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sentry-sdk is imported unconditionally by the CLI, but not part of install_requires #2411

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effigies opened this issue May 15, 2021 · 0 comments
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@effigies
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See: https://neurostars.org/t/fmriprep-error-using-ubuntu-20-04-2/19294

The issue is that sentry-sdk is imported unconditionally, but not part of install_requires.

  1. If it's intended to be optional, we should guard against ImportErrors.
  2. If it's required, we should add to install_requires.
  3. If we want people to be able to install fMRIPrep as a library and not purely as a runtime CLI, then we should update the installation instructions to install fmriprep[sentry]. Possibly move sentry to [cli] or something to make it clearer that the reason for adding it is to enable the CLI.

What version of fMRIPrep are you using?

20.2.1

What kind of installation are you using? Containers (Singularity, Docker), or "bare-metal"?

bare-metal

What is the exact command-line you used?

bids_root_dir=$HOME/openneuro_tutorial/ds000102
preprocess_output_dir=$HOME/openneuro_tutorial/ds000102/fmriprep
subj=01
 
export TEMPLATEFLOW_HOME=$HOME/openneuro_tutorial/templateflow
export FS_LICENSE=$HOME/openneuro_tutorial/license.txt

fmriprep   $bids_root_dir $preprocess_output_dir participant \
   --participant-label $subj \
   --skip_bids_validation \
   --md-only-boilerplate \
   --fs-license-file $HOME/openneuro_tutorial/license.txt \
   --fs-no-reconall \
   --output-spaces MNI152NLin2009cAsym:res-1 \
   --nthreads $nthreads \
   --stop-on-first-crash \
   -w $HOME

Have you checked that your inputs are BIDS valid?

Unknown

Did fMRIPrep generate the visual report for this particular subject? If yes, could you share it?

No

Can you find some traces of the error reported in the visual report (at the bottom) or in crashfiles?

No

Are you reusing previously computed results (e.g., FreeSurfer, Anatomical derivatives, work directory of previous run)?

Unknown

fMRIPrep log

If you have access to the output logged by fMRIPrep, please make sure to attach it as a text file to this issue.

    File "/home/taliw/.local/bin/fmriprep", line 11, in <module>
    load_entry_point('fmriprep==20.2.1', 'console_scripts', 'fmriprep')()
      File "/home/taliw/.local/lib/python3.8/site-packages/fmriprep-20.2.1-py3.8.egg/fmriprep/cli/run.py", line 21, in main
    ModuleNotFoundError: No module named 'sentry_sdk'
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