fmriprep-docker 0.3.2__tar.gz

fmriprep-docker-0.3.2/PKG-INFO

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+Metadata-Version: 1.1
+Name: fmriprep-docker
+Version: 0.3.2
+Summary: fMRIprep is a functional magnetic resonance image pre-processing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to differences in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.
+Home-page: https://github.com/poldracklab/fmriprep
+Author: Christopher J. Markiewicz
+Author-email: crn.poldracklab@gmail.com
+License: 3-clause BSD
+Description: This package is a basic wrapper for fMRIprep that generates the appropriate
+        Docker commands, providing an intuitive interface to running the fMRIprep
+        workflow in a Docker environment.
+Platform: UNKNOWN
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 2.7
+Classifier: Programming Language :: Python :: 3.5
+Classifier: Programming Language :: Python :: 3.6

fmriprep-docker-0.3.2/fmriprep_docker.egg-info/PKG-INFO

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+Metadata-Version: 1.1
+Name: fmriprep-docker
+Version: 0.3.2
+Summary: fMRIprep is a functional magnetic resonance image pre-processing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to differences in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.
+Home-page: https://github.com/poldracklab/fmriprep
+Author: Christopher J. Markiewicz
+Author-email: crn.poldracklab@gmail.com
+License: 3-clause BSD
+Description: This package is a basic wrapper for fMRIprep that generates the appropriate
+        Docker commands, providing an intuitive interface to running the fMRIprep
+        workflow in a Docker environment.
+Platform: UNKNOWN
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 2.7
+Classifier: Programming Language :: Python :: 3.5
+Classifier: Programming Language :: Python :: 3.6

fmriprep-docker-0.3.2/fmriprep_docker.egg-info/SOURCES.txt

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+fmriprep_docker.py
+setup.py
+fmriprep_docker.egg-info/PKG-INFO
+fmriprep_docker.egg-info/SOURCES.txt
+fmriprep_docker.egg-info/dependency_links.txt
+fmriprep_docker.egg-info/entry_points.txt
+fmriprep_docker.egg-info/not-zip-safe
+fmriprep_docker.egg-info/requires.txt
+fmriprep_docker.egg-info/top_level.txt

fmriprep-docker-0.3.2/fmriprep_docker.egg-info/dependency_links.txt

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+

fmriprep-docker-0.3.2/fmriprep_docker.egg-info/entry_points.txt

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+[console_scripts]
+fmriprep-docker = fmriprep_docker:main
+

fmriprep-docker-0.3.2/fmriprep_docker.egg-info/not-zip-safe

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+

fmriprep-docker-0.3.2/fmriprep_docker.egg-info/requires.txt

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+future

fmriprep-docker-0.3.2/fmriprep_docker.egg-info/top_level.txt

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+fmriprep_docker

fmriprep-docker-0.3.2/fmriprep_docker.py

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+#!/usr/bin/env python
+from __future__ import print_function, unicode_literals, division, absolute_import
+from builtins import int, map, input, zip
+from future import standard_library
+import sys
+import os
+import re
+import argparse
+import subprocess
+
+standard_library.install_aliases()
+
+__version__ = '0.3.2'
+__packagename__ = 'fmriprep-docker'
+__author__ = 'The CRN developers'
+__copyright__ = 'Copyright 2017, Center for Reproducible Neuroscience, Stanford University'
+__credits__ = ['Craig Moodie', 'Ross Blair', 'Oscar Esteban', 'Chris Gorgolewski',
+               'Shoshana Berleant', 'Christopher J. Markiewicz', 'Russell A. Poldrack']
+__license__ = '3-clause BSD'
+__maintainer__ = 'Christopher J. Markiewicz'
+__email__ = 'crn.poldracklab@gmail.com'
+__url__ = 'https://github.com/poldracklab/fmriprep'
+__bugreports__ = 'https://github.com/poldracklab/fmriprep/issues'
+
+__description__ = """\
+fMRIprep is a functional magnetic resonance image pre-processing pipeline \
+that is designed to provide an easily accessible, state-of-the-art interface \
+that is robust to differences in scan acquisition protocols and that requires \
+minimal user input, while providing easily interpretable and comprehensive \
+error and output reporting."""
+__longdesc__ = """\
+This package is a basic wrapper for fMRIprep that generates the appropriate
+Docker commands, providing an intuitive interface to running the fMRIprep
+workflow in a Docker environment."""
+
+DOWNLOAD_URL = (
+    'https://pypi.python.org/packages/source/{name[0]}/{name}/{name}-{ver}.tar.gz'.format(
+        name=__packagename__, ver=__version__))
+
+CLASSIFIERS = [
+    'Development Status :: 3 - Alpha',
+    'Intended Audience :: Science/Research',
+    'License :: OSI Approved :: BSD License',
+    'Programming Language :: Python :: 2.7',
+    'Programming Language :: Python :: 3.5',
+    'Programming Language :: Python :: 3.6',
+]
+
+
+MISSING = """
+Image '{}' is missing
+Would you like to download? [Y/n] """
+PKG_PATH = '/usr/local/miniconda/lib/python3.6/site-packages'
+
+# Monkey-patch Py2 subprocess
+if not hasattr(subprocess, 'DEVNULL'):
+    subprocess.DEVNULL = -3
+
+if not hasattr(subprocess, 'run'):
+    # Reimplement minimal functionality for usage in this file
+    def _run(args, stdout=None, stderr=None):
+        from collections import namedtuple
+        result = namedtuple('CompletedProcess', 'stdout stderr returncode')
+
+        devnull = None
+        if subprocess.DEVNULL in (stdout, stderr):
+            devnull = open(os.devnull, 'r+')
+            if stdout == subprocess.DEVNULL:
+                stdout = devnull
+            if stderr == subprocess.DEVNULL:
+                stderr = devnull
+
+        proc = subprocess.Popen(args, stdout=stdout, stderr=stderr)
+        stdout, stderr = proc.communicate()
+        res = result(stdout, stderr, proc.returncode)
+
+        if devnull is not None:
+            devnull.close()
+
+        return res
+    subprocess.run = _run
+
+
+def check_docker():
+    """Verify that docker is installed and the user has permission to
+    run docker images.
+
+    Returns
+    -------
+    -1  Docker can't be found
+     0  Docker found, but user can't connect to daemon
+     1  Test run OK
+     """
+    try:
+        ret = subprocess.run(['docker', 'version'], stdout=subprocess.PIPE,
+                             stderr=subprocess.PIPE)
+    except OSError as e:
+        from errno import ENOENT
+        if e.errno == ENOENT:
+            return -1
+        raise e
+    if ret.stderr.startswith(b"Cannot connect to the Docker daemon."):
+        return 0
+    return 1
+
+
+def check_image(image):
+    """Check whether image is present on local system"""
+    ret = subprocess.run(['docker', 'images', '-q', image],
+                         stdout=subprocess.PIPE)
+    return bool(ret.stdout)
+
+
+def check_memory(image):
+    """Check total memory from within a docker container"""
+    ret = subprocess.run(['docker', 'run', '--rm', '--entrypoint=free',
+                          image, '-m'],
+                         stdout=subprocess.PIPE,
+                         stderr=subprocess.DEVNULL)
+    mem = [line.decode().split()[1]
+           for line in ret.stdout.splitlines()
+           if line.startswith(b'Mem:')][0]
+    return int(mem)
+
+
+def merge_help(wrapper_help, target_help):
+    # Matches all flags with up to one nested square bracket
+    opt_re = re.compile(r'(\[--?[\w-]+(?:[^\[\]]+(?:\[[^\[\]]+\])?)?\])')
+    # Matches flag name only
+    flag_re = re.compile(r'\[--?([\w-]+)[ \]]')
+
+    # Normalize to Unix-style line breaks
+    w_help = wrapper_help.rstrip().replace('\r', '')
+    t_help = target_help.rstrip().replace('\r', '')
+
+    w_usage, w_details = w_help.split('\n\n', 1)
+    w_groups = w_details.split('\n\n')
+    t_usage, t_details = t_help.split('\n\n', 1)
+    t_groups = t_details.split('\n\n')
+
+    w_posargs = w_usage.split('\n')[-1].lstrip()
+    t_posargs = t_usage.split('\n')[-1].lstrip()
+
+    w_options = opt_re.findall(w_usage)
+    w_flags = sum(map(flag_re.findall, w_options), [])
+    t_options = opt_re.findall(t_usage)
+    t_flags = sum(map(flag_re.findall, t_options), [])
+
+    # The following code makes this assumption
+    assert w_flags[:2] == ['h', 'v']
+    assert w_posargs.replace(']', '').replace('[', '') == t_posargs
+
+    # Make sure we're not clobbering options we don't mean to
+    overlap = set(w_flags).intersection(t_flags)
+    assert overlap == set('hvw'), "Clobbering options: {}".format(
+        ', '.join(overlap - set('hvw')))
+
+    sections = []
+
+    # Construct usage
+    start = w_usage[:w_usage.index(' [')]
+    indent = ' ' * len(start)
+    new_options = sum((
+        w_options[:2],
+        [opt for opt, flag in zip(t_options, t_flags) if flag not in overlap],
+        w_options[2:]
+        ), [])
+    opt_line_length = 79 - len(start)
+    length = 0
+    opt_lines = [start]
+    for opt in new_options:
+        opt = ' ' + opt
+        olen = len(opt)
+        if length + olen <= opt_line_length:
+            opt_lines[-1] += opt
+            length += olen
+        else:
+            opt_lines.append(indent + opt)
+            length = olen
+    opt_lines.append(indent + ' ' + t_posargs)
+    sections.append('\n'.join(opt_lines))
+
+    # Use target description and positional args
+    sections.extend(t_groups[:2])
+
+    for line in t_groups[2].split('\n')[1:]:
+        content = line.lstrip().split(',', 1)[0]
+        if content[1:] not in overlap:
+            w_groups[2] += '\n' + line
+
+    sections.append(w_groups[2])
+
+    # All remaining sections, show target then wrapper (skipping duplicates)
+    sections.extend(t_groups[3:] + w_groups[5:])
+    return '\n\n'.join(sections)
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description='fMRI Preprocessing workflow',
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        add_help=False)
+
+    # Standard FMRIPREP arguments
+    parser.add_argument('bids_dir', nargs='?', type=str, default='')
+    parser.add_argument('output_dir', nargs='?', type=str, default='')
+    parser.add_argument('analysis_level', nargs='?', choices=['participant'],
+                        default='participant')
+
+    parser.add_argument('-h', '--help', action='store_true',
+                        help="show this help message and exit")
+    parser.add_argument('-v', '--version', action='store_true',
+                        help="show program's version number and exit")
+
+    # Allow alternative images (semi-developer)
+    parser.add_argument('-i', '--image', metavar='IMG', type=str,
+                        default='poldracklab/fmriprep:{}'.format(__version__),
+                        help='image name')
+
+    g_wrap = parser.add_argument_group(
+        'Wrapper options',
+        'Standard options that require mapping files into the container')
+    g_wrap.add_argument('-w', '--work-dir', action='store',
+                        help='path where intermediate results should be stored')
+
+    # Developer patch/shell options
+    g_dev = parser.add_argument_group(
+        'Developer options',
+        'Tools for testing and debugging FMRIPREP')
+    g_dev.add_argument('-f', '--patch-fmriprep', metavar='PATH',
+                       type=os.path.abspath,
+                       help='working fmriprep repository')
+    g_dev.add_argument('-n', '--patch-niworkflows', metavar='PATH',
+                       type=os.path.abspath,
+                       help='working niworkflows repository')
+    g_dev.add_argument('-p', '--patch-nipype', metavar='PATH',
+                       type=os.path.abspath,
+                       help='working nipype repository')
+    g_dev.add_argument('--shell', action='store_true',
+                       help='open shell in image instead of running FMRIPREP')
+    g_dev.add_argument('--config', metavar='PATH', action='store',
+                       type=os.path.abspath, help='Use custom nipype.cfg file')
+
+    # Capture additional arguments to pass inside container
+    opts, unknown_args = parser.parse_known_args()
+
+    # Set help if no directories set
+    if (opts.bids_dir, opts.output_dir) == ('', ''):
+        opts.help = True
+
+    # Stop if no docker / docker fails to run
+    check = check_docker()
+    if check < 1:
+        if opts.version:
+            print('fmriprep wrapper {!s}'.format(__version__))
+        if opts.help:
+            parser.print_help()
+        print("fmriprep: ", end='')
+        if check == -1:
+            print("Could not find docker command... Is it installed?")
+        else:
+            print("Make sure you have permission to run 'docker'")
+        return 1
+
+    # For --help or --version, ask before downloading an image
+    if not check_image(opts.image):
+        resp = 'Y'
+        if opts.version:
+            print('fmriprep wrapper {!s}'.format(__version__))
+        if opts.help:
+            parser.print_help()
+        if opts.version or opts.help:
+            try:
+                resp = input(MISSING.format(opts.image))
+            except KeyboardInterrupt:
+                print()
+                return 1
+        if resp not in ('y', 'Y', ''):
+            return 0
+
+    # Warn on low memory allocation
+    mem_total = check_memory(opts.image)
+    if mem_total < 8000:
+        print('Warning: <8GB of RAM is available within your Docker '
+              'environment.\nSome parts of fMRIprep may fail to complete.')
+        resp = 'N'
+        try:
+            resp = input('Continue anyway? [y/N]')
+        except KeyboardInterrupt:
+            print()
+            return 1
+        if resp not in ('y', 'Y', ''):
+            return 0
+
+    command = ['docker', 'run', '--rm', '-it']
+
+    # Patch working repositories into installed package directories
+    for pkg in ('fmriprep', 'niworkflows', 'nipype'):
+        repo_path = getattr(opts, 'patch_' + pkg)
+        pkg_path = '{}/{}'.format(PKG_PATH, pkg)  # Always POSIX path
+        if repo_path is not None:
+            command.extend(['-v', '{}:{}:ro'.format(repo_path, pkg_path)])
+
+    main_args = []
+    if opts.bids_dir:
+        command.extend(['-v', ':'.join((opts.bids_dir, '/data', 'ro'))])
+        main_args.append('/data')
+    if opts.output_dir:
+        command.extend(['-v', ':'.join((opts.output_dir, '/out'))])
+        main_args.append('/out')
+    main_args.append(opts.analysis_level)
+
+    if opts.work_dir:
+        command.extend(['-v', ':'.join((opts.work_dir, '/scratch'))])
+        unknown_args.extend(['-w', '/scratch'])
+
+    if opts.config:
+        command.extend(['-v', ':'.join((opts.config,
+                                        '/root/.nipype/nipype.cfg', 'ro'))])
+
+    if opts.shell:
+        command.append('--entrypoint=bash')
+
+    command.append(opts.image)
+
+    # Override help and version to describe underlying program
+    # Respects '-i' flag, so will retrieve information from any image
+    if opts.help:
+        command.append('-h')
+        targethelp = subprocess.check_output(command).decode()
+        print(merge_help(parser.format_help(), targethelp))
+        return 0
+    elif opts.version:
+        # Get version to be run and exit
+        command.append('-v')
+        ret = subprocess.run(command)
+        return ret.returncode
+
+    if not opts.shell:
+        command.extend(main_args)
+        command.extend(unknown_args)
+
+    print("RUNNING: " + ' '.join(command))
+    ret = subprocess.run(command)
+    if ret.returncode:
+        print("fmriprep: Please report errors to {}".format(__bugreports__))
+    return ret.returncode
+
+
+if __name__ == '__main__':
+    sys.exit(main())

fmriprep-docker-0.3.2/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

fmriprep-docker-0.3.2/setup.py

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+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+""" fmriprep wrapper setup script """
+
+from setuptools import setup, find_packages
+from os import path as op
+import runpy
+
+
+def main():
+    """ Install entry-point """
+    this_path = op.abspath(op.dirname(__file__))
+
+    info = runpy.run_path(op.join(this_path, 'fmriprep_docker.py'))
+
+    setup(
+        name=info['__packagename__'],
+        version=info['__version__'],
+        description=info['__description__'],
+        long_description=info['__longdesc__'],
+        author=info['__author__'],
+        author_email=info['__email__'],
+        maintainer=info['__maintainer__'],
+        maintainer_email=info['__email__'],
+        url=info['__url__'],
+        license=info['__license__'],
+        classifiers=info['CLASSIFIERS'],
+        # Dependencies handling
+        setup_requires=[],
+        install_requires=['future'],
+        tests_require=[],
+        extras_require={},
+        dependency_links=[],
+        package_data={},
+        py_modules=["fmriprep_docker"],
+        entry_points={'console_scripts': ['fmriprep-docker=fmriprep_docker:main']},
+        packages=find_packages(),
+        zip_safe=False
+    )
+
+
+if __name__ == '__main__':
+    main()