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PeerHerholz / BIDSonym

a BIDS app for pseudo-anonymization of neuroimaging data
https://peerherholz.github.io/BIDSonym/
BSD 3-Clause "New" or "Revised" License
51 stars 14 forks source link

Add codespell support: config, workflow + make it fix all typos #78

Closed yarikoptic closed 2 months ago

yarikoptic commented 7 months ago

originally ran into a problem while copy pasting the proposed by error option:

❯ datalad containers-run -n bids-bidsonym . participant --participant_label 0001
[INFO   ] Making sure inputs are available (this may take some time) 
[INFO   ] == Command start (output follows) ===== 
Traceback (most recent call last):
  File "/opt/miniconda-latest/envs/bidsonym/bin/bidsonym", line 33, in <module>
    sys.exit(load_entry_point('bidsonym', 'console_scripts', 'bidsonym')())
  File "/home/bm/bidsonym/run_deeid.py", line 77, in run_deeid
    raise Exception("For post defacing quality it is required to run a form of brainextraction"
Exception: For post defacing quality it is required to run a form of brainextractionon the non-deindentified data. Thus please either indicate bet(--brainextration bet) or nobrainer (--brainextraction nobrainer).
[INFO   ] == Command exit (modification check follows) ===== 
run(error): /home/yoh/datasets/1076_spacetop (dataset) [./code/containers/scripts/singularity_cm...]
action summary:
  get (notneeded: 2)
  run (error: 1)
❯ datalad containers-run -n bids-bidsonym . participant --participant_label 0001 --brainextration bet
[INFO   ] Making sure inputs are available (this may take some time) 
[INFO   ] == Command start (output follows) ===== 
usage: bidsonym [-h]
                [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                [--deid {pydeface,mri_deface,quickshear,mridefacer,deepdefacer}]
                [--deface_t2w] [--check_meta CHECK_META [CHECK_META ...]]
                [--del_meta DEL_META [DEL_META ...]]
                [--brainextraction {bet,nobrainer}] [--bet_frac BET_FRAC]
                [--skip_bids_validation] [-v]
                bids_dir {participant,group}
bidsonym: error: unrecognized arguments: --brainextration bet

hence came to my regular codespell rampage

yarikoptic commented 2 months ago

Hey @PeerHerholz -- may be merge this simple one?

PeerHerholz commented 2 months ago

Sorry, missed it. Done and thanks for all the help!