[ENH] Pypi packaging

CHANGES.rst

@@ -1,10 +1,12 @@
+Release 0.0.2
+=============
+
 Release 0.0.1
 =============
 
 * [ENH] Added Docker images
 * [DOC] Added base code for automatic publication to RTD.
-* Set up CircleCI
-* Added downsampled dataset for running smoke tests.
+* Set up CircleCI with a first smoke test on one subject.
 * BIDS tree scrubbing and subject-session-run selection.
 * Refactored big workflow into consistent pieces.
 * Migrated Craig's original code

MANIFEST.in

@@ -0,0 +1,7 @@
+#documentation
+recursive-include docs/_build/html *
+
+#Misc
+include requirements.txt
+include CHANGES.rst
+include LICENSE

fmriprep/__init__.py

@@ -11,15 +11,39 @@
 
 from .workflows.base import fmri_preprocess
 
+__version__ = '0.0.2'
+
 
 __author__ = 'The CRN developers'
 __copyright__ = 'Copyright 2016, Center for Reproducible Neuroscience, Stanford University'
 __credits__ = ['Craig Moodie', 'Ross Blair', 'Oscar Esteban', 'Chris F. Gorgolewski',
                'Russell A. Poldrack']
 __license__ = '3-clause BSD'
-__version__ = '0.0.1'
-__maintainer__ = 'Oscar Esteban'
+__maintainer__ = 'Ross Blair'
 __email__ = 'crn.poldracklab@gmail.com'
 __status__ = 'Prototype'
 __url__ = 'https://github.com/poldracklab/preprocessing-workflow'
 __packagename__ = 'fmriprep'
+
+__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 functional magnetic resonance image preprocessing 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. This open-source neuroimaging data processing tool
+is being developed as a part of the MRI image analysis and reproducibility platform offered by the
+CRN. This pipeline is heavily influenced by the `Human Connectome Project analysis pipelines
+<https://github.com/Washington-University/Pipelines>`_ and, as such, the backbone of this pipeline
+is a python reimplementation of the HCP `GenericfMRIVolumeProcessingPipeline.sh` script. However, a
+major difference is that this pipeline is executed using a `nipype workflow framework
+<http://nipype.readthedocs.io/en/latest/>`_. This allows for each call to a software module or binary
+to be controlled within the workflows, which removes the need for manual curation at every stage, while
+still providing all the output and error information that would be necessary for debugging and interpretation
+purposes. The fmriprep pipeline primarily utilizes FSL tools, but also utilizes ANTs tools at several stages
+such as skull stripping and template registration. This pipeline was designed to provide the best software
+implementation for each state of preprocessing, and will be updated as newer and better neuroimaging software
+become available.
+"""

fmriprep/run_workflow.py

@@ -3,12 +3,16 @@
 # @Author: oesteban
 # @Date:   2015-11-19 16:44:27
 # @Last Modified by:   oesteban
-# @Last Modified time: 2016-05-11 12:05:47
-
+# @Last Modified time: 2016-05-11 13:30:01
 """
 fMRI preprocessing workflow
 =====
 """
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
+
 from argparse import ArgumentParser
 from argparse import RawTextHelpFormatter
 from multiprocessing import cpu_count
@@ -23,6 +27,7 @@
 from .utils.misc import get_subject
 from .viz.pipeline_reports import generate_report_workflow
 
+
 def preproc_and_reports(imaging_data, name='preproc_and_reports', settings=None):
     preproc_wf = fmri_preprocess_single(settings=settings)
     report_wf = generate_report_workflow()

requirements.txt

@@ -1,37 +1,5 @@
-cycler==0.10.0
-decorator==4.0.9
--e git+https://github.com/rwblair/preprocessing-workflow.git@d4bf97c6d69e01a73569c4f238b9ce890175832c#egg=fmriprep
-funcsigs==0.4
-future==0.15.2
-html5lib==0.9999999
-lockfile==0.12.2
-lxml==3.6.0
-matplotlib==1.5.1
-mock==1.3.0
-mriqc==0.0.4a1
-networkx==1.11
-nibabel==2.0.2
+numpy
+matplotlib
+nibabel
 -e git+https://github.com/oesteban/nipype@3b8528cb2eac0b5d321ea90d1094ebdc1cec7d1a#egg=nipype
-nilearn==0.2.4
-nitime==0.6
-nose==1.3.7
-numpy==1.10.4
-pandas==0.18.0
-pbr==1.8.1
-pi==0.1.2
-Pillow==3.1.1
-prov==1.4.0
-pyparsing==2.1.0
-PyPDF2==1.25.1
-python-dateutil==2.5.0
-pytz==2016.1
-PyYAML==3.11
-reportlab==3.3.0
-scipy==0.17.0
-seaborn==0.7.0
-sklearn==0.0
-simplejson==3.8.2
-six==1.10.0
-traits==4.5.0
-xhtml2pdf==0.0.6
-xvfbwrapper==0.2.8
+

setup.py

@@ -3,12 +3,13 @@
 # @Author: oesteban
 # @Date:   2015-11-19 16:44:27
 # @Last Modified by:   oesteban
-# @Last Modified time: 2016-05-11 13:41:58
+# @Last Modified time: 2016-05-11 14:32:37
 """ fmriprep setup script """
 import os
 import sys
 
-from fmriprep import __version__, __email__, __url__, __packagename__, __license__
+from fmriprep import (__version__, __email__, __url__, __packagename__, __license__,
+                      __description__, __longdesc__)
 
 
 REQ_LINKS = []
@@ -31,7 +32,8 @@ def main():
     setup(
         name=__packagename__,
         version=__version__,
-        description='',
+        description=__description__,
+        long_description=__longdesc__,
         author_email=__email__,
         url=__url__,
         download_url='https://pypi.python.org/packages/source/f/fmriprep/'
@@ -49,6 +51,7 @@ def main():
             'Topic :: Scientific/Engineering :: Biomedical Imaging',
             'License :: OSI Approved :: 3-clause BSD License',
             'Programming Language :: Python :: 2.7',
+            'Programming Language :: Python :: 3.5'
         ],
     )