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Added skip_citation_process flag to skip processing citation.md #1876

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merged 3 commits into from Nov 25, 2019
Merged

Added skip_citation_process flag to skip processing citation.md #1876

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6fabb5a
added skip_citation_process flag to skip processing citation.md which
soichih Nov 22, 2019
f9056e4
renamed skip_citation_process to md_only_biolerplate and storing it
soichih Nov 24, 2019
1c6335d
shorten help line
soichih Nov 24, 2019
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5 changes: 4 additions & 1 deletion fmriprep/cli/run.py
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Expand Up @@ -73,6 +73,9 @@ def get_parser():
g_bids.add_argument('--skip_bids_validation', '--skip-bids-validation', action='store_true',
default=False,
help='assume the input dataset is BIDS compliant and skip the validation')
g_bids.add_argument('--skip_citation_process', '--skip-citation-process', action='store_true',
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Suggested change
g_bids.add_argument('--skip_citation_process', '--skip-citation-process', action='store_true',
g_bids.add_argument('--skip-citation-process', action='store_true',

Usually the _ one is there for backwards compatibility with old submission scripts. - is preferred, so we can use it on new options.

And this should go in g_perfm, not g_bids.

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I will update the PR. Testing the update now.

default=False,
help='skip processing HTML and LaTeX formatted citation with pandoc')
g_bids.add_argument('--participant_label', '--participant-label', action='store', nargs='+',
help='a space delimited list of participant identifiers or a single '
'identifier (the sub- prefix can be removed)')
Expand Down Expand Up @@ -444,7 +447,7 @@ def main():
for ext in ('bib', 'tex', 'md', 'html')
}

if citation_files['md'].exists():
if not opts.skip_citation_process and citation_files['md'].exists():
# Generate HTML file resolving citations
cmd = ['pandoc', '-s', '--bibliography',
pkgrf('fmriprep', 'data/boilerplate.bib'),
Expand Down