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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.

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 workflow:

.. workflow ::
    :graph2use: flat
    :simple_form: no

    from nipype.workflows.dmri.camino.connectivity_mapping import create_connectivity_pipeline
    wf = create_connectivity_pipeline()

For example, the following graph has been generated inserting the previous code block in this documentation:

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
    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:

  • 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
    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.

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