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42358 Commits
Author SHA1 Message Date
Aysam Guerler f05c8a83bc Merge pull request #20914 from guerler/allow_creating_visualizations 
Allow creation of visualizations without dataset
 2025-09-17 14:58:23 +03:00
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
guerler e70546bb3e Allow creation of visualizations without dataset 2025-09-16 18:56:08 +03:00
Aysam Guerler 979ae54b0b Merge pull request #20907 from guerler/add_alignmentviewer 
Add Multiple Sequence Alignment Viewer 2.0
 2025-09-16 11:09:08 +03:00
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
John Davis 9c0ef303ab Merge pull request #20845 from AustralianBioCommons/oidc-pipeline-config 
OIDC authentication pipeline - allow adding extra steps to the default pipeline
 2025-09-15 21:31:15 -04:00
marius-mather 1f4cd32967 Rebuild config and skip pre-commit changes 2025-09-16 08:58:52 +10:00
Ahmed Awan ea22c0e765 drop eager param from get_invocation in error report method 2025-09-15 17:16:55 -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
John Chilton 66852487fa Merge pull request #20862 from jmchilton/pulsar_15_10 
Various Container Execution Enhancements (including GCP Batch support)
 2025-09-15 15:03:34 -04:00
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
marius-mather 2700989c56 Use attribute access to get app_config value 2025-09-15 11:02:18 +10:00
marius-mather 0a2399cb3e Improve config descriptions 2025-09-15 10:48:11 +10:00
Nicola Soranzo 7f569cdb43 Type annotation fixes for mypy 1.18.1 2025-09-14 22:14:39 +01:00
guerler 2c55e74d8a Fix datatype description 2025-09-14 13:15:26 +03:00
guerler c6ae06d5d0 Add a2m file format as fasta subclass 2025-09-14 12:50:11 +03:00
galaxybot 060f48e1d9 Update Python dependencies 
by running `make update-dependencies`.
 2025-09-13 03:09:59 +00:00
John Davis 89b9a50da9 Merge pull request #20827 from arash77/add-pptx-datatype 
[25.0] Fix DOCX detection and add PPTX support
 2025-09-11 23:36:49 -04:00
John Davis c47bb0c4f6 Merge pull request #20895 from mvdbeek/add_ldda_purged 
[25.0] Add LDDA purged property
 2025-09-11 12:27:40 -04:00
John Davis fb46c0a866 Merge pull request #20893 from cat-bro/custos_authnz_compare_email_case_insensitive 
[25.0] Make check for existing user in custos_authnz.py case insensitive
 2025-09-11 12:01:54 -04:00
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 DavisandMarius van den Beek d94bfe4df8 Update lib/galaxy/authnz/custos_authnz.py 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2025-09-11 10:18:10 -04:00
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
mvdbeek 9dac51b62e add LDDA purged property 
Fixes https://github.com/galaxyproject/galaxy/issues/20894
 2025-09-11 13:35:48 +02:00
mvdbeek 7a0539560d Speed up ImplicitCollectionJobs.job_list 
Minor tweak, for 100 items this goes from 500ms to 80ms and I assume
this becomes more significant the more jobs there are.

No changes to the API, we should probably paginate this and just return
relevant fields, but this should address the 12s load time on the
backend when you click on a 8000+ job step.
 2025-09-11 09:09:04 +02:00
cat-bro 2ad1570059 Make check for existing user in custos_authnz.py case insensitive 2025-09-11 14:58:32 +10:00
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 Davis ddee1a2a90 Merge branch 'release_24.2' into release_25.0 2025-09-10 09:54:38 -04:00
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 59b5b6beca Merge pull request #20874 from abretaud/hic_datatype 
[25.0] Add HiC datatype
 2025-09-10 15:03:17 +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 7ab6320f7f Merge pull request #20778 from nilchia/fix_anndata 
fix anndata metadata
 2025-09-10 12:01:53 +02:00
John Davis ee749b9dfd Check if role has description before editing 2025-09-09 17:17:23 -04:00
John Chilton a8df2c8ea7 Validate column definitions. 2025-09-09 12:32:47 -04:00
Martin Cech 2a4609c19a fix description link of maf 2025-09-09 14:43:48 +02:00
Marius van den Beek d4a4562a2c Merge pull request #20872 from mvdbeek/perf_fix_anton_invocation_2 
[25.0] Use ``populated_optimized`` when serializing collection
 2025-09-09 08:43:58 +02:00
mvdbeek c6e52c0703 Use outerjoins to replicate old populated method 2025-09-08 20:03:53 +02:00
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
John Chilton 4e2112355c Extract functionality from k8s runner for reuse. 2025-09-08 09:59:51 -04:00
John Chilton 7ebb964ab5 Eliminate copy-paste from Kubernetes runner. 2025-09-08 09:59:51 -04:00
John Chilton fcf1654468 Remove unused kubernetes helper method. 2025-09-08 09:59:51 -04:00
John Chilton a2afb2ceef Co-execution update - implement GCP, improve TES. 2025-09-08 09:59:37 -04:00
John Chilton 93bbc008ad Remove deprecated line. 2025-09-08 09:58:04 -04:00
Anthony Bretaudeau 4045f56914 Add HiC datatype 2025-09-08 15:46:04 +02:00
mvdbeek 2860a55c36 Make populated_state query more robust 2025-09-08 15:14:32 +02:00
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
mvdbeek 1f97a51846 Use `populated_optimized` when serializing collection 
The slow collection in question has 8000+ paired elements, where each
element would need to be lazy-loaded before this change.
 2025-09-08 14:03:00 +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