Improved documentation

Author: chrisgorgo

CHANGES

@@ -28,6 +28,7 @@ Next Release
 * ENH: New data grabbing interface that works over SSH connections, SSHDataGrabber
 * ENH: New color mode for write_graph
 * ENH: You can now force MapNodes to be run serially
+* ENH: Support for headless mode using Xvfb
 * FIX: MRTrix tracking algorithms were ignoring mask parameters.
 * FIX: FNIRT registration pathway and associated OpenFMRI example script
 * FIX: spm12b compatibility for Model estimate

doc/devel/interface_specs.rst

@@ -404,6 +404,9 @@ If you used genfile:
 
 And optionally:
 
+* ``_redirect_x``: If set to True it will make Nipype start Xvfb before running the interface and redirect X output to it. This is useful for
+commandlines that spawn a graphical user interface.
+
 * ``_format_arg(name, spec, value)``: For extra formatting of the input values before passing them to generic ``_parse_inputs()`` method.
 
 For example this is the class definition for Flirt, minus the docstring::

doc/users/index.rst

@@ -36,6 +36,7 @@
    model_specification
    saving_workflows
    spmmcr
+   mipav
 
 
 

nipype/testing/data/pyscript.m

@@ -1,6 +1,14 @@
 fprintf(1,'Executing %s at %s:\n',mfilename,datestr(now));
 ver,
-try,a=1;
+try,
+if isempty(which('spm')),
+throw(MException('SPMCheck:NotFound','SPM not in matlab path'));
+end;
+spm_path = spm('dir');
+[name, version] = spm('ver');
+fprintf(1, 'NIPYPE path:%s|name:%s|release:%s', spm_path, name, version);
+exit;
+        
 ,catch ME,
 fprintf(2,'MATLAB code threw an exception:\n');
 fprintf(2,'%s\n',ME.message);

tools/run_examples.py

@@ -26,7 +26,7 @@ def run_examples(example, pipelines, plugin):
                 'fmri_spm_nested':['level1','l2pipeline'],
                 'fmri_spm_dartel':['level1','l2pipeline'],
                 'fmri_fsl_feeds':['l1pipeline']}
-    plugins = ['Linear', 'MultiProc', 'IPython']
+    plugins = ['IPython']
     for plugin in plugins:
         for example, pipelines in examples.items():
             run_examples(example, pipelines, plugin)