How to use the smriprep.__about__.__version__ function in smriprep

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github poldracklab / smriprep / smriprep / cli / run.py View on Github external
# Arguments as specified by BIDS-Apps
    # required, positional arguments
    # IMPORTANT: they must go directly with the parser object
    parser.add_argument('bids_dir', action='store', type=Path,
                        help='the root folder of a BIDS valid dataset (sub-XXXXX folders should '
                             'be found at the top level in this folder).')
    parser.add_argument('output_dir', action='store', type=Path,
                        help='the output path for the outcomes of preprocessing and visual '
                             'reports')
    parser.add_argument('analysis_level', choices=['participant'],
                        help='processing stage to be run, only "participant" in the case of '
                             'sMRIPrep (see BIDS-Apps specification).')

    # optional arguments
    parser.add_argument('--version', action='version', version='smriprep v{}'.format(__version__))

    g_bids = parser.add_argument_group('Options for filtering BIDS queries')
    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)')
    g_bids.add_argument(
        '--bids-filter-file', action='store', type=Path, metavar='PATH',
        help='a JSON file describing custom BIDS input filters using pybids '
             '{:{:
github poldracklab / smriprep / smriprep / cli / run.py View on Github external
retval['run_uuid'] = run_uuid
    retval['workflow'] = None

    # Called with reports only
    if opts.reports_only:
        from niworkflows.reports import generate_reports

        logger.log(25, 'Running --reports-only on participants %s', ', '.join(subject_list))
        if opts.run_uuid is not None:
            run_uuid = opts.run_uuid
        retval['return_code'] = generate_reports(subject_list, str(output_dir), run_uuid,
                                                 packagename="smriprep")
        return retval

    logger.log(25, INIT_MSG(
        version=__version__,
        bids_dir=bids_dir,
        subject_list=subject_list,
        uuid=run_uuid,
        spaces=opts.output_spaces)
    )

    # Build main workflow
    retval['workflow'] = init_smriprep_wf(
        debug=opts.sloppy,
        fast_track=opts.fast_track,
        freesurfer=opts.run_reconall,
        fs_subjects_dir=opts.fs_subjects_dir,
        hires=opts.hires,
        layout=layout,
        longitudinal=opts.longitudinal,
        low_mem=opts.low_mem,
github poldracklab / smriprep / smriprep / utils / bids.py View on Github external
"""
    import os
    from pathlib import Path
    import json
    from ..__about__ import __version__, __url__, DOWNLOAD_URL

    bids_dir = Path(bids_dir)
    deriv_dir = Path(deriv_dir)
    desc = {
        'Name': 'sMRIPrep - Structural MRI PREProcessing workflow',
        'BIDSVersion': '1.1.1',
        'PipelineDescription': {
            'Name': 'sMRIPrep',
            'Version': __version__,
            'CodeURL': DOWNLOAD_URL,
        },
        'CodeURL': __url__,
        'HowToAcknowledge':
            'Please cite our paper (https://doi.org/10.1101/306951), and '
            'include the generated citation boilerplate within the Methods '
            'section of the text.',
    }

    # Keys that can only be set by environment
    if 'SMRIPREP_DOCKER_TAG' in os.environ:
        desc['DockerHubContainerTag'] = os.environ['SMRIPREP_DOCKER_TAG']
    if 'SMRIPREP_SINGULARITY_URL' in os.environ:
        singularity_url = os.environ['SMRIPREP_SINGULARITY_URL']
        desc['SingularityContainerURL'] = singularity_url
github poldracklab / smriprep / smriprep / workflows / base.py View on Github external
else:
        subject_data = collect_data(layout, subject_id, bids_filters=bids_filters)[0]

    if not subject_data['t1w']:
        raise Exception("No T1w images found for participant {}. "
                        "All workflows require T1w images.".format(subject_id))

    workflow = Workflow(name=name)
    workflow.__desc__ = """
Results included in this manuscript come from preprocessing
performed using *sMRIPprep* {smriprep_ver}
(@fmriprep1; @fmriprep2; RRID:SCR_016216),
which is based on *Nipype* {nipype_ver}
(@nipype1; @nipype2; RRID:SCR_002502).

""".format(smriprep_ver=__version__, nipype_ver=nipype_ver)
    workflow.__postdesc__ = """

For more details of the pipeline, see [the section corresponding
to workflows in *sMRIPrep*'s documentation]\
(https://smriprep.readthedocs.io/en/latest/workflows.html \
"sMRIPrep's documentation").


### References

"""

    deriv_cache = None
    if fast_track:
        from ..utils.bids import collect_derivatives
        std_spaces = spaces.get_spaces(nonstandard=False, dim=(3,))