From 76eb88165b6faa0f06115f751f5c3b4864a8d955 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Mon, 20 Mar 2017 19:28:18 -0700
Subject: [PATCH 1/9] [ENH] Sphinx extension to plot workflows

Close #1873
---
 doc/conf.py                       |   1 +
 nipype/sphinxext/__init__.py      |   5 +
 nipype/sphinxext/plot_workflow.py | 670 ++++++++++++++++++++++++++++++
 3 files changed, 676 insertions(+)
 create mode 100644 nipype/sphinxext/__init__.py
 create mode 100644 nipype/sphinxext/plot_workflow.py

diff --git a/doc/conf.py b/doc/conf.py
index 9ed5c87da9..b69379d9a0 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -52,6 +52,7 @@
               'numpy_ext.numpydoc',
               'matplotlib.sphinxext.plot_directive',
               'matplotlib.sphinxext.only_directives',
+              'nipype.sphinxext.plot_workflow',
               #'IPython.sphinxext.ipython_directive',
               #'IPython.sphinxext.ipython_console_highlighting'
               ]
diff --git a/nipype/sphinxext/__init__.py b/nipype/sphinxext/__init__.py
new file mode 100644
index 0000000000..b2033960f3
--- /dev/null
+++ b/nipype/sphinxext/__init__.py
@@ -0,0 +1,5 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+from __future__ import print_function, division, absolute_import, unicode_literals
diff --git a/nipype/sphinxext/plot_workflow.py b/nipype/sphinxext/plot_workflow.py
new file mode 100644
index 0000000000..11428858da
--- /dev/null
+++ b/nipype/sphinxext/plot_workflow.py
@@ -0,0 +1,670 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""
+A directive for including a nipype workflow graph in a Sphinx document.
+
+By default, in HTML output, `workflow` will include a .png file with a
+link to a high-res .png.  In LaTeX output, it will include a
+.pdf.
+The source code for the workflow may be included as **inline content** to
+the directive::
+       .. workflow::
+          from mriqc.workflows.anatomical import airmsk_wf
+          wf = airmsk_wf()
+
+
+Options
+-------
+
+The ``workflow`` directive supports the following options:
+    format : {'python', 'doctest'}
+        Specify the format of the input
+    include-source : bool
+        Whether to display the source code. The default can be changed
+        using the `workflow_include_source` variable in conf.py
+    encoding : str
+        If this source file is in a non-UTF8 or non-ASCII encoding,
+        the encoding must be specified using the `:encoding:` option.
+        The encoding will not be inferred using the ``-*- coding -*-``
+        metacomment.
+
+Additionally, this directive supports all of the options of the
+`image` directive, except for `target` (since workflow will add its own
+target).  These include `alt`, `height`, `width`, `scale`, `align` and
+`class`.
+
+Configuration options
+---------------------
+The workflow directive has the following configuration options:
+    wf_include_source
+        Default value for the include-source option
+    wf_html_show_source_link
+        Whether to show a link to the source in HTML.
+    wf_pre_code
+        Code that should be executed before each workflow.
+    wf_basedir
+        Base directory, to which ``workflow::`` file names are relative
+        to.  (If None or empty, file names are relative to the
+        directory where the file containing the directive is.)
+    wf_formats
+        File formats to generate. List of tuples or strings::
+            [(suffix, dpi), suffix, ...]
+        that determine the file format and the DPI. For entries whose
+        DPI was omitted, sensible defaults are chosen. When passing from
+        the command line through sphinx_build the list should be passed as
+        suffix:dpi,suffix:dpi, ....
+    wf_html_show_formats
+        Whether to show links to the files in HTML.
+    wf_rcparams
+        A dictionary containing any non-standard rcParams that should
+        be applied before each workflow.
+    wf_apply_rcparams
+        By default, rcParams are applied when `context` option is not used in
+        a workflow directive.  This configuration option overrides this behavior
+        and applies rcParams before each workflow.
+    wf_working_directory
+        By default, the working directory will be changed to the directory of
+        the example, so the code can get at its data files, if any.  Also its
+        path will be added to `sys.path` so it can import any helper modules
+        sitting beside it.  This configuration option can be used to specify
+        a central directory (also added to `sys.path`) where data files and
+        helper modules for all code are located.
+    wf_template
+        Provide a customized template for preparing restructured text.
+
+"""
+from __future__ import print_function, division, absolute_import, unicode_literals
+
+import sys, os, shutil, io, re, textwrap
+from os.path import relpath
+import traceback
+
+from docutils.parsers.rst import directives
+from docutils.parsers.rst.directives.images import Image
+
+from mriqc.utils.misc import check_folder as mkdirs
+
+
+
+try:
+    # Sphinx depends on either Jinja or Jinja2
+    import jinja2
+    def format_template(template, **kw):
+        return jinja2.Template(template).render(**kw)
+except ImportError:
+    import jinja
+    def format_template(template, **kw):
+        return jinja.from_string(template, **kw)
+
+from builtins import str, bytes
+align = Image.align
+
+PY2 = sys.version_info[0] == 2
+PY3 = sys.version_info[0] == 3
+
+
+def wf_directive(name, arguments, options, content, lineno,
+                   content_offset, block_text, state, state_machine):
+    return run(arguments, content, options, state_machine, state, lineno)
+wf_directive.__doc__ = __doc__
+
+def _option_boolean(arg):
+    if not arg or not arg.strip():
+        # no argument given, assume used as a flag
+        return True
+    elif arg.strip().lower() in ('no', '0', 'false'):
+        return False
+    elif arg.strip().lower() in ('yes', '1', 'true'):
+        return True
+    else:
+        raise ValueError('"%s" unknown boolean' % arg)
+
+
+def _option_context(arg):
+    if arg in [None, 'reset', 'close-figs']:
+        return arg
+    raise ValueError("argument should be None or 'reset' or 'close-figs'")
+
+
+def _option_format(arg):
+    return directives.choice(arg, ('python', 'doctest'))
+
+
+def _option_align(arg):
+    return directives.choice(arg, ("top", "middle", "bottom", "left", "center",
+                                   "right"))
+
+
+def mark_wf_labels(app, document):
+    """
+    To make graphs referenceable, we need to move the reference from
+    the "htmlonly" (or "latexonly") node to the actual figure node
+    itself.
+    """
+    for name, explicit in list(document.nametypes.items()):
+        if not explicit:
+            continue
+        labelid = document.nameids[name]
+        if labelid is None:
+            continue
+        node = document.ids[labelid]
+        if node.tagname in ('html_only', 'latex_only'):
+            for n in node:
+                if n.tagname == 'figure':
+                    sectname = name
+                    for c in n:
+                        if c.tagname == 'caption':
+                            sectname = c.astext()
+                            break
+
+                    node['ids'].remove(labelid)
+                    node['names'].remove(name)
+                    n['ids'].append(labelid)
+                    n['names'].append(name)
+                    document.settings.env.labels[name] = \
+                        document.settings.env.docname, labelid, sectname
+                    break
+
+
+def setup(app):
+    setup.app = app
+    setup.config = app.config
+    setup.confdir = app.confdir
+
+    options = {'alt': directives.unchanged,
+               'height': directives.length_or_unitless,
+               'width': directives.length_or_percentage_or_unitless,
+               'scale': directives.nonnegative_int,
+               'align': _option_align,
+               'class': directives.class_option,
+               'include-source': _option_boolean,
+               'format': _option_format,
+               'context': _option_context,
+               'nofigs': directives.flag,
+               'encoding': directives.encoding
+               }
+
+    app.add_directive('workflow', wf_directive, True, (0, 2, False), **options)
+    app.add_config_value('wf_pre_code', None, True)
+    app.add_config_value('wf_include_source', False, True)
+    app.add_config_value('wf_html_show_source_link', True, True)
+    app.add_config_value('wf_formats', ['png', 'hires.png', 'pdf'], True)
+    app.add_config_value('wf_basedir', None, True)
+    app.add_config_value('wf_html_show_formats', True, True)
+    app.add_config_value('wf_rcparams', {}, True)
+    app.add_config_value('wf_apply_rcparams', False, True)
+    app.add_config_value('wf_working_directory', None, True)
+    app.add_config_value('wf_template', None, True)
+
+    app.connect('doctree-read'.encode() if PY2 else 'doctree-read', mark_wf_labels)
+
+    metadata = {'parallel_read_safe': True, 'parallel_write_safe': True}
+    return metadata
+
+
+#------------------------------------------------------------------------------
+# Doctest handling
+#------------------------------------------------------------------------------
+
+def contains_doctest(text):
+    try:
+        # check if it's valid Python as-is
+        compile(text, '<string>', 'exec')
+        return False
+    except SyntaxError:
+        pass
+    r = re.compile(r'^\s*>>>', re.M)
+    m = r.search(text)
+    return bool(m)
+
+
+def unescape_doctest(text):
+    """
+    Extract code from a piece of text, which contains either Python code
+    or doctests.
+    """
+    if not contains_doctest(text):
+        return text
+
+    code = ""
+    for line in text.split("\n"):
+        m = re.match(r'^\s*(>>>|\.\.\.) (.*)$', line)
+        if m:
+            code += m.group(2) + "\n"
+        elif line.strip():
+            code += "# " + line.strip() + "\n"
+        else:
+            code += "\n"
+    return code
+
+
+def remove_coding(text):
+    """
+    Remove the coding comment, which exec doesn't like.
+    """
+    sub_re = re.compile("^#\s*-\*-\s*coding:\s*.*-\*-$", flags=re.MULTILINE)
+    return sub_re.sub("", text)
+
+#------------------------------------------------------------------------------
+# Template
+#------------------------------------------------------------------------------
+
+
+TEMPLATE = """
+{{ source_code }}
+{{ only_html }}
+   {% if source_link or (html_show_formats and not multi_image) %}
+   (
+   {%- if source_link -%}
+   `Source code <{{ source_link }}>`__
+   {%- endif -%}
+   {%- if html_show_formats and not multi_image -%}
+     {%- for img in images -%}
+       {%- for fmt in img.formats -%}
+         {%- if source_link or not loop.first -%}, {% endif -%}
+         `{{ fmt }} <{{ dest_dir }}/{{ img.basename }}.{{ fmt }}>`__
+       {%- endfor -%}
+     {%- endfor -%}
+   {%- endif -%}
+   )
+   {% endif %}
+   {% for img in images %}
+   .. figure:: {{ build_dir }}/{{ img.basename }}.{{ default_fmt }}
+      {% for option in options -%}
+      {{ option }}
+      {% endfor %}
+      {% if html_show_formats and multi_image -%}
+        (
+        {%- for fmt in img.formats -%}
+        {%- if not loop.first -%}, {% endif -%}
+        `{{ fmt }} <{{ dest_dir }}/{{ img.basename }}.{{ fmt }}>`__
+        {%- endfor -%}
+        )
+      {%- endif -%}
+      {{ caption }}
+   {% endfor %}
+{{ only_latex }}
+   {% for img in images %}
+   {% if 'pdf' in img.formats -%}
+   .. figure:: {{ build_dir }}/{{ img.basename }}.pdf
+      {% for option in options -%}
+      {{ option }}
+      {% endfor %}
+      {{ caption }}
+   {% endif -%}
+   {% endfor %}
+{{ only_texinfo }}
+   {% for img in images %}
+   .. image:: {{ build_dir }}/{{ img.basename }}.png
+      {% for option in options -%}
+      {{ option }}
+      {% endfor %}
+   {% endfor %}
+"""
+
+exception_template = """
+.. htmlonly::
+   [`source code <%(linkdir)s/%(basename)s.py>`__]
+Exception occurred rendering plot.
+"""
+
+# the context of the plot for all directives specified with the
+# :context: option
+wf_context = dict()
+
+class ImageFile(object):
+    def __init__(self, basename, dirname):
+        self.basename = basename
+        self.dirname = dirname
+        self.formats = []
+
+    def filename(self, fmt):
+        return os.path.join(self.dirname, "%s.%s" % (self.basename, fmt))
+
+    def filenames(self):
+        return [self.filename(fmt) for fmt in self.formats]
+
+
+def out_of_date(original, derived):
+    """
+    Returns True if derivative is out-of-date wrt original,
+    both of which are full file paths.
+    """
+    return (not os.path.exists(derived) or
+            (os.path.exists(original) and
+             os.stat(derived).st_mtime < os.stat(original).st_mtime))
+
+
+class GraphError(RuntimeError):
+    pass
+
+
+def run_code(code, code_path, ns=None, function_name=None):
+    """
+    Import a Python module from a path, and run the function given by
+    name, if function_name is not None.
+    """
+
+    # Change the working directory to the directory of the example, so
+    # it can get at its data files, if any.  Add its path to sys.path
+    # so it can import any helper modules sitting beside it.
+    pwd = str(os.getcwd())
+    old_sys_path = list(sys.path)
+    if setup.config.wf_working_directory is not None:
+        try:
+            os.chdir(setup.config.wf_working_directory)
+        except OSError as err:
+            raise OSError(str(err) + '\n`wf_working_directory` option in'
+                          'Sphinx configuration file must be a valid '
+                          'directory path')
+        except TypeError as err:
+            raise TypeError(str(err) + '\n`wf_working_directory` option in '
+                            'Sphinx configuration file must be a string or '
+                            'None')
+        sys.path.insert(0, setup.config.wf_working_directory)
+    elif code_path is not None:
+        dirname = os.path.abspath(os.path.dirname(code_path))
+        os.chdir(dirname)
+        sys.path.insert(0, dirname)
+
+    # Reset sys.argv
+    old_sys_argv = sys.argv
+    sys.argv = [code_path]
+
+    # Redirect stdout
+    stdout = sys.stdout
+    if PY3:
+        sys.stdout = io.StringIO()
+    else:
+        from cStringIO import StringIO
+        sys.stdout = StringIO()
+
+    # Assign a do-nothing print function to the namespace.  There
+    # doesn't seem to be any other way to provide a way to (not) print
+    # that works correctly across Python 2 and 3.
+    def _dummy_print(*arg, **kwarg):
+        pass
+
+    try:
+        try:
+            code = unescape_doctest(code)
+            if ns is None:
+                ns = {}
+            if not ns:
+                if setup.config.wf_pre_code is not None:
+                    exec(str(setup.config.wf_pre_code), ns)
+            ns['print'] = _dummy_print
+            if "__main__" in code:
+                exec("__name__ = '__main__'", ns)
+            code = remove_coding(code)
+            exec(code, ns)
+            if function_name is not None:
+                exec(function_name + "()", ns)
+        except (Exception, SystemExit) as err:
+            raise GraphError(traceback.format_exc())
+    finally:
+        os.chdir(pwd)
+        sys.argv = old_sys_argv
+        sys.path[:] = old_sys_path
+        sys.stdout = stdout
+    return ns
+
+
+def get_wf_formats(config):
+    default_dpi = {'png': 80, 'hires.png': 200, 'pdf': 200}
+    formats = []
+    wf_formats = config.wf_formats
+    if isinstance(wf_formats, (str, bytes)):
+        # String Sphinx < 1.3, Split on , to mimic
+        # Sphinx 1.3 and later. Sphinx 1.3 always
+        # returns a list.
+        wf_formats = wf_formats.split(',')
+    for fmt in wf_formats:
+        if isinstance(fmt, (str, bytes)):
+            if ':' in fmt:
+                suffix, dpi = fmt.split(':')
+                formats.append((str(suffix), int(dpi)))
+            else:
+                formats.append((fmt, default_dpi.get(fmt, 80)))
+        elif isinstance(fmt, (tuple, list)) and len(fmt) == 2:
+            formats.append((str(fmt[0]), int(fmt[1])))
+        else:
+            raise GraphError('invalid image format "%r" in wf_formats' % fmt)
+    return formats
+
+
+def render_figures(code, code_path, output_dir, output_base, context,
+                   function_name, config, context_reset=False,
+                   close_figs=False):
+    """
+    Run a nipype workflow creation script and save the graph in *output_dir*.
+    Save the images under *output_dir* with file names derived from
+    *output_base*
+    """
+    formats = get_wf_formats(config)
+
+    ns = wf_context if context else {}
+    if context_reset:
+        wf_context.clear()
+
+    run_code(code, code_path, ns, function_name)
+    img = ImageFile(output_base, output_dir)
+
+    for fmt, dpi in formats:
+        try:
+            img_path = img.filename(fmt)
+            imgname, ext = os.path.splitext(os.path.basename(img_path))
+            ns['wf'].base_dir = output_dir
+            ns['wf'].write_graph(imgname, format=ext[1:])
+
+            src = os.path.join(os.path.dirname(img_path), ns['wf'].name,
+                               os.path.basename(img_path))
+            print(src, img_path)
+            shutil.move(src, img_path)
+        except Exception as err:
+            raise GraphError(traceback.format_exc())
+
+        img.formats.append(fmt)
+
+    return [(code, [img])]
+
+
+def run(arguments, content, options, state_machine, state, lineno):
+    document = state_machine.document
+    config = document.settings.env.config
+    nofigs = 'nofigs' in options
+
+    formats = get_wf_formats(config)
+    default_fmt = formats[0][0]
+
+    options.setdefault('include-source', config.wf_include_source)
+    keep_context = 'context' in options
+    context_opt = None if not keep_context else options['context']
+
+    rst_file = document.attributes['source']
+    rst_dir = os.path.dirname(rst_file)
+
+    if len(arguments):
+        if not config.wf_basedir:
+            source_file_name = os.path.join(setup.app.builder.srcdir,
+                                            directives.uri(arguments[0]))
+        else:
+            source_file_name = os.path.join(setup.confdir, config.wf_basedir,
+                                            directives.uri(arguments[0]))
+
+        # If there is content, it will be passed as a caption.
+        caption = '\n'.join(content)
+
+        # If the optional function name is provided, use it
+        if len(arguments) == 2:
+            function_name = arguments[1]
+        else:
+            function_name = None
+
+        with io.open(source_file_name, 'r', encoding='utf-8') as fd:
+            code = fd.read()
+        output_base = os.path.basename(source_file_name)
+    else:
+        source_file_name = rst_file
+        code = textwrap.dedent("\n".join([str(c) for c in content]))
+        counter = document.attributes.get('_wf_counter', 0) + 1
+        document.attributes['_wf_counter'] = counter
+        base, _ = os.path.splitext(os.path.basename(source_file_name))
+        output_base = '%s-%d.py' % (base, counter)
+        function_name = None
+        caption = ''
+
+    base, source_ext = os.path.splitext(output_base)
+    if source_ext in ('.py', '.rst', '.txt'):
+        output_base = base
+    else:
+        source_ext = ''
+
+    # ensure that LaTeX includegraphics doesn't choke in foo.bar.pdf filenames
+    output_base = output_base.replace('.', '-')
+
+    # is it in doctest format?
+    is_doctest = contains_doctest(code)
+    if 'format' in options:
+        if options['format'] == 'python':
+            is_doctest = False
+        else:
+            is_doctest = True
+
+    # determine output directory name fragment
+    source_rel_name = relpath(source_file_name, setup.confdir)
+    source_rel_dir = os.path.dirname(source_rel_name)
+    while source_rel_dir.startswith(os.path.sep):
+        source_rel_dir = source_rel_dir[1:]
+
+    # build_dir: where to place output files (temporarily)
+    build_dir = os.path.join(os.path.dirname(setup.app.doctreedir),
+                             'wf_directive',
+                             source_rel_dir)
+    # get rid of .. in paths, also changes pathsep
+    # see note in Python docs for warning about symbolic links on Windows.
+    # need to compare source and dest paths at end
+    build_dir = os.path.normpath(build_dir)
+
+    if not os.path.exists(build_dir):
+        os.makedirs(build_dir)
+
+    # output_dir: final location in the builder's directory
+    dest_dir = os.path.abspath(os.path.join(setup.app.builder.outdir,
+                                            source_rel_dir))
+    if not os.path.exists(dest_dir):
+        os.makedirs(dest_dir) # no problem here for me, but just use built-ins
+
+    # how to link to files from the RST file
+    dest_dir_link = os.path.join(relpath(setup.confdir, rst_dir),
+                                 source_rel_dir).replace(os.path.sep, '/')
+    try:
+        build_dir_link = relpath(build_dir, rst_dir).replace(os.path.sep, '/')
+    except ValueError:
+        # on Windows, relpath raises ValueError when path and start are on
+        # different mounts/drives
+        build_dir_link = build_dir
+    source_link = dest_dir_link + '/' + output_base + source_ext
+
+    # make figures
+    try:
+        results = render_figures(code,
+                                 source_file_name,
+                                 build_dir,
+                                 output_base,
+                                 keep_context,
+                                 function_name,
+                                 config,
+                                 context_reset=context_opt == 'reset',
+                                 close_figs=context_opt == 'close-figs')
+        errors = []
+    except GraphError as err:
+        reporter = state.memo.reporter
+        sm = reporter.system_message(
+            2, "Exception occurred in plotting %s\n from %s:\n%s" % (output_base,
+                                                source_file_name, err),
+            line=lineno)
+        results = [(code, [])]
+        errors = [sm]
+
+    # Properly indent the caption
+    caption = '\n'.join('      ' + line.strip()
+                        for line in caption.split('\n'))
+
+    # generate output restructuredtext
+    total_lines = []
+    for j, (code_piece, images) in enumerate(results):
+        if options['include-source']:
+            if is_doctest:
+                lines = ['']
+                lines += [row.rstrip() for row in code_piece.split('\n')]
+            else:
+                lines = ['.. code-block:: python', '']
+                lines += ['    %s' % row.rstrip()
+                          for row in code_piece.split('\n')]
+            source_code = "\n".join(lines)
+        else:
+            source_code = ""
+
+        if nofigs:
+            images = []
+
+        opts = [':%s: %s' % (key, val) for key, val in list(options.items())
+                if key in ('alt', 'height', 'width', 'scale', 'align', 'class')]
+
+        only_html = ".. only:: html"
+        only_latex = ".. only:: latex"
+        only_texinfo = ".. only:: texinfo"
+
+        # Not-None src_link signals the need for a source link in the generated
+        # html
+        if j == 0 and config.wf_html_show_source_link:
+            src_link = source_link
+        else:
+            src_link = None
+
+        result = format_template(
+            config.wf_template or TEMPLATE,
+            default_fmt=default_fmt,
+            dest_dir=dest_dir_link,
+            build_dir=build_dir_link,
+            source_link=src_link,
+            multi_image=len(images) > 1,
+            only_html=only_html,
+            only_latex=only_latex,
+            only_texinfo=only_texinfo,
+            options=opts,
+            images=images,
+            source_code=source_code,
+            html_show_formats=config.wf_html_show_formats and len(images),
+            caption=caption)
+
+        total_lines.extend(result.split("\n"))
+        total_lines.extend("\n")
+
+    if total_lines:
+        state_machine.insert_input(total_lines, source=source_file_name)
+
+    # copy image files to builder's output directory, if necessary
+    if not os.path.exists(dest_dir):
+        mkdirs(dest_dir)
+
+    for code_piece, images in results:
+        for img in images:
+            for fn in img.filenames():
+                destimg = os.path.join(dest_dir, os.path.basename(fn))
+                if fn != destimg:
+                    shutil.copyfile(fn, destimg)
+
+    # copy script (if necessary)
+    target_name = os.path.join(dest_dir, output_base + source_ext)
+    with io.open(target_name, 'w', encoding="utf-8") as f:
+        if source_file_name == rst_file:
+            code_escaped = unescape_doctest(code)
+        else:
+            code_escaped = code
+        f.write(code_escaped)
+
+    return errors

From 805ba528614273201a8084f878007b9c4d7b63c4 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Mon, 20 Mar 2017 23:38:22 -0700
Subject: [PATCH 2/9] support graph2html and simple_form options

---
 doc/conf.py                         |  3 +-
 nipype/info.py                      |  2 +-
 nipype/pipeline/engine/utils.py     | 24 ++++++-----
 nipype/pipeline/engine/workflows.py | 10 +++--
 nipype/sphinxext/plot_workflow.py   | 65 +++++++++++++++++------------
 5 files changed, 62 insertions(+), 42 deletions(-)

diff --git a/doc/conf.py b/doc/conf.py
index b69379d9a0..116ff3f36e 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -42,12 +42,11 @@
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = ['sphinx.ext.todo',
-              'sphinx.ext.pngmath',
+              'sphinx.ext.imgmath',
               'sphinx.ext.inheritance_diagram',
               'sphinx.ext.graphviz',
               'sphinx.ext.autodoc',
               'sphinx.ext.doctest',
-              'sphinx.ext.pngmath',
               'sphinx.ext.autosummary',
               'numpy_ext.numpydoc',
               'matplotlib.sphinxext.plot_directive',
diff --git a/nipype/info.py b/nipype/info.py
index 81a8adce0a..c70b555ee3 100644
--- a/nipype/info.py
+++ b/nipype/info.py
@@ -152,7 +152,7 @@ def get_nipype_gitversion():
 ]
 
 EXTRA_REQUIRES = {
-    'doc': ['Sphinx>=0.3', 'matplotlib', 'pydotplus'],
+    'doc': ['Sphinx>=1.4', 'matplotlib', 'pydotplus'],
     'tests': TESTS_REQUIRES,
     'fmri': ['nitime', 'nilearn', 'dipy', 'nipy', 'matplotlib'],
     'profiler': ['psutil'],
diff --git a/nipype/pipeline/engine/utils.py b/nipype/pipeline/engine/utils.py
index ce2f927b15..0211de16f6 100644
--- a/nipype/pipeline/engine/utils.py
+++ b/nipype/pipeline/engine/utils.py
@@ -1018,20 +1018,18 @@ def export_graph(graph_in, base_dir=None, show=False, use_execgraph=False,
                                suffix='_detailed.dot',
                                use_ext=False,
                                newpath=base_dir)
-    logger.info('Creating detailed dot file: %s' % outfname)
     _write_detailed_dot(graph, outfname)
     cmd = 'dot -T%s -O %s' % (format, outfname)
     res = CommandLine(cmd, terminal_output='allatonce').run()
     if res.runtime.returncode:
         logger.warn('dot2png: %s', res.runtime.stderr)
     pklgraph = _create_dot_graph(graph, show_connectinfo, simple_form)
-    outfname = fname_presuffix(dotfilename,
-                               suffix='.dot',
-                               use_ext=False,
-                               newpath=base_dir)
-    nx.drawing.nx_pydot.write_dot(pklgraph, outfname)
-    logger.info('Creating dot file: %s' % outfname)
-    cmd = 'dot -T%s -O %s' % (format, outfname)
+    simplefname = fname_presuffix(dotfilename,
+                                  suffix='.dot',
+                                  use_ext=False,
+                                  newpath=base_dir)
+    nx.drawing.nx_pydot.write_dot(pklgraph, simplefname)
+    cmd = 'dot -T%s -O %s' % (format, simplefname)
     res = CommandLine(cmd, terminal_output='allatonce').run()
     if res.runtime.returncode:
         logger.warn('dot2png: %s', res.runtime.stderr)
@@ -1041,6 +1039,10 @@ def export_graph(graph_in, base_dir=None, show=False, use_execgraph=False,
         if show_connectinfo:
             nx.draw_networkx_edge_labels(pklgraph, pos)
 
+    if format != 'dot':
+        outfname += '.%s' % format
+    return outfname
+
 
 def format_dot(dotfilename, format=None):
     """Dump a directed graph (Linux only; install via `brew` on OSX)"""
@@ -1052,8 +1054,10 @@ def format_dot(dotfilename, format=None):
             raise IOError("Cannot draw directed graph; executable 'dot' is unavailable")
         else:
             raise ioe
-    else:
-        logger.info('Converting dotfile: %s to %s format' % (dotfilename, format))
+
+    if format != 'dot':
+        dotfilename += '.%s' % format
+    return dotfilename
 
 
 def make_output_dir(outdir):
diff --git a/nipype/pipeline/engine/workflows.py b/nipype/pipeline/engine/workflows.py
index 5a8c5eed56..50b47c63a9 100644
--- a/nipype/pipeline/engine/workflows.py
+++ b/nipype/pipeline/engine/workflows.py
@@ -429,15 +429,19 @@ def write_graph(self, dotfilename='graph.dot', graph2use='hierarchical',
             self.write_hierarchical_dotfile(dotfilename=dotfilename,
                                             colored=graph2use == "colored",
                                             simple_form=simple_form)
-            format_dot(dotfilename, format=format)
+            outfname = format_dot(dotfilename, format=format)
         else:
             graph = self._graph
             if graph2use in ['flat', 'exec']:
                 graph = self._create_flat_graph()
             if graph2use == 'exec':
                 graph = generate_expanded_graph(deepcopy(graph))
-            export_graph(graph, base_dir, dotfilename=dotfilename,
-                         format=format, simple_form=simple_form)
+            outfname = export_graph(graph, base_dir, dotfilename=dotfilename,
+                                    format=format, simple_form=simple_form)
+
+        logger.info('Generated workflow graph: %s (graph2use=%s, simple_form=%s).' % (
+            outfname, graph2use, simple_form))
+        return outfname
 
     def write_hierarchical_dotfile(self, dotfilename=None, colored=False,
                                    simple_form=True):
diff --git a/nipype/sphinxext/plot_workflow.py b/nipype/sphinxext/plot_workflow.py
index 11428858da..1d7aed5082 100644
--- a/nipype/sphinxext/plot_workflow.py
+++ b/nipype/sphinxext/plot_workflow.py
@@ -10,6 +10,7 @@
 .pdf.
 The source code for the workflow may be included as **inline content** to
 the directive::
+
        .. workflow::
           from mriqc.workflows.anatomical import airmsk_wf
           wf = airmsk_wf()
@@ -38,6 +39,11 @@
 Configuration options
 ---------------------
 The workflow directive has the following configuration options:
+    graph2use
+        Select a graph type to use
+    simple_form
+        determines if the node name shown in the visualization is either of the form nodename
+        (package) when set to True or nodename.Class.package when set to False.
     wf_include_source
         Default value for the include-source option
     wf_html_show_source_link
@@ -121,6 +127,8 @@ def _option_boolean(arg):
     else:
         raise ValueError('"%s" unknown boolean' % arg)
 
+def _option_graph2use(arg):
+    return directives.choice(arg, ('hierarchical', 'colored', 'flat', 'orig', 'exec'))
 
 def _option_context(arg):
     if arg in [None, 'reset', 'close-figs']:
@@ -183,14 +191,18 @@ def setup(app):
                'format': _option_format,
                'context': _option_context,
                'nofigs': directives.flag,
-               'encoding': directives.encoding
+               'encoding': directives.encoding,
+               'graph2use': _option_graph2use,
+               'simple_form': _option_boolean
                }
 
     app.add_directive('workflow', wf_directive, True, (0, 2, False), **options)
+    app.add_config_value('graph2use', 'hierarchical', 'html')
+    app.add_config_value('simple_form', True, 'html')
     app.add_config_value('wf_pre_code', None, True)
     app.add_config_value('wf_include_source', False, True)
     app.add_config_value('wf_html_show_source_link', True, True)
-    app.add_config_value('wf_formats', ['png', 'hires.png', 'pdf'], True)
+    app.add_config_value('wf_formats', ['png', 'svg', 'pdf'], True)
     app.add_config_value('wf_basedir', None, True)
     app.add_config_value('wf_html_show_formats', True, True)
     app.add_config_value('wf_rcparams', {}, True)
@@ -255,21 +267,6 @@ def remove_coding(text):
 TEMPLATE = """
 {{ source_code }}
 {{ only_html }}
-   {% if source_link or (html_show_formats and not multi_image) %}
-   (
-   {%- if source_link -%}
-   `Source code <{{ source_link }}>`__
-   {%- endif -%}
-   {%- if html_show_formats and not multi_image -%}
-     {%- for img in images -%}
-       {%- for fmt in img.formats -%}
-         {%- if source_link or not loop.first -%}, {% endif -%}
-         `{{ fmt }} <{{ dest_dir }}/{{ img.basename }}.{{ fmt }}>`__
-       {%- endfor -%}
-     {%- endfor -%}
-   {%- endif -%}
-   )
-   {% endif %}
    {% for img in images %}
    .. figure:: {{ build_dir }}/{{ img.basename }}.{{ default_fmt }}
       {% for option in options -%}
@@ -285,6 +282,21 @@ def remove_coding(text):
       {%- endif -%}
       {{ caption }}
    {% endfor %}
+   {% if source_link or (html_show_formats and not multi_image) %}
+   (
+   {%- if source_link -%}
+   `Source code <{{ source_link }}>`__
+   {%- endif -%}
+   {%- if html_show_formats and not multi_image -%}
+     {%- for img in images -%}
+       {%- for fmt in img.formats -%}
+         {%- if source_link or not loop.first -%}, {% endif -%}
+         `{{ fmt }} <{{ dest_dir }}/{{ img.basename }}.{{ fmt }}>`__
+       {%- endfor -%}
+     {%- endfor -%}
+   {%- endif -%}
+   )
+   {% endif %}
 {{ only_latex }}
    {% for img in images %}
    {% if 'pdf' in img.formats -%}
@@ -411,7 +423,6 @@ def _dummy_print(*arg, **kwarg):
         sys.stdout = stdout
     return ns
 
-
 def get_wf_formats(config):
     default_dpi = {'png': 80, 'hires.png': 200, 'pdf': 200}
     formats = []
@@ -436,15 +447,14 @@ def get_wf_formats(config):
 
 
 def render_figures(code, code_path, output_dir, output_base, context,
-                   function_name, config, context_reset=False,
-                   close_figs=False):
+                   function_name, config, graph2use, simple_form,
+                   context_reset=False, close_figs=False):
     """
     Run a nipype workflow creation script and save the graph in *output_dir*.
     Save the images under *output_dir* with file names derived from
     *output_base*
     """
     formats = get_wf_formats(config)
-
     ns = wf_context if context else {}
     if context_reset:
         wf_context.clear()
@@ -457,11 +467,9 @@ def render_figures(code, code_path, output_dir, output_base, context,
             img_path = img.filename(fmt)
             imgname, ext = os.path.splitext(os.path.basename(img_path))
             ns['wf'].base_dir = output_dir
-            ns['wf'].write_graph(imgname, format=ext[1:])
-
-            src = os.path.join(os.path.dirname(img_path), ns['wf'].name,
-                               os.path.basename(img_path))
-            print(src, img_path)
+            src = ns['wf'].write_graph(imgname, format=ext[1:],
+                                       graph2use=graph2use,
+                                       simple_form=simple_form)
             shutil.move(src, img_path)
         except Exception as err:
             raise GraphError(traceback.format_exc())
@@ -479,6 +487,9 @@ def run(arguments, content, options, state_machine, state, lineno):
     formats = get_wf_formats(config)
     default_fmt = formats[0][0]
 
+    graph2use = options.get('graph2use', 'hierarchical')
+    simple_form = options.get('simple_form', True)
+
     options.setdefault('include-source', config.wf_include_source)
     keep_context = 'context' in options
     context_opt = None if not keep_context else options['context']
@@ -577,6 +588,8 @@ def run(arguments, content, options, state_machine, state, lineno):
                                  keep_context,
                                  function_name,
                                  config,
+                                 graph2use,
+                                 simple_form,
                                  context_reset=context_opt == 'reset',
                                  close_figs=context_opt == 'close-figs')
         errors = []

From b0b9d84b692a91df70a4c011a69e4eeb6a3f3e5f Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Mon, 20 Mar 2017 23:52:00 -0700
Subject: [PATCH 3/9] update CHANGES

---
 CHANGES | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGES b/CHANGES
index 970422b3b4..891df66bb6 100644
--- a/CHANGES
+++ b/CHANGES
@@ -1,6 +1,7 @@
 Upcoming Release
 =====================
 
+* ENH: Sphinx extension to plot workflows (https://github.com/nipy/nipype/pull/1896)
 * ENH: Added non-steady state detector for EPI data (https://github.com/nipy/nipype/pull/1839)
 * ENH: Enable new BBRegister init options for FSv6+ (https://github.com/nipy/nipype/pull/1811)
 * REF: Splits nipype.interfaces.utility into base, csv, and wrappers (https://github.com/nipy/nipype/pull/1828)
@@ -22,7 +23,7 @@ Upcoming Release
 
 0.13.0-rc1 (January 4, 2017)
 ===============================
- 
+
 * FIX: Compatibility with traits 4.6 (https://github.com/nipy/nipype/pull/1770)
 * FIX: Multiproc deadlock (https://github.com/nipy/nipype/pull/1756)
 * TST: Replace nose and unittest with pytest (https://github.com/nipy/nipype/pull/1722, https://github.com/nipy/nipype/pull/1751)

From 35c2e5db82c04491c7b5741995de31a914c6f051 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Tue, 21 Mar 2017 09:21:10 -0700
Subject: [PATCH 4/9] remove mriqc leftovers

---
 nipype/sphinxext/plot_workflow.py | 41 ++++++++++++++++++++++++-------
 nipype/utils/filemanip.py         | 13 ++++++++++
 2 files changed, 45 insertions(+), 9 deletions(-)

diff --git a/nipype/sphinxext/plot_workflow.py b/nipype/sphinxext/plot_workflow.py
index 1d7aed5082..0aea845f01 100644
--- a/nipype/sphinxext/plot_workflow.py
+++ b/nipype/sphinxext/plot_workflow.py
@@ -3,23 +3,49 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """
+
+
+:mod:`nipype.sphinxext.plot_workflow` -- Workflow plotting extension
+====================================================================
+
+
 A directive for including a nipype workflow graph in a Sphinx document.
 
+This code is forked from the plot_figure sphinx extension of matplotlib.
+
 By default, in HTML output, `workflow` will include a .png file with a
 link to a high-res .png.  In LaTeX output, it will include a
 .pdf.
 The source code for the workflow may be included as **inline content** to
-the directive::
+the directive `workflow`::
+
+  .. workflow:
+      :graph2use: flat
+      :simple_form: no
+
+      from nipype.workflows.dmri.camino.connectivity_mapping import create_connectivity_pipeline
+      wf = create_connectivity_pipeline()
 
-       .. workflow::
-          from mriqc.workflows.anatomical import airmsk_wf
-          wf = airmsk_wf()
+
+For example, the following graph has been generated inserting the previous
+code block in this documentation:
+
+.. workflow:
+  :graph2use: flat
+  :simple_form: no
+
+  from nipype.workflows.dmri.camino.connectivity_mapping import create_connectivity_pipeline
+  wf = create_connectivity_pipeline()
 
 
 Options
 -------
 
 The ``workflow`` directive supports the following options:
+    graph2use : {'hierarchical', 'colored', 'flat', 'orig', 'exec'}
+        Specify the type of graph to be generated.
+    simple_form: bool
+        Whether the graph will be in detailed or simple form.
     format : {'python', 'doctest'}
         Specify the format of the input
     include-source : bool
@@ -90,8 +116,7 @@
 from docutils.parsers.rst import directives
 from docutils.parsers.rst.directives.images import Image
 
-from mriqc.utils.misc import check_folder as mkdirs
-
+from nipype.utils.filemanip import mkdirp
 
 
 try:
@@ -661,9 +686,7 @@ def run(arguments, content, options, state_machine, state, lineno):
         state_machine.insert_input(total_lines, source=source_file_name)
 
     # copy image files to builder's output directory, if necessary
-    if not os.path.exists(dest_dir):
-        mkdirs(dest_dir)
-
+    mkdirp(dest_dir)
     for code_piece, images in results:
         for img in images:
             for fn in img.filenames():
diff --git a/nipype/utils/filemanip.py b/nipype/utils/filemanip.py
index cbf32392eb..8ac4b5dda0 100644
--- a/nipype/utils/filemanip.py
+++ b/nipype/utils/filemanip.py
@@ -16,6 +16,7 @@
 import hashlib
 from hashlib import md5
 import os
+from errno import EEXIST
 import re
 import shutil
 import posixpath
@@ -425,6 +426,18 @@ def copyfiles(filelist, dest, copy=False, create_new=False):
             newfiles.insert(i, destfile)
     return newfiles
 
+def mkdirp(folder):
+    """
+    Equivalent to bash's mkdir -p
+    """
+    if not os.path.exists(folder):
+        try:
+            os.makedirs(folder)
+        except OSError as exc:
+            if not exc.errno == EEXIST:
+                raise
+    return folder
+
 
 def filename_to_list(filename):
     """Returns a list given either a string or a list

From 5ed4683635a6bc04b8ea59100bd4e44379feacd4 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Tue, 21 Mar 2017 09:21:26 -0700
Subject: [PATCH 5/9] add documentation

---
 doc/documentation.rst    |  2 ++
 doc/users/index.rst      |  2 ++
 doc/users/sphinx_ext.rst | 15 +++++++++++++++
 3 files changed, 19 insertions(+)
 create mode 100644 doc/users/sphinx_ext.rst

diff --git a/doc/documentation.rst b/doc/documentation.rst
index 8ca2e503c8..3468525492 100644
--- a/doc/documentation.rst
+++ b/doc/documentation.rst
@@ -24,10 +24,12 @@ Previous versions:  `0.12.0 <http://nipype.readthedocs.io/en/0.12.0/>`_ `0.11.0
             :maxdepth: 2
 
             users/index
+            
          .. toctree::
             :maxdepth: 1
 
             changes
+
        * Developer
 
          .. toctree::
diff --git a/doc/users/index.rst b/doc/users/index.rst
index c9cbcd961b..3c39ce08b2 100644
--- a/doc/users/index.rst
+++ b/doc/users/index.rst
@@ -39,6 +39,8 @@
    mipav
    nipypecmd
    aws
+   resource_sched_profiler
+   sphinx_ext
 
 
 
diff --git a/doc/users/sphinx_ext.rst b/doc/users/sphinx_ext.rst
new file mode 100644
index 0000000000..11748287d0
--- /dev/null
+++ b/doc/users/sphinx_ext.rst
@@ -0,0 +1,15 @@
+
+.. _sphinx_ext:
+
+Sphinx extensions
+-----------------
+
+
+To help users document their *Nipype*-based code, the software is shipped
+with a set of extensions (currently only one) to customize the appearance
+and simplify the generation process.
+
+.. automodule:: nipype.sphinxext.plot_workflow
+    :members:
+    :undoc-members:
+    :show-inheritance:

From 88b3ec4bcf9ec117787cfc7437ae9b4385a3d697 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Tue, 21 Mar 2017 09:34:47 -0700
Subject: [PATCH 6/9] added resource profiling to user docs, example not
 working

close #1526
---
 doc/users/sphinx_ext.rst          | 3 +--
 nipype/sphinxext/plot_workflow.py | 3 +--
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/doc/users/sphinx_ext.rst b/doc/users/sphinx_ext.rst
index 11748287d0..6326a6041a 100644
--- a/doc/users/sphinx_ext.rst
+++ b/doc/users/sphinx_ext.rst
@@ -10,6 +10,5 @@ with a set of extensions (currently only one) to customize the appearance
 and simplify the generation process.
 
 .. automodule:: nipype.sphinxext.plot_workflow
-    :members:
     :undoc-members:
-    :show-inheritance:
+    :noindex:
\ No newline at end of file
diff --git a/nipype/sphinxext/plot_workflow.py b/nipype/sphinxext/plot_workflow.py
index 0aea845f01..e50a4dfdd8 100644
--- a/nipype/sphinxext/plot_workflow.py
+++ b/nipype/sphinxext/plot_workflow.py
@@ -3,8 +3,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """
-
-
 :mod:`nipype.sphinxext.plot_workflow` -- Workflow plotting extension
 ====================================================================
 
@@ -64,6 +62,7 @@
 
 Configuration options
 ---------------------
+
 The workflow directive has the following configuration options:
     graph2use
         Select a graph type to use

From 5e7fac9424e1af3562463da251ced0945585cdbf Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Tue, 21 Mar 2017 12:39:01 -0700
Subject: [PATCH 7/9] fix example of use of the new workflow directive

---
 nipype/sphinxext/plot_workflow.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nipype/sphinxext/plot_workflow.py b/nipype/sphinxext/plot_workflow.py
index e50a4dfdd8..726c5df88c 100644
--- a/nipype/sphinxext/plot_workflow.py
+++ b/nipype/sphinxext/plot_workflow.py
@@ -17,7 +17,7 @@
 The source code for the workflow may be included as **inline content** to
 the directive `workflow`::
 
-  .. workflow:
+  .. workflow ::
       :graph2use: flat
       :simple_form: no
 
@@ -28,7 +28,7 @@
 For example, the following graph has been generated inserting the previous
 code block in this documentation:
 
-.. workflow:
+.. workflow ::
   :graph2use: flat
   :simple_form: no
 

From e173327b256dcdd5293e64129920b394f749d4c3 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Wed, 22 Mar 2017 10:44:25 -0700
Subject: [PATCH 8/9] check that folder is a folder in mkdirp

---
 nipype/utils/filemanip.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/nipype/utils/filemanip.py b/nipype/utils/filemanip.py
index 8ac4b5dda0..3d31ac66fd 100644
--- a/nipype/utils/filemanip.py
+++ b/nipype/utils/filemanip.py
@@ -430,12 +430,12 @@ def mkdirp(folder):
     """
     Equivalent to bash's mkdir -p
     """
-    if not os.path.exists(folder):
-        try:
-            os.makedirs(folder)
-        except OSError as exc:
-            if not exc.errno == EEXIST:
-                raise
+    try:
+        os.makedirs(folder)
+    except OSError as exc:
+        if exc.errno != EEXIST or not os.path.isdir(folder):
+            raise
+
     return folder
 
 

From 1f6335bdcc6ced28593ad4c4b2d823453d062662 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Wed, 22 Mar 2017 19:13:45 -0700
Subject: [PATCH 9/9] make mkdirp private

---
 nipype/sphinxext/plot_workflow.py | 21 ++++++++++++++++++---
 nipype/utils/filemanip.py         | 13 -------------
 2 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/nipype/sphinxext/plot_workflow.py b/nipype/sphinxext/plot_workflow.py
index 726c5df88c..1ed10aef42 100644
--- a/nipype/sphinxext/plot_workflow.py
+++ b/nipype/sphinxext/plot_workflow.py
@@ -110,13 +110,12 @@
 
 import sys, os, shutil, io, re, textwrap
 from os.path import relpath
+from errno import EEXIST
 import traceback
 
 from docutils.parsers.rst import directives
 from docutils.parsers.rst.directives.images import Image
 
-from nipype.utils.filemanip import mkdirp
-
 
 try:
     # Sphinx depends on either Jinja or Jinja2
@@ -134,6 +133,22 @@ def format_template(template, **kw):
 PY2 = sys.version_info[0] == 2
 PY3 = sys.version_info[0] == 3
 
+def _mkdirp(folder):
+    """
+    Equivalent to bash's mkdir -p
+    """
+    if sys.version_info > (3, 4, 1):
+        os.makedirs(folder, exist_ok=True)
+        return folder
+
+    try:
+        os.makedirs(folder)
+    except OSError as exc:
+        if exc.errno != EEXIST or not os.path.isdir(folder):
+            raise
+
+    return folder
+
 
 def wf_directive(name, arguments, options, content, lineno,
                    content_offset, block_text, state, state_machine):
@@ -685,7 +700,7 @@ def run(arguments, content, options, state_machine, state, lineno):
         state_machine.insert_input(total_lines, source=source_file_name)
 
     # copy image files to builder's output directory, if necessary
-    mkdirp(dest_dir)
+    _mkdirp(dest_dir)
     for code_piece, images in results:
         for img in images:
             for fn in img.filenames():
diff --git a/nipype/utils/filemanip.py b/nipype/utils/filemanip.py
index 3d31ac66fd..cbf32392eb 100644
--- a/nipype/utils/filemanip.py
+++ b/nipype/utils/filemanip.py
@@ -16,7 +16,6 @@
 import hashlib
 from hashlib import md5
 import os
-from errno import EEXIST
 import re
 import shutil
 import posixpath
@@ -426,18 +425,6 @@ def copyfiles(filelist, dest, copy=False, create_new=False):
             newfiles.insert(i, destfile)
     return newfiles
 
-def mkdirp(folder):
-    """
-    Equivalent to bash's mkdir -p
-    """
-    try:
-        os.makedirs(folder)
-    except OSError as exc:
-        if exc.errno != EEXIST or not os.path.isdir(folder):
-            raise
-
-    return folder
-
 
 def filename_to_list(filename):
     """Returns a list given either a string or a list