Merge pull request #152 from oesteban/py3/setup.py

[FIX] setup.py in python 3

Dockerfile

@@ -50,7 +50,7 @@ RUN pip install -r requirements.txt
 
 COPY . fmriprep/
 RUN cd fmriprep && \
-    pip install -e .
+    pip install -e .[all]
 
 WORKDIR /root/
 COPY build/files/run_* /usr/bin/

fmriprep/info.py

@@ -1,10 +1,10 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """
 Base module variables
 """
+from __future__ import unicode_literals
 
 __version__ = '0.1.1a3'
 __author__ = 'The CRN developers'
@@ -39,3 +39,46 @@
 implementation for each state of preprocessing, and will be updated as newer and better neuroimaging software
 become available.
 """
+
+DOWNLOAD_URL = ('https://pypi.python.org/packages/source/f/fmriprep/' +
+                'fmriprep-%s.tar.gz').format('__version__')
+
+REQUIRES = [
+    'numpy',
+    'lockfile',
+    'future',
+    'scikit-learn',
+    'matplotlib',
+    'nilearn',
+    'sklearn',
+    'nibabel',
+    'niworkflows>=0.0.3a3',
+    'grabbit'
+]
+
+LINKS_REQUIRES = [
+    'git+https://github.com/nipy/nipype.git@master#egg=nipype',
+    'git+https://github.com/incf/pybids.git@master#egg=pybids'
+]
+
+TESTS_REQUIRES = [
+    "mock",
+    "codecov"
+]
+
+EXTRA_REQUIRES = {
+    'doc': ['sphinx'],
+    'tests': TESTS_REQUIRES,
+    'duecredit': ['duecredit']
+}
+
+# Enable a handle to install all extra dependencies at once
+EXTRA_REQUIRES['all'] = [val for _, val in list(EXTRA_REQUIRES.items())]
+CLASSIFIERS = [
+    'Development Status :: 3 - Alpha',
+    'Intended Audience :: MRI processing',
+    'Topic :: Scientific/Engineering :: Biomedical Imaging',
+    'License :: OSI Approved :: 3-clause BSD License',
+    'Programming Language :: Python :: 2.7',
+    'Programming Language :: Python :: 3.5'
+]

fmriprep/run_workflow.py

@@ -3,33 +3,26 @@
 # @Author: oesteban
 # @Date:   2015-11-19 16:44:27
 # @Last Modified by:   oesteban
-# @Last Modified time: 2016-08-30 16:52:12
+# @Last Modified time: 2016-09-13 13:37:43
 """
 fMRI preprocessing workflow
 =====
 """
-from __future__ import absolute_import
-from __future__ import division
-from __future__ import print_function
-from __future__ import unicode_literals
+from __future__ import absolute_import, division, print_function, unicode_literals
 
+import os
+import os.path as op
+import glob
 from argparse import ArgumentParser
 from argparse import RawTextHelpFormatter
+from multiprocessing import cpu_count
 from lockfile import LockFile
 
-import logging
-from multiprocessing import cpu_count
-import os
-import os.path as op
-import glob
+
 
 def main():
     """Entry point"""
-    from nipype import config as ncfg
-    from nipype.pipeline import engine as pe
     from fmriprep import __version__
-    from fmriprep.workflows import base as fwb
-    from fmriprep.workflows.base import base_workflow_enumerator
     parser = ArgumentParser(description='fMRI Preprocessing workflow',
                             formatter_class=RawTextHelpFormatter)
 
@@ -74,6 +67,14 @@ def main():
                          help='use ANTs-based skull-stripping')
 
     opts = parser.parse_args()
+    create_workflow(opts)
+
+
+def create_workflow(opts):
+    import logging
+    from nipype import config as ncfg
+    from fmriprep.workflows import base as fwb
+    from fmriprep.workflows.base import base_workflow_enumerator
 
     settings = {
         'bids_root': op.abspath(opts.bids_dir),
@@ -115,10 +116,6 @@ def main():
 
     logger.addHandler(logging.FileHandler(op.join(log_dir, 'run_workflow')))
 
-    # Warn for default work/output directories
-    if settings['work_dir'] == parser.get_default('work_dir'):
-        logger.info('Using default working directory (%s)', settings['work_dir'])
-
     # Set nipype config
     ncfg.update_config({
         'logging': {'log_directory': log_dir, 'log_to_file': True},
@@ -157,6 +154,5 @@ def main():
     if opts.write_graph:
         preproc_wf.write_graph()
 
-
 if __name__ == '__main__':
     main()

requirements.txt

@@ -1,11 +1,2 @@
 -e git+https://github.com/nipy/nipype.git@master#egg=nipype
 -e git+https://github.com/incf/pybids.git@master#egg=pybids
-numpy
-lockfile
-future
-scikit-learn
-matplotlib
-nilearn
-sklearn
-nibabel
-niworkflows>=0.0.3a3

setup.py

@@ -2,70 +2,53 @@
 # -*- coding: utf-8 -*-
 # @Author: oesteban
 # @Date:   2015-11-19 16:44:27
-# @Last Modified by:   oesteban
-# @Last Modified time: 2016-08-29 18:50:54
 """ fmriprep setup script """
-import os
-import sys
 
 
 def main():
     """ Install entry-point """
+    from io import open
+    from os import path as op
     from glob import glob
     from inspect import getfile, currentframe
     from setuptools import setup, find_packages
 
-    this_path = os.path.dirname(os.path.abspath(getfile(currentframe())))
-    # Read vars from info file
-    module_file =os.path.join(this_path, 'fmriprep', 'info.py')
-    with open(module_file) as fvars:
-       exec(compile(fvars.read(), module_file, 'exec'))
+    this_path = op.dirname(op.abspath(getfile(currentframe())))
 
-    REQ_LINKS = []
-    with open('requirements.txt', 'r') as rfile:
-        REQUIREMENTS = [line.strip() for line in rfile.readlines()]
-
-    for i, req in enumerate(REQUIREMENTS):
-        if req.startswith('-e'):
-            REQUIREMENTS[i] = req.split('=')[1]
-            REQ_LINKS.append(req.split()[1])
-
-    if REQUIREMENTS is None:
-        REQUIREMENTS = []
+    # Python 3: use a locals dictionary
+    # http://stackoverflow.com/a/1463370/6820620
+    ldict = locals()
+    # Get version and release info, which is all stored in fmriprep/info.py
+    module_file = op.join(this_path, 'fmriprep', 'info.py')
+    with open(module_file) as infofile:
+        pythoncode = [line for line in infofile.readlines() if not line.strip().startswith('#')]
+        exec('\n'.join(pythoncode), globals(), ldict)
 
     setup(
-        name=__packagename__,
-        version=__version__,
-        description=__description__,
-        long_description=__longdesc__,
-        author=__author__,
-        author_email='cmoodie@stanford.edu',
-        email=__email__,
-        maintainer=__maintainer__,
-        maintainer_email=__email__,
-        url=__url__,
-        download_url='https://pypi.python.org/packages/source/f/fmriprep/'
-                     'fmriprep-%s.tar.gz' % __version__,
-        license=__license__,
+        name=ldict['__packagename__'],
+        version=ldict['__version__'],
+        description=ldict['__description__'],
+        long_description=ldict['__longdesc__'],
+        author=ldict['__author__'],
+        author_email=ldict['__email__'],
+        email=ldict['__email__'],
+        maintainer=ldict['__maintainer__'],
+        maintainer_email=ldict['__email__'],
+        url=ldict['__url__'],
+        license=ldict['__license__'],
+        classifiers=ldict['CLASSIFIERS'],
+        download_url=ldict['DOWNLOAD_URL'],
+        # Dependencies handling
+        setup_requires=[],
+        install_requires=ldict['REQUIRES'],
+        tests_require=ldict['TESTS_REQUIRES'],
+        extras_require=ldict['EXTRA_REQUIRES'],
+        dependency_links=ldict['LINKS_REQUIRES'],
+        package_data={'fmriprep': ['data/*.json']},
         entry_points={'console_scripts': ['fmriprep=fmriprep.run_workflow:main',]},
         packages=find_packages(),
-        package_data={'fmriprep': ['data/*.json']},
-        install_requires=REQUIREMENTS,
-        dependency_links=REQ_LINKS,
-        zip_safe=False,
-        classifiers=[
-            'Development Status :: 3 - Alpha',
-            'Intended Audience :: MRI processing',
-            'Topic :: Scientific/Engineering :: Biomedical Imaging',
-            'License :: OSI Approved :: 3-clause BSD License',
-            'Programming Language :: Python :: 2.7',
-            'Programming Language :: Python :: 3.5'
-        ],
+        zip_safe=False
     )
 
 if __name__ == '__main__':
-    LOCAL_PATH = os.path.dirname(os.path.abspath(sys.argv[0]))
-    os.chdir(LOCAL_PATH)
-    sys.path.insert(0, LOCAL_PATH)
-
     main()