--yes option doesn't do anything?

[JohannesWiesner]

Just discovered that in our current script, the --yes option does not have any effect on the generated Dockerfile. See this issue: JohannesWiesner/csp_docker#12 (comment)

[kaczmarj]

hi @JohannesWiesner the --yes flag is meant for any alerts that a neurodocker template might have. for example, the fsl template alerts the user that fsl is non-free software for commercial purposes. see

neurodocker/neurodocker/templates/fsl.yaml

Line 13 in c92634f

alert: FSL is non-free. If you are considering commercial use of FSL, please consult the relevant license(s).

without the --yes flag, the user will be prompted to agree by typing y. with the --yes flag, the yes response is automatic.

neurodocker/neurodocker/cli/generate.py

Lines 389 to 398 in c92634f

	if tmpl.alert:
	# If user provides --yes flag, print message but do not ask for
	# confirmation.
	yes = ctx.params.get("yes")
	if yes:
	click.secho(tmpl.alert, fg="yellow", err=True)
	else:
	# TODO: add color to this to make it visible, perhaps yellow. But
	# there is no color option in `click.confirm`.
	click.confirm(f"{tmpl.alert} Proceed?", abort=True, err=True)

perhaps we can rename the --yes flag to clarify its purpose.

[JohannesWiesner]

Aaah, interesting, then I got that totally wrong. Yup, the docs are quite sparse, maybe we should update the docs?

docker run -i --rm repronim/neurodocker:0.9.4 generate docker --help
  --yes                        Reply yes to all prompts.