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Merged
merged 3 commits into from
May 24, 2016
Merged

DOC:add instructions to install; fix doc build for python 3 #1478

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a95c5de
add instructions to install; fix doc build for python 3
May 17, 2016
7c25f3e
more installation instructions; fix link to nose
May 18, 2016
542f681
remove confusing references to nibabel in install instructions
May 18, 2016
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2 changes: 1 addition & 1 deletion doc/links_names.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@
.. _doctest-mode: http://www.cis.upenn.edu/~edloper/projects/doctestmode/
.. _bazaar: http://bazaar-vcs.org/
.. _subversion: http://subversion.tigris.org/
.. _nose: http://somethingaboutorange.com/mrl/projects/nose
.. _nose: http://nose.readthedocs.io/en/latest/
.. _`python coverage tester`: http://nedbatchelder.com/code/modules/coverage.html

.. Other python projects
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6 changes: 3 additions & 3 deletions doc/sphinxext/numpy_ext/numpydoc.py
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Expand Up @@ -40,7 +40,7 @@ def mangle_docstrings(app, what, name, obj, options, lines,

if what == 'module':
# Strip top title
title_re = re.compile(ur'^\s*[#*=]{4,}\n[a-z0-9 -]+\n[#*=]{4,}\s*',
title_re = re.compile(r'^\s*[#*=]{4,}\n[a-z0-9 -]+\n[#*=]{4,}\s*',
re.I | re.S)
lines[:] = title_re.sub(u'', u"\n".join(lines)).split(u"\n")
else:
Expand All @@ -61,7 +61,7 @@ def mangle_docstrings(app, what, name, obj, options, lines,
references = []
for line in lines:
line = line.strip()
m = re.match(ur'^.. \[([a-z0-9_.-])\]', line, re.I)
m = re.match(r'^.. \[([a-z0-9_.-])\]', line, re.I)
if m:
references.append(m.group(1))

Expand All @@ -70,7 +70,7 @@ def mangle_docstrings(app, what, name, obj, options, lines,
if references:
for i, line in enumerate(lines):
for r in references:
if re.match(ur'^\d+$', r):
if re.match(r'^\d+$', r):
new_r = u"R%d" % (reference_offset[0] + int(r))
else:
new_r = u"%s%d" % (r, reference_offset[0])
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31 changes: 20 additions & 11 deletions doc/users/install.rst
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Expand Up @@ -21,6 +21,10 @@ To check out the latest development version::

git clone git://github.com/nipy/nipype.git

or::

git clone https://github.com/nipy/nipype.git

Install
-------

Expand All @@ -46,9 +50,8 @@ Mac OS X
~~~~~~~~

The easiest way to get nipype running on Mac OS X is to install Anaconda_ or
Canopy_ and then add nibabel and nipype by executing::
Canopy_ and then add nipype by executing::

easy_install nibabel
easy_install nipype

From source
Expand All @@ -58,6 +61,7 @@ If you downloaded the source distribution named something
like ``nipype-x.y.tar.gz``, then unpack the tarball, change into the
``nipype-x.y`` directory and install nipype using::

pip install -r requirements.txt
python setup.py install

**Note:** Depending on permissions you may need to use ``sudo``.
Expand Down Expand Up @@ -107,10 +111,15 @@ recommendations.
Must Have
~~~~~~~~~

Python_ 2.7
.. note::

Full distributions of Nipype, such as the ones in Anaconda_ or Canopy_, provide
the following packages automatically.

Nibabel_ 1.0 - 1.4
Neuroimaging file i/o library
Neuroimaging file i/o library.

Python_ 2.7

NetworkX_ 1.0 - 1.8
Python package for working with complex networks.
Expand All @@ -124,10 +133,6 @@ Enthought_ Traits_ 4.0.0 - 4.3.0

Dateutil 1.5 -

.. note::

Full distributions such as Anaconda_ or Canopy_ provide the above packages,
except Nibabel_.

Strong Recommendations
~~~~~~~~~~~~~~~~~~~~~~
Expand All @@ -140,18 +145,22 @@ Matplotlib_ 1.0 - 1.2
Plotting library

`RDFLib <http://rdflib.readthedocs.org/en/latest/>`_ 4.1
RDFLibrary required for provenance export as RDF
RDFLibrary required for provenance export as RDF

Sphinx_ 1.1
Required for building the documentation

`Graphviz <http://www.graphviz.org/>`_
Required for building the documentation
Required for building the documentation. The python wrapper package (``graphviz``)
and the program itself both need to be installed.

Interface Dependencies
~~~~~~~~~~~~~~~~~~~~~~

These are the software packages that nipype.interfaces wraps:
You might not need some of the following packages, depending on what exactly you
want to use nipype for. If you do need any of them, install nipype's wrapper package
(``nipype.interfaces``), then install the programs separately onto your computer, just
like you would install any other app.

FSL_
4.1.0 or later
Expand Down