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Fixes to updatepetjson and ecatheaderupdate #369

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Merged
merged 3 commits into from
Nov 21, 2025
Merged

Fixes to updatepetjson and ecatheaderupdate #369

merged 3 commits into from
Nov 21, 2025

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@pwighton
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@pwighton pwighton commented Nov 20, 2025 •
edited by github-actions bot
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Running updatepetjson gives:

Traceback (most recent call last):
  File "/home/paul/miniconda3/envs/pet2bids/bin/updatepetjson", line 3, in <module>
    from pypet2bids.update_json import update_json_cli
ModuleNotFoundError: No module named 'pypet2bids.update_json'

And running ecatheaderupdate gives:

Traceback (most recent call last):
  File "/home/paul/miniconda3/envs/pet2bids/bin/updatepetjson", line 3, in <module>
    from pypet2bids.update_json import update_json_cli
ModuleNotFoundError: No module named 'pypet2bids.update_json'

These errors can be fixed by the changes to pyproject.toml

But then, trying to run updatepetjson gives the following error:

Traceback (most recent call last):
  File "/home/paul/lcn/git/pet2bids/pypet2bids/pypet2bids/update_json_pet_file.py", line 17, in <module>
    import helper_functions
ModuleNotFoundError: No module named 'helper_functions'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/paul/lcn/git/pet2bids/pypet2bids/pypet2bids/is_pet.py", line 15, in <module>
    import helper_functions
ModuleNotFoundError: No module named 'helper_functions'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/paul/lcn/git/pet2bids/pypet2bids/pypet2bids/ecat.py", line 19, in <module>
    import helper_functions
ModuleNotFoundError: No module named 'helper_functions'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/paul/lcn/git/pet2bids/pypet2bids/pypet2bids/dcm2niix4pet.py", line 34, in <module>
    import helper_functions
ModuleNotFoundError: No module named 'helper_functions'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/paul/miniconda3/envs/pet2bids/bin/updatepetjson", line 3, in <module>
    from pypet2bids.update_json_pet_file import update_json_cli
  File "/home/paul/lcn/git/pet2bids/pypet2bids/pypet2bids/update_json_pet_file.py", line 22, in <module>
    import pypet2bids.is_pet as is_pet
  File "/home/paul/lcn/git/pet2bids/pypet2bids/pypet2bids/is_pet.py", line 21, in <module>
    import pypet2bids.ecat as ecat
  File "/home/paul/lcn/git/pet2bids/pypet2bids/pypet2bids/ecat.py", line 34, in <module>
    import pypet2bids.dcm2niix4pet as dcm2niix4pet
  File "/home/paul/lcn/git/pet2bids/pypet2bids/pypet2bids/dcm2niix4pet.py", line 54, in <module>
    from pypet2bids.update_json_pet_file import (
ImportError: cannot import name 'check_json' from partially initialized module 'pypet2bids.update_json_pet_file' (most likely due to a circular import) (/home/paul/lcn/git/pet2bids/pypet2bids/pypet2bids/update_json_pet_file.py)

This is due to a circular dependency:

  • update_json_pet_file.py imports from is_pet.py
  • is_pet.py imports ecat.py
  • ecat.py imports dcm2niix4pet.py
  • dcm2niix4pet.py imports from update_json_pet_file.py

Deferring the import of is_pet to the function where it's used, get_metadata_from_spreadsheet() resolves this.

Running ecatheaderupdate gives:

Traceback (most recent call last):
  File "/home/paul/lcn/git/pet2bids/pypet2bids/pypet2bids/ecat_header_update.py", line 2, in <module>
    import ecat
ModuleNotFoundError: No module named 'ecat'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/paul/miniconda3/envs/pet2bids/bin/ecatheaderupdate", line 3, in <module>
    from pypet2bids.ecat_header_update import cli
  File "/home/paul/lcn/git/pet2bids/pypet2bids/pypet2bids/ecat_header_update.py", line 7, in <module>
    from pypet2bids.ecat import ecat
ImportError: cannot import name 'ecat' from 'pypet2bids.ecat' (/home/paul/lcn/git/pet2bids/pypet2bids/pypet2bids/ecat.py)

Fixing the import statement to import the modules themselves instead of objetcs from modules resolves this.

📚 Documentation preview 📚: https://pet2bids--369.org.readthedocs.build/en/369/

@bendhouseart
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bendhouseart commented Nov 20, 2025

I thought I fixed this, but I must have dreamed that I moved all the import try excepts to pypet2bids/pypet2bids/__init__.py Thanks Paul, will test and merge later today.

bendhouseart
bendhouseart approved these changes Nov 21, 2025
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👍

@bendhouseart bendhouseart merged commit f7a7ffe into openneuropet:main Nov 21, 2025
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2 participants

@pwighton @bendhouseart