Merge pull request #1478 from shoshber/installation

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

Author: chrisgorgo

doc/links_names.txt

@@ -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

doc/sphinxext/numpy_ext/numpydoc.py

@@ -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:
@@ -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))
 
@@ -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])

doc/users/install.rst

@@ -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
 -------
 
@@ -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
@@ -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``.
@@ -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.
@@ -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
 ~~~~~~~~~~~~~~~~~~~~~~
@@ -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