nipy / heudiconv

Flexible DICOM conversion into structured directory layouts
https://heudiconv.readthedocs.io
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Run tests weekly to ensure we are still good #781

Closed yarikoptic closed 2 months ago

yarikoptic commented 2 months ago

also to check what the current state is since in fresh runs for

_____________________ test_embed_dicom_and_nifti_metadata ______________________
/home/runner/work/heudiconv/heudiconv/heudiconv/tests/test_dicoms.py:57: in test_embed_dicom_and_nifti_metadata
    embed_dicom_and_nifti_metadata(dcmfiles, out_prefix + ".nii.gz", infofile, None)
/home/runner/work/heudiconv/heudiconv/heudiconv/dicoms.py:659: in embed_dicom_and_nifti_metadata
    stack = ds.parse_and_stack(dcmfiles, force=True).values()
/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dcmstack/dcmstack.py:1156: in parse_and_stack
    results = parse_and_group(src_paths,
/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dcmstack/dcmstack.py:1046: in parse_and_group
    dcm = pydicom.read_file(dcm_path, force=force)
E   AttributeError: module 'pydicom' has no attribute 'read_file'

that is with

Downloading pydicom-3.0.0-py3-none-any.whl.metadata (9.4 kB)

and pydicom released 5 days ago :-/ https://github.com/pydicom/pydicom/releases/tag/v3.0.0 says

heh, so we should also fix codebase (in a separate PR)

codecov[bot] commented 2 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 82.03%. Comparing base (a0a3635) to head (84694c1). Report is 6 commits behind head on master.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #781 +/- ## ========================================== - Coverage 82.08% 82.03% -0.06% ========================================== Files 42 42 Lines 4215 4214 -1 ========================================== - Hits 3460 3457 -3 - Misses 755 757 +2 ```

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yarikoptic commented 2 months ago

d'oh we have replaced those already in

github-actions[bot] commented 2 months ago

:rocket: PR was released in v1.2.0 :rocket: