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setup.py
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#!/usr/bin/env python
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Nipype : Neuroimaging in Python pipelines and interfaces package.
Nipype intends to create python interfaces to other neuroimaging
packages and create an API for specifying a full analysis pipeline in
python.
Much of the machinery at the beginning of this file has been copied over from
nibabel denoted by ## START - COPIED FROM NIBABEL and a corresponding ## END
"""
# Build helper
from __future__ import print_function
import os
from os.path import join as pjoin
import sys
from glob import glob
from functools import partial
from io import open
# BEFORE importing distutils, remove MANIFEST. distutils doesn't properly
# update it when the contents of directories change.
if os.path.exists('MANIFEST'):
os.remove('MANIFEST')
# For some commands, use setuptools.
if len(set(('develop', 'bdist_egg', 'bdist_rpm', 'bdist', 'bdist_dumb',
'install_egg_info', 'egg_info', 'easy_install', 'bdist_wheel',
'bdist_mpkg')).intersection(sys.argv)) > 0:
# import setuptools setup, thus monkeypatching distutils.
import setup_egg
from setuptools import setup
else:
from distutils.core import setup
# Commit hash writing, and dependency checking
''' Distutils / setuptools helpers from nibabel.nisext'''
from distutils.version import LooseVersion
from distutils.command.build_py import build_py
from distutils import log
PY3 = sys.version_info[0] >= 3
if PY3:
string_types = (str, bytes)
else:
string_types = (basestring, str, unicode)
def get_comrec_build(pkg_dir, build_cmd=build_py):
""" Return extended build command class for recording commit
The extended command tries to run git to find the current commit, getting
the empty string if it fails. It then writes the commit hash into a file
in the `pkg_dir` path, named ``COMMIT_INFO.txt``.
In due course this information can be used by the package after it is
installed, to tell you what commit it was installed from if known.
To make use of this system, you need a package with a COMMIT_INFO.txt file -
e.g. ``myproject/COMMIT_INFO.txt`` - that might well look like this::
# This is an ini file that may contain information about the code state
[commit hash]
# The line below may contain a valid hash if it has been substituted during 'git archive'
archive_subst_hash=$Format:%h$
# This line may be modified by the install process
install_hash=
The COMMIT_INFO file above is also designed to be used with git substitution
- so you probably also want a ``.gitattributes`` file in the root directory
of your working tree that contains something like this::
myproject/COMMIT_INFO.txt export-subst
That will cause the ``COMMIT_INFO.txt`` file to get filled in by ``git
archive`` - useful in case someone makes such an archive - for example with
via the github 'download source' button.
Although all the above will work as is, you might consider having something
like a ``get_info()`` function in your package to display the commit
information at the terminal. See the ``pkg_info.py`` module in the nipy
package for an example.
"""
class MyBuildPy(build_cmd):
''' Subclass to write commit data into installation tree '''
def run(self):
import subprocess
try:
from configparser import ConfigParser
except ImportError:
from ConfigParser import ConfigParser
build_cmd.run(self)
proc = subprocess.Popen('git rev-parse --short HEAD',
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True)
repo_commit, _ = proc.communicate()
# Fix for python 3
repo_commit = '{}'.format(repo_commit)
# We write the installation commit even if it's empty
cfg_parser = ConfigParser()
cfg_parser.read(pjoin(pkg_dir, 'COMMIT_INFO.txt'))
cfg_parser.set('commit hash', 'install_hash', repo_commit)
out_pth = pjoin(self.build_lib, pkg_dir, 'COMMIT_INFO.txt')
if PY3:
cfg_parser.write(open(out_pth, 'wt'))
else:
cfg_parser.write(open(out_pth, 'wb'))
return MyBuildPy
def _add_append_key(in_dict, key, value):
""" Helper for appending dependencies to setuptools args """
# If in_dict[key] does not exist, create it
# If in_dict[key] is a string, make it len 1 list of strings
# Append value to in_dict[key] list
if key not in in_dict:
in_dict[key] = []
elif isinstance(in_dict[key], string_types):
in_dict[key] = [in_dict[key]]
in_dict[key].append(value)
# Dependency checks
def package_check(pkg_name, version=None,
optional=False,
checker=LooseVersion,
version_getter=None,
messages=None,
setuptools_args=None
):
''' Check if package `pkg_name` is present and has good enough version
Has two modes of operation. If `setuptools_args` is None (the default),
raise an error for missing non-optional dependencies and log warnings for
missing optional dependencies. If `setuptools_args` is a dict, then fill
``install_requires`` key value with any missing non-optional dependencies,
and the ``extras_requires`` key value with optional dependencies.
This allows us to work with and without setuptools. It also means we can
check for packages that have not been installed with setuptools to avoid
installing them again.
Parameters
----------
pkg_name : str
name of package as imported into python
version : {None, str}, optional
minimum version of the package that we require. If None, we don't
check the version. Default is None
optional : bool or str, optional
If ``bool(optional)`` is False, raise error for absent package or wrong
version; otherwise warn. If ``setuptools_args`` is not None, and
``bool(optional)`` is not False, then `optional` should be a string
giving the feature name for the ``extras_require`` argument to setup.
checker : callable, optional
callable with which to return comparable thing from version
string. Default is ``distutils.version.LooseVersion``
version_getter : {None, callable}:
Callable that takes `pkg_name` as argument, and returns the
package version string - as in::
``version = version_getter(pkg_name)``
If None, equivalent to::
mod = __import__(pkg_name); version = mod.__version__``
messages : None or dict, optional
dictionary giving output messages
setuptools_args : None or dict
If None, raise errors / warnings for missing non-optional / optional
dependencies. If dict fill key values ``install_requires`` and
``extras_require`` for non-optional and optional dependencies.
'''
setuptools_mode = setuptools_args is not None
optional_tf = bool(optional)
if version_getter is None:
def version_getter(pkg_name):
mod = __import__(pkg_name)
return mod.__version__
if messages is None:
messages = {}
msgs = {
'missing': 'Cannot import package "%s" - is it installed?',
'missing opt': 'Missing optional package "%s"',
'opt suffix': '; you may get run-time errors',
'version too old': 'You have version %s of package "%s"'
' but we need version >= %s', }
msgs.update(messages)
status, have_version = _package_status(pkg_name,
version,
version_getter,
checker)
if status == 'satisfied':
return
if not setuptools_mode:
if status == 'missing':
if not optional_tf:
raise RuntimeError(msgs['missing'] % pkg_name)
log.warn(msgs['missing opt'] % pkg_name +
msgs['opt suffix'])
return
elif status == 'no-version':
raise RuntimeError('Cannot find version for %s' % pkg_name)
assert status == 'low-version'
if not optional_tf:
raise RuntimeError(msgs['version too old'] % (have_version,
pkg_name,
version))
log.warn(msgs['version too old'] % (have_version,
pkg_name,
version) +
msgs['opt suffix'])
return
# setuptools mode
if optional_tf and not isinstance(optional, string_types):
raise RuntimeError('Not-False optional arg should be string')
dependency = pkg_name
if version:
dependency += '>=' + version
if optional_tf:
if 'extras_require' not in setuptools_args:
setuptools_args['extras_require'] = {}
_add_append_key(setuptools_args['extras_require'],
optional,
dependency)
return
# add_append_key(setuptools_args, 'install_requires', dependency)
return
def _package_status(pkg_name, version, version_getter, checker):
try:
__import__(pkg_name)
except ImportError:
return 'missing', None
if not version:
return 'satisfied', None
try:
have_version = version_getter(pkg_name)
except AttributeError:
return 'no-version', None
if checker(have_version) < checker(version):
return 'low-version', have_version
return 'satisfied', have_version
cmdclass = {'build_py': get_comrec_build('nipype')}
# Get version and release info, which is all stored in nipype/info.py
ver_file = os.path.join('nipype', 'info.py')
exec(open(ver_file).read(), locals())
# Prepare setuptools args
if 'setuptools' in sys.modules:
extra_setuptools_args = dict(
tests_require=['nose'],
test_suite='nose.collector',
zip_safe=False,
extras_require=dict(
doc='Sphinx>=0.3',
test='nose>=0.10.1'),
)
pkg_chk = partial(package_check, setuptools_args=extra_setuptools_args)
else:
extra_setuptools_args = {}
pkg_chk = package_check
# Do dependency checking
pkg_chk('networkx', NETWORKX_MIN_VERSION)
pkg_chk('nibabel', NIBABEL_MIN_VERSION)
pkg_chk('numpy', NUMPY_MIN_VERSION)
pkg_chk('scipy', SCIPY_MIN_VERSION)
pkg_chk('traits', TRAITS_MIN_VERSION)
pkg_chk('nose', NOSE_MIN_VERSION)
pkg_chk('future', FUTURE_MIN_VERSION)
pkg_chk('simplejson', SIMPLEJSON_MIN_VERSION)
pkg_chk('prov', PROV_MIN_VERSION)
custom_dateutil_messages = {'missing opt': ('Missing optional package "%s"'
' provided by package '
'"python-dateutil"')}
pkg_chk('dateutil', DATEUTIL_MIN_VERSION,
messages=custom_dateutil_messages)
def main(**extra_args):
thispath, _ = os.path.split(__file__)
testdatafiles = [pjoin('testing', 'data', val)
for val in os.listdir(pjoin(thispath, 'nipype', 'testing', 'data'))
if not os.path.isdir(pjoin(thispath, 'nipype', 'testing', 'data', val))]
testdatafiles+=[
pjoin('testing', 'data', 'dicomdir', '*'),
pjoin('testing', 'data', 'bedpostxout', '*'),
pjoin('testing', 'data', 'tbss_dir', '*'),
pjoin('workflows', 'data', '*'),
pjoin('pipeline', 'engine', 'report_template.html'),
pjoin('external', 'd3.js'),
pjoin('interfaces', 'script_templates', '*'),
pjoin('interfaces', 'tests', 'realign_json.json'),
pjoin('interfaces', 'tests', 'use_resources'),
]
setup(name=NAME,
maintainer=MAINTAINER,
maintainer_email=MAINTAINER_EMAIL,
description=DESCRIPTION,
long_description=LONG_DESCRIPTION,
url=URL,
download_url=DOWNLOAD_URL,
license=LICENSE,
classifiers=CLASSIFIERS,
author=AUTHOR,
author_email=AUTHOR_EMAIL,
platforms=PLATFORMS,
version=VERSION,
install_requires=REQUIRES,
provides=PROVIDES,
packages=['nipype',
'nipype.algorithms',
'nipype.algorithms.tests',
'nipype.caching',
'nipype.caching.tests',
'nipype.external',
'nipype.fixes',
'nipype.fixes.numpy',
'nipype.fixes.numpy.testing',
'nipype.interfaces',
'nipype.interfaces.afni',
'nipype.interfaces.afni.tests',
'nipype.interfaces.ants',
'nipype.interfaces.ants.tests',
'nipype.interfaces.camino',
'nipype.interfaces.camino.tests',
'nipype.interfaces.camino2trackvis',
'nipype.interfaces.camino2trackvis.tests',
'nipype.interfaces.cmtk',
'nipype.interfaces.cmtk.tests',
'nipype.interfaces.diffusion_toolkit',
'nipype.interfaces.diffusion_toolkit.tests',
'nipype.interfaces.dipy',
'nipype.interfaces.dipy.tests',
'nipype.interfaces.elastix',
'nipype.interfaces.elastix.tests',
'nipype.interfaces.freesurfer',
'nipype.interfaces.freesurfer.tests',
'nipype.interfaces.fsl',
'nipype.interfaces.fsl.tests',
'nipype.interfaces.minc',
'nipype.interfaces.minc.tests',
'nipype.interfaces.mipav',
'nipype.interfaces.mipav.tests',
'nipype.interfaces.mne',
'nipype.interfaces.mne.tests',
'nipype.interfaces.mrtrix',
'nipype.interfaces.mrtrix3',
'nipype.interfaces.mrtrix.tests',
'nipype.interfaces.mrtrix3.tests',
'nipype.interfaces.nipy',
'nipype.interfaces.nipy.tests',
'nipype.interfaces.nitime',
'nipype.interfaces.nitime.tests',
'nipype.interfaces.script_templates',
'nipype.interfaces.semtools',
'nipype.interfaces.semtools.brains',
'nipype.interfaces.semtools.brains.tests',
'nipype.interfaces.semtools.diffusion',
'nipype.interfaces.semtools.diffusion.tests',
'nipype.interfaces.semtools.diffusion.tractography',
'nipype.interfaces.semtools.diffusion.tractography.tests',
'nipype.interfaces.semtools.filtering',
'nipype.interfaces.semtools.filtering.tests',
'nipype.interfaces.semtools.legacy',
'nipype.interfaces.semtools.legacy.tests',
'nipype.interfaces.semtools.registration',
'nipype.interfaces.semtools.registration.tests',
'nipype.interfaces.semtools.segmentation',
'nipype.interfaces.semtools.segmentation.tests',
'nipype.interfaces.semtools.testing',
'nipype.interfaces.semtools.tests',
'nipype.interfaces.semtools.utilities',
'nipype.interfaces.semtools.utilities.tests',
'nipype.interfaces.slicer',
'nipype.interfaces.slicer.diffusion',
'nipype.interfaces.slicer.diffusion.tests',
'nipype.interfaces.slicer.filtering',
'nipype.interfaces.slicer.filtering.tests',
'nipype.interfaces.slicer.legacy',
'nipype.interfaces.slicer.legacy.diffusion',
'nipype.interfaces.slicer.legacy.diffusion.tests',
'nipype.interfaces.slicer.legacy.tests',
'nipype.interfaces.slicer.quantification',
'nipype.interfaces.slicer.quantification.tests',
'nipype.interfaces.slicer.registration',
'nipype.interfaces.slicer.registration.tests',
'nipype.interfaces.slicer.segmentation',
'nipype.interfaces.slicer.segmentation.tests',
'nipype.interfaces.slicer.tests',
'nipype.interfaces.spm',
'nipype.interfaces.spm.tests',
'nipype.interfaces.tests',
'nipype.interfaces.vista',
'nipype.interfaces.vista.tests',
'nipype.pipeline',
'nipype.pipeline.engine',
'nipype.pipeline.engine.tests',
'nipype.pipeline.plugins',
'nipype.pipeline.plugins.tests',
'nipype.testing',
'nipype.testing.data',
'nipype.testing.data.bedpostxout',
'nipype.testing.data.dicomdir',
'nipype.testing.data.tbss_dir',
'nipype.utils',
'nipype.utils.tests',
'nipype.workflows',
'nipype.workflows.data',
'nipype.workflows.dmri',
'nipype.workflows.dmri.camino',
'nipype.workflows.dmri.connectivity',
'nipype.workflows.dmri.dipy',
'nipype.workflows.dmri.fsl',
'nipype.workflows.dmri.fsl.tests',
'nipype.workflows.dmri.mrtrix',
'nipype.workflows.fmri',
'nipype.workflows.fmri.fsl',
'nipype.workflows.fmri.fsl.tests',
'nipype.workflows.fmri.spm',
'nipype.workflows.fmri.spm.tests',
'nipype.workflows.graph',
'nipype.workflows.misc',
'nipype.workflows.rsfmri',
'nipype.workflows.rsfmri.fsl',
'nipype.workflows.smri',
'nipype.workflows.smri.ants',
'nipype.workflows.smri.freesurfer',
'nipype.workflows.warp'],
# The package_data spec has no effect for me (on python 2.6) -- even
# changing to data_files doesn't get this stuff included in the source
# distribution -- not sure if it has something to do with the magic
# above, but distutils is surely the worst piece of code in all of
# python -- duplicating things into MANIFEST.in but this is admittedly
# only a workaround to get things started -- not a solution
package_data={'nipype': testdatafiles},
scripts=glob('bin/*') + ['nipype/external/fsl_imglob.py'],
cmdclass=cmdclass,
**extra_args
)
if __name__ == "__main__":
main(**extra_setuptools_args)