fix: docs build without any sphinx errors or warnings

Author: satra

INSTALL

@@ -1,33 +1,8 @@
 .. -*- rst -*- rest mode for emacs
 .. _development-quickstart:
 
-========================
- Development quickstart
-========================
+For installation instructions see documentation:
 
-Source Code
-===========
+http://nipy.org/nipype/
 
-Nipype uses sourceforge_ for our code hosting.  For immediate access
-to the source code, see `the nipype developer wiki
-<http://sourceforge.net/apps/trac/nipy/wiki>`_.
-
-For information on coding style, writing documentation, writing tests
-or using nipy tools, please see the `NIPY developer resources`_ site.
-
-.. _trunk_download:
-
-Check out the current version
-=============================
-
-To access the source code you need subversion_.  You can check out the
-current trunk with the following command::
-
-    svn co https://nipy.svn.sourceforge.net/svnroot/nipy/nipype/trunk/ nipype
-
-Then change into the source directory and install nipype::
-
-    cd nipype
-    python setup.py install
-
-.. include:: doc/links_names.txt
+or doc/users/install.rst

doc/devel/development_quickstart.rst

@@ -76,10 +76,10 @@ Slicer_
   3.6 or later
 
 Nipy_ 
-  0.1.2+20110404 or later (required for doc building)
+  0.1.2+20110404 or later
 
 Nitime_ 
-  (optional; required for doc building)
+  (optional)
 
 Camino_
 
@@ -170,5 +170,4 @@ where, $pathtomatlabdir is the path to your matlab installation and
 $platform is the directory referring to x86 or x64 installations
 (typically glnxa64 on 64-bit installations).
 
-
 .. include:: ../links_names.txt

doc/users/install.rst

@@ -174,7 +174,7 @@ which provides information on each of the options one can assign.
     realignment_parameters: Estimated translation and rotation parameters
 
 
-Our :ref:`interfaces` documentation provides html versions of our
+Our :ref:`interface-index` documentation provides html versions of our
 docstrings and includes links to the specific package
 documentation. For instance, the :class:`nipype.interfaces.fsl.Bet`
 docstring has a direct link to the online BET Documentation.

doc/users/interface_tutorial.rst

@@ -81,8 +81,8 @@ or with amplitudes::
 
 Together with this information, one needs to specify:
 
-- whether the durations and event onsets are specified in terms of scan volumes or
-secs.
+- whether the durations and event onsets are specified in terms of scan volumes
+  or secs.
 
 - the high-pass filter cutoff, 
 

doc/users/model_specification.rst

@@ -66,7 +66,7 @@ Once the clients have been started, any pipeline executed with::
 
 will automatically start getting distributed to the
 clients. Alternatively, a config file may be used to define the
-plugin. See :ref:`config_file_` for details.
+plugin. See :ref:`config_file` for details.
 
 To prevent prevent parallel execution type::
 
@@ -89,7 +89,7 @@ sending a dictionary containing any of the following keys::
  qsub_args - any other command line args to be passed to qsub.
 
 For example, the following snippet executes the workflow on myqueue with
-a custom template:
+a custom template::
  
        workflow.run(plugin='SGE',
           plugin_args=dict(template='mytemplate.sh', qsub_args='-q myqueue')

doc/users/parallel_processing.rst

@@ -47,7 +47,7 @@ Requirements
   Analysis tutorials
 
   - FSL_, FreeSurfer_, Camino_, ConnectomeViewer and MATLAB_ are available and
-  callable from the command line
+    callable from the command line
 
   - SPM_ 5/8 is installed and callable in matlab
 

doc/users/pipeline_tutorial.rst

@@ -4,10 +4,8 @@
    A pipeline example that uses intergrates several interfaces to
    perform a first and second level analysis on a two-subject data
    set.
-"""
 
 
-"""
 1. Tell python where to find the appropriate functions.
 """
 
@@ -45,6 +43,7 @@
 in the provided data set, the nose is behind the head and causes problems for
 segmentation routines
 """
+
 nosestrip = pe.Node(interface=fsl.BET(frac=0.3),
                     name = 'nosestrip')
 skullstrip = pe.Node(interface=fsl.BET(mask = True),
@@ -64,6 +63,7 @@
 """
 skull strip functional data
 """
+
 func_skullstrip = pe.Node(interface=fsl.BET(functional = True),
                           name='stripfunc')
                              #iterfield = ['in_file'])
@@ -72,24 +72,28 @@
 Run FAST on T1 anatomical image to obtain CSF mask.
 Create mask for three tissue types.
 """
+
 getCSFmasks = pe.Node(interface=fsl.FAST(no_pve=True,segments=True),
                       name = 'segment')
 
 """
 Apply registration matrix to CSF segmentation mask.
 """
+
 applyReg2CSFmask = pe.Node(interface=fsl.ApplyXfm(apply_xfm=True),
                            name = 'applyreg2csfmask')
 
 """
 Threshold CSF segmentation mask from  .90 to 1
 """
+
 threshCSFseg = pe.Node(interface = fsl.ImageMaths(op_string = ' -thr .90 -uthr 1 -bin '),
                        name = 'threshcsfsegmask')
 
 """
 Extract CSF timeseries
 """
+
 avgCSF = pe.Node(interface = fsl.ImageMeants(), name='extractcsfts')
 
 
@@ -100,6 +104,7 @@ def pickfirst(files):
 """
 Create the workflow
 """
+
 csffilter = pe.Workflow(name='csffilter')
 csffilter.connect([(extract_ref, motion_correct,[('roi_file', 'ref_file')]),
                    (extract_ref, refskullstrip,[('roi_file', 'in_file')]),
@@ -122,24 +127,28 @@ def pickfirst(files):
    c. Use :class:`nipype.interfaces.spm.SpecifyModel` to generate
    SPM-specific design information.
 """
+
 modelspec = pe.Node(interface=model.SpecifyModel(),  name="modelspec")
 
 """
    d. Use :class:`nipype.interfaces.fsl.Level1Design` to generate a
    run specific fsf file for analysis
 """
+
 level1design = pe.Node(interface=fsl.Level1Design(), name="fsfdesign")
 
 """
    e. Use :class:`nipype.interfaces.fsl.FEATModel` to generate a
    run specific mat file for use by FILMGLS
 """
+
 modelgen = pe.Node(interface=fsl.FEATModel(), name='modelgen')
 
 """
    f. Use :class:`nipype.interfaces.fsl.FILMGLS` to estimate a model
    specified by a mat file and a functional run
 """
+
 modelestimate = pe.Node(interface=fsl.FILMGLS(), name='modelestimate')
                            #iterfield = ['design_file','in_file'])
 
@@ -270,11 +279,3 @@ def subjectinfo(meantsfile):
 
 l1pipeline.run()
 l1pipeline.write_graph()
-
-"""
-Store significant result-files in a special directory
-"""
-#datasink = pe.Node(interface=nio.DataSink(),name='datasink')
-#datasink.inputs.base_directory = os.path.abspath('csffiltered')
-#def getstripdir(subject_id):
-#    return os.path.join(os.path.abspath('nataliaPipeline'),'_subject_id_%s' % subject_id)

examples/afni_dicomconvert.py

@@ -172,6 +172,13 @@ def exfile2rstfile(filename, opts):
     # write converted ReST
     dfile.write(exfile2rst(filename))
 
+    links = """
+
+.. include:: ../../links_names.txt
+
+"""
+    dfile.write(links)
+
     if opts.sourceref:
         # write post example see also box
         msg = """

examples/bet_inputs_gui.py

@@ -33,7 +33,10 @@
 
 .. _examples:
 
-   note_about_examples
+Examples
+========
+
+.. note_about_examples
 """
 #-----------------------------------------------------------------------------
 # Function defintions
@@ -68,6 +71,7 @@ def show():
 sh('../../../tools/ex2rst --project Nipype --outdir . ../../../examples/frontiers_paper')
 
 # Make the index.rst file
+"""
 index = open('index.rst', 'w')
 index.write(examples_header)
 for name in [os.path.splitext(f)[0] for f in glob('*.rst')]:
@@ -76,6 +80,8 @@ def show():
     if name not in(['index','note_about_examples']):
         index.write('   %s\n' % name)
 index.close()
+"""
+
 # Execute each python script in the directory.
 if '--no-exec' in sys.argv:
     pass