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containers-run example on script.py is errorring out #849

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yarikoptic opened this issue Jul 7, 2022 · 1 comment · Fixed by #854
Closed

containers-run example on script.py is errorring out #849

yarikoptic opened this issue Jul 7, 2022 · 1 comment · Fixed by #854

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@yarikoptic
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reported on https://neurostars.org/t/problems-with-datalad-handbooks-containers-run/23011

(base) twutz@mate:~/vtwutz_ext/DataLad-101/midterm_project$ datalad containers-run -m "rerun analysis in container" \
>   --container-name midterm-software \
>   --input "input/iris.csv" \
>   --output "prediction_report.csv" \
>   --output "pairwise_relationships.png" \
>   "python3 code/script.py"
/home/twutz/miniconda3/lib/python3.9/site-packages/requests/__init__.py:102: RequestsDependencyWarning: urllib3 (1.26.8) or chardet (5.0.0)/charset_normalizer (2.0.4) doesn't match a supported version!
  warnings.warn("urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported "
[INFO   ] Making sure inputs are available (this may take some time) 
unlock(ok): pairwise_relationships.png (file)
unlock(ok): prediction_report.csv (file)
[INFO   ] == Command start (output follows) ===== 
usage: script.py [-h] data output_figure output_report
script.py: error: the following arguments are required: data, output_figure, output_report
[INFO   ] == Command exit (modification check follows) ===== 
run(error): /home/twutz/vtwutz_ext/DataLad-101/midterm_project (dataset) [singularity exec .datalad/environments/m...]
add(ok): pairwise_relationships.png (file)                                      
add(ok): prediction_report.csv (file)                                           
action summary:                                                                 
  add (ok: 2)
  get (notneeded: 4)
  run (error: 1)
  save (notneeded: 2)
  unlock (ok: 2)

and indeed script used there from http://handbook.datalad.org/en/latest/basics/101-130-yodaproject.html#yoda-project seems to need positional arguments

@adswa
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adswa commented Jul 31, 2022

Sorry - for some reason this issue went right passed me. Will push a fix right away.

adswa added a commit that referenced this issue Jul 31, 2022
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2 participants