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Author SHA1 Message Date
galaxybot 060f48e1d9 Update Python dependencies 
by running `make update-dependencies`.
 2025-09-13 03:09:59 +00:00
Marius van den Beek 3b215326eb Merge pull request #20880 from jmchilton/validate_columns 
Validate sample sheet column definitions in workflow definitions on backend.
 2025-09-11 16:43:57 +02:00
John Chilton 29898badf0 Merge pull request #20890 from jmchilton/transient_selenium_published_histories 
Likely fix for transiently failing published histories test.
 2025-09-11 10:13:54 -04:00
Marius van den Beek e9af2f3e9d Merge pull request #20892 from nsoranzo/update_sort1_requirements 
Update requirements of sort1 tool
 2025-09-11 08:50:39 +02:00
Nicola Soranzo 857948c033 Update requirements of sort1 tool 
Otherwise the conda environment for it fails to solve with the following
error:

```
Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - package grep-2.14-h470a237_2 is excluded by strict repo priority
```

This is due to the fact that grep 2.14 is only available on the bioconda
channel, while newer versions are on conda-forge, which has a higher
priority.

Reported by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20876/files#r2336209775 .
 2025-09-11 01:44:30 +01:00
Nicola Soranzo 12f81e97a8 Merge pull request #20891 from nsoranzo/replace_codecs.open 
Replace deprecated ``codecs.open()``
 2025-09-10 17:59:48 +01:00
David López 78f47c5c3c Merge pull request #20886 from davelopez/improve_user_sharing_default 
Set default option to make datasets accessible only to individual users when sharing histories with particular users
 2025-09-10 18:23:58 +02:00
David López bfcc46a36d Merge pull request #20888 from davelopez/improve_typing_in_share_ui 
Refactor sharing logic for unified type handling
 2025-09-10 18:23:33 +02:00
Nicola Soranzo b0d04d2ac2 Replace deprecated `codecs.open()` 
with ``open()``. See

https://docs.python.org/3.14/whatsnew/3.14.html#deprecated
https://docs.python.org/3.14/library/codecs.html#codecs.open
 2025-09-10 15:20:51 +01:00
John Chilton 5d31aedcc4 Likely fix for transiently failing published histories test. 
The failing error:

```
self = <galaxy_test.selenium.test_histories_published.TestPublishedHistories object at 0x7f4ae3449e80>

    @selenium_test
    def test_published_histories_username_filter(self):
        self._login()
        self.navigate_to_published_histories()
        username = self.user2_email.split("@")[0]
        self.components.published_histories.search_input.wait_for_and_send_keys(f"user:{username}")
>       self.assert_histories_present([self.history2_name])
```
 2025-09-10 09:49:34 -04:00
Marius van den Beek 0b743f88e7 Merge pull request #20884 from nsoranzo/main_tool_CI_tests 
Add main tool CI tests
 2025-09-10 15:00:31 +02:00
Marius van den Beek dbcf3e3668 Merge pull request #20875 from richard-burhans/auto_compress_maf_axt 
adding axt and maf to auto_compressed_types
 2025-09-10 14:58:48 +02:00
Marius van den Beek a32fd305a1 Merge pull request #20881 from dannon/viz-nav-guard 
Viz nav guard
 2025-09-10 14:48:18 +02:00
davelopez 3878fac000 Refactors sharing logic for unified type handling 
Replacing custom types with backend generated types and using guards for type handling.
 2025-09-10 14:39:30 +02:00
davelopez 049e343d77 Updates default sharing option to 'make_accessible_to_shared' 
This seems like the sensible default when sharing an item with individual users.
 2025-09-10 14:07:54 +02:00
Marius van den Beek 7ab6320f7f Merge pull request #20778 from nilchia/fix_anndata 
fix anndata metadata
 2025-09-10 12:01:53 +02:00
Aysam Guerler 9afb25c651 Merge pull request #20877 from guerler/update_jupyterlite 
Update JupyterLite version to 0.6.4
 2025-09-10 12:05:56 +03:00
Nicola Soranzo 26e6a17a17 Fix skipping of empty lines in gtf_filter_by_attribute_values_list tool 
Introduced in https://github.com/galaxyproject/galaxy/pull/11365 .
 2025-09-10 03:45:54 +01:00
Nicola Soranzo bafa6de88e Fix incorrect test for Grep1 tool 2025-09-10 03:22:09 +01:00
Nicola Soranzo eb0a33ff39 Fix gff_filter_by_attribute and gff_filter_by_feature_count tools for recent Python 
Original fix by @natefoo in
https://github.com/galaxyproject/galaxy/pull/20840 .
 2025-09-10 03:21:14 +01:00
Nicola Soranzo 0abc2f7d97 Fix ldtools if tool path contains spaces 2025-09-10 02:14:50 +01:00
Nicola Soranzo 922bbdc741 Add main tool CI tests 
Also:
- Use the same cached venv for main tools, tool framework and
  workflow framework tests.
 2025-09-09 22:28:48 +01:00
Dannon Baker e982c519ad Fix linting issue, just setting an empty truthy value lets the browser 
handle this appropriately.  Simplify emits and rely on local change
handling.
 2025-09-09 12:55:45 -04:00
Dannon Baker 76ac175191 Add navigation guards to prevent data loss in visualizations 
Detects unsaved changes in visualization iframes using DOM observers and event listeners. Shows confirmation when navigating away with unsaved work.
 2025-09-09 12:43:58 -04:00
John Chilton a8df2c8ea7 Validate column definitions. 2025-09-09 12:32:47 -04:00
guerler 3eb3ad8ec7 Update JupyterLite version to 0.6.4 2025-09-09 17:12:46 +03:00
Martin Cech 2a4609c19a fix description link of maf 2025-09-09 14:43:48 +02:00
Marius van den Beek 8a8112e6e8 Merge pull request #20876 from nsoranzo/sort1_drop_Python_script 
Drop Python helper script from sort1 tool
 2025-09-09 08:45:16 +02:00
Nicola Soranzo 4768d3d1db Drop Python helper script from sort1 tool 
Also:
- Incidentally address the deprecation of the `argparse.FileType` type
  converter in Python 3.14 , see
  https://docs.python.org/3.14/whatsnew/3.14.html#deprecated
  https://github.com/galaxyproject/galaxy/issues/16854
- Drop the now unnecessary Python requirement.
- Use CDATA.
 2025-09-08 23:47:46 +01:00
Richard C. Burhans e75b51f8b5 adding axt and maf to auto_compressed_types 2025-09-08 13:32:44 -04:00
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
Marius van den Beek 8aade45d00 Merge pull request #20853 from davelopez/explore_file_source_hashes 
Support remote file source hashes
 2025-09-08 14:37:58 +02:00
Marius van den Beek b2beae577e Merge pull request #20873 from nsoranzo/fix_configfile_user_defined_test 
Fix test in ``configfile_user_defined.yml``
 2025-09-08 14:30:38 +02:00
Nicola Soranzo 06245f4f08 Fix test in `configfile_user_defined.yml` 
Introduced in commit 0308f25b43 .
 2025-09-08 11:56:34 +01:00
Marius van den Beek cba4d1dd5a Merge pull request #20871 from nsoranzo/type_annot_job_runners 
Improve type annotation for job runners and ``InteractiveToolManager``
 2025-09-08 09:57:54 +02:00
Nicola Soranzo aa13a63352 Improve type annotation for job runners and `InteractiveToolManager` 
Also:
- Fix bug in `KubernetesJobRunner.check_watched_item()` introduced in
  commit da100d3b27 .
- Drop unused `InteractiveToolManager.configure_entry_point()` method.
- Drop unnecessary `trans` parameter from `_get_entry_point_url_elements()`,
  `get_entry_point_subdomain()` and `get_entry_point_path()` methods of
  `InteractiveToolManager`.
 2025-09-07 22:19:07 +01:00
Nuwan Goonasekera 46485203d8 Fix incorrect done check in aws batch based on review comment 2025-09-07 22:19:07 +01:00
Nuwan Goonasekera 5293a34ebc Put ajs instead of tuple into watch queue 2025-09-07 22:19:06 +01:00
Nicola Soranzo 76b714d2ef Merge pull request #20869 from galaxybot/dev_auto_update_dependencies 
Update Python dependencies
 2025-09-07 14:05:41 +01:00
Marius van den Beek 7fc4545de4 Merge pull request #13570 from natefoo/tool-version-comparison-fix 
Workaround to numeric sorting in the local portion of tool versions if they are galaxy "build" numbers
 2025-09-06 11:18:11 +02:00
galaxybot 2f27fd0171 Update Python dependencies 
by running `make update-dependencies`.
 2025-09-06 03:14:24 +00:00
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
John Davis c91fce6a49 Add required fields to test file 2025-09-05 11:50:25 -04:00
Keith Suderman 3388259352 Remove test for invalid notebook. Fix format of test file. 2025-09-05 11:44:32 -04:00
Keith Suderman 14188b8402 Run make format to fix linting errors 2025-09-05 11:27:40 -04:00
Marius van den Beek 70b455bda1 Merge pull request #20866 from t1mk1k/add-support-for-hierarchical-module-systems 
Add support for hierarchical module systems in lmod + module dependency resolvers
 2025-09-05 15:58:49 +02:00
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