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Commit Graph
42301 Commits
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
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 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 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
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
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 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
mvdbeek 5142d276f9 Simply special case version suffix `+galaxy` 2025-09-05 10:26:00 +02:00
Nate Coraor 491bb53447 Don't add . to +galaxy local version if there is already a . 2025-09-05 10:23:25 +02:00
Nate Coraor 09442ce7f1 Attempt a workaround to numeric sorting in the local portion of tool 
versions if they are galaxy "build" numbers.
 2025-09-05 10:23:20 +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
davelopez 2519efaa62 Implement support for optional file hashes in fsspec-based remote file entries 
Introduces the ability to include optional file hashes in remote file
entries by adding a new `_get_file_hashes` method. This method can be
overridden by subclasses to extract and provide hash information from
the remote filesystem.

For Hugging Face, integrates SHA-256 hash extraction for files stored
using Git LFS
 2025-09-04 16:04:09 +02:00
davelopez e1a1b2a117 Adds support for precomputed file hashes in remote file schema 
This update improves compatibility with systems requiring file integrity verification or file deduplication and enables better handling of hash-based operations.

No breaking changes introduced; the `hashes` field is optional.
 2025-09-04 16:04:08 +02:00
davelopez 9c11d58c30 Replace hardcoded hash function names with reusable type alias 
Introduces a `HashFunctionNames` type alias to centralize the definition of supported hash functions, ensuring consistency across the codebase. Updates references to use this alias instead of hardcoding values.

This change improves maintainability by linking the type alias with the `HashFunctionNameEnum`, making it easier to keep them synchronized.
 2025-09-04 16:04:07 +02:00
mvdbeek 5ccf97752b Verify collection is correctly consumed 2025-09-04 14:48:44 +02:00
mvdbeek d679127310 Deserialize collection input into multiple="true" as hdca, not list of hdca 2025-09-01 20:27:35 +02:00
mvdbeek eb823365bb Don't load custom tools into toolbox 2025-09-01 17:36:11 +02:00
mvdbeek ea9fde1636 Add selenium test for creating and running custom tool 2025-09-01 17:36:10 +02:00
mvdbeek 9b0d97e33e Don't return step tool uuid when downloading workflow 
We want to rebuild from `tool_representation`.
 2025-09-01 17:36:10 +02:00
mvdbeek 2c19e16994 Assert dynamic tool error message specificity 2025-09-01 17:36:10 +02:00
mvdbeek 60d12acb7d Serialize step tool_uuid as string, not UUID class instance 2025-09-01 17:36:10 +02:00
mvdbeek 4cf80afcaa Fix invocation step view with custom tools 2025-09-01 17:36:09 +02:00
mvdbeek ec186820cc Rebuild openapi schema 2025-09-01 17:36:09 +02:00
mvdbeek 4d75e3b066 Default to skip if data style unspecified 2025-09-01 17:36:08 +02:00
mvdbeek 0308f25b43 Implement templatable configfiles for yaml tools 2025-09-01 17:36:08 +02:00
mvdbeek b801dfe94b Fix tool form loading 2025-09-01 17:36:08 +02:00
Amirhossein Naghsh Nilchi 8ec0610b65 fix anndata 
update shape attr

add test for new update
 2025-09-01 17:31:09 +02:00
galaxybot d49bc365c4 Update Python dependencies 
by running `make update-dependencies`.
 2025-08-30 03:16:24 +00:00
mvdbeek 30af8fb6ea Merge branch 'release_25.0' into dev 2025-08-29 20:00:19 +02:00
mvdbeek 4225e4b0fa Merge branch 'release_24.2' into release_25.0 2025-08-29 19:59:33 +02:00
Marius van den Beek 4ea216f0e1 Merge pull request #20836 from mvdbeek/include_user_agent 
[24.2] Include galaxy user agent in data source tools
 2025-08-29 19:40:44 +02:00
mvdbeek 541d70acf6 Include galaxy user agent in data source tools 
Closes https://github.com/galaxyproject/galaxy/issues/20833
 2025-08-29 17:22:28 +02:00
Nicola Soranzo dcd415a293 Merge pull request #20834 from bernt-matthias/bump-directory-converters 
Bump requirement of directory converters
 2025-08-29 16:55:41 +02:00
Matthias Bernt d76747df7d bump requirement of directory converters 
with conda I get

```
Traceback (most recent call last):
  File "<string>", line 1, in <module>
    from galaxy.util.compression_utils import CompressedFile; CompressedFile('/tmp/tmp3v2nuot4/files/a/9/7/dataset_a97aebb4-46f7-47a9-b418-11ff1deeed74.dat').extract('.')
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/berntm/miniforge3/envs/__galaxy-util@23.2.1/lib/python3.13/site-packages/galaxy/util/compression_utils.py", line 29, in <module>
    from .checkers import (
    ...<2 lines>...
    )
  File "/home/berntm/miniforge3/envs/__galaxy-util@23.2.1/lib/python3.13/site-packages/galaxy/util/checkers.py", line 20, in <module>
    from galaxy.util.image_util import image_type
  File "/home/berntm/miniforge3/envs/__galaxy-util@23.2.1/lib/python3.13/site-packages/galaxy/util/image_util.py", line 3, in <module>
    import imghdr
ModuleNotFoundError: No module named 'imghdr'
```
 2025-08-29 13:03:00 +02:00
John Chilton fcb5e414da Merge pull request #20805 from davelopez/add_huggingface_file_source 
Add Hugging Face 🤗 file source and user-defined template
 2025-08-28 09:36:32 -04:00