdbeek e83e6b72a1 Return states and deleted status with HDCA 2025-08-11 10:32:11 +02:00
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