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@bernt-matthias bernt-matthias commented Aug 29, 2025

with conda I get (because it chooses a python without imghdr). We dropped the need for this module in 24.2 #18449

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/[email protected]/lib/python3.13/site-packages/galaxy/util/compression_utils.py", line 29, in <module>
    from .checkers import (
    ...<2 lines>...
    )
  File "/home/berntm/miniforge3/envs/[email protected]/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/[email protected]/lib/python3.13/site-packages/galaxy/util/image_util.py", line 3, in <module>
    import imghdr
ModuleNotFoundError: No module named 'imghdr'

How to test the changes?

(Select all options that apply)

  • I've included appropriate automated tests.
  • This is a refactoring of components with existing test coverage.
  • Instructions for manual testing are as follows:
    1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

  • I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

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/[email protected]/lib/python3.13/site-packages/galaxy/util/compression_utils.py", line 29, in <module>
    from .checkers import (
    ...<2 lines>...
    )
  File "/home/berntm/miniforge3/envs/[email protected]/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/[email protected]/lib/python3.13/site-packages/galaxy/util/image_util.py", line 3, in <module>
    import imghdr
ModuleNotFoundError: No module named 'imghdr'
```
@github-actions github-actions bot added this to the 25.1 milestone Aug 29, 2025
@nsoranzo
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I don't think we need to bump the tool versions since these are internal tools, but just mentioning it in case someone disagrees.

@nsoranzo nsoranzo merged commit dcd415a into galaxyproject:dev Aug 29, 2025
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This PR was merged without a "kind/" label, please correct.

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3 participants