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A Guide to NumPy/SciPy Documentation

Note

For an accompanying example, see example.py.

Overview

In general, we follow the standard Python style conventions as described here:
Additional PEPs of interest regarding documentation of code:
Use a code checker:

The following import conventions are used throughout the NumPy source and documentation:

import numpy as np
import scipy as sp
import matplotlib as mpl
import matplotlib.pyplot as plt

It is not necessary to do import numpy as np at the beginning of an example. However, some sub-modules, such as fft, are not imported by default, and you have to include them explicitly:

import numpy.fft

after which you may use it:

np.fft.fft2(...)

Docstring Standard

A documentation string (docstring) is a string that describes a module, function, class, or method definition. The docstring is a special attribute of the object (object.__doc__) and, for consistency, is surrounded by triple double quotes, i.e.:

"""This is the form of a docstring.

It can be spread over several lines.

"""

NumPy, SciPy, and the scikits follow a common convention for docstrings that provides for consistency, while also allowing our toolchain to produce well-formatted reference guides. This document describes the current community consensus for such a standard. If you have suggestions for improvements, post them on the numpy-discussion list.

Our docstring standard uses re-structured text (reST) syntax and is rendered using Sphinx (a pre-processor that understands the particular documentation style we are using). While a rich set of markup is available, we limit ourselves to a very basic subset, in order to provide docstrings that are easy to read on text-only terminals.

A guiding principle is that human readers of the text are given precedence over contorting docstrings so our tools produce nice output. Rather than sacrificing the readability of the docstrings, we have written pre-processors to assist Sphinx in its task.

The length of docstring lines should be kept to 75 characters to facilitate reading the docstrings in text terminals.

Status

We are busy converting existing docstrings to the new format, expanding them where they are lacking, as well as writing new ones for undocumented functions. Volunteers are welcome to join the effort on our new documentation system (see the Documentation Editor and the Developer Zone).

Sections

The sections of the docstring are:

  1. Short summary

    A one-line summary that does not use variable names or the function name, e.g.

    def add(a, b):
       """The sum of two numbers.
    
       """
    

    The function signature is normally found by introspection and displayed by the help function. For some functions (notably those written in C) the signature is not available, so we have to specify it as the first line of the docstring:

    """
    add(a, b)
    
    The sum of two numbers.
    
    """
    
  2. Extended summary

    A few sentences giving an extended description. This section should be used to clarify functionality, not to discuss implementation detail or background theory, which should rather be explored in the notes section below. You may refer to the parameters and the function name, but parameter descriptions still belong in the parameters section.

  3. Parameters

    Description of the function arguments, keywords and their respective types.

    Parameters
    ----------
    x : type
       Description of parameter `x`.
    

    Enclose variables in single backticks.

    For the parameter types, be as preciese as possible. Below are a few examples of parameters and their types.

    Parameters
    ----------
    filename : str
    copy : bool
    dtype : data-type
    iterable : iterable object
    shape : int or tuple of int
    files : list of str
    

    If it is not necessary to specify a keyword argument, use optional:

    x : int, optional
    

    Optional keyword parameters have default values, which are displayed as part of the function signature. They can also be detailed in the description:

    Description of parameter `x` (the default is -1, which implies summation
    over all axes).
    

    When a parameter can only assume one of a fixed set of values, those values can be listed in braces:

    order : {'C', 'F', 'A'}
        Description of `order`.
    

    When two or more input parameters have exactly the same type, shape and description, they can be combined:

    x1, x2 : array_like
        Input arrays, description of `x1`, `x2`.
    
  4. Returns

    Explanation of the returned values and their types, of the same format as parameters.

  5. Other parameters

    An optional section used to describe infrequently used parameters. It should only be used if a function has a large number of keyword prameters, to prevent cluttering the parameters section.

  6. Raises

    An optional section detailing which errors get raised and under what conditions:

    Raises
    ------
    LinAlgException
        If the matrix is not numerically invertible.
    

    This section should be used judiciously, i.e only for errors that are non-obvious or have a large chance of getting raised.

  7. See Also

    An optional section used to refer to related code. This section can be very useful, but should be used judiciously. The goal is to direct users to other functions they may not be aware of, or have easy means of discovering (by looking at the module docstring, for example). Routines whose docstrings further explain parameters used by this function are good candidates.

    As an example, for numpy.mean we would have:

    See Also
    --------
    average : Weighted average
    

    When referring to functions in the same sub-module, no prefix is needed, and the tree is searched upwards for a match.

    Prefix functions from other sub-modules appropriately. E.g., whilst documenting the random module, refer to a function in fft by

    fft.fft2 : 2-D fast discrete Fourier transform
    

    When referring to an entirely different module:

    scipy.random.norm : Random variates, PDFs, etc.
    

    Functions may be listed without descriptions, and this is preferable if the functionality is clear from the function name:

    See Also
    --------
    func_a : Function a with its description.
    func_b, func_c_, func_d
    func_e
    
  8. Notes

    An optional section that provides additional information about the code, possibly including a discussion of the algorithm. This section may include mathematical equations, written in LaTeX format:

    The FFT is a fast implementation of the discrete Fourier transform:
    
    .. math:: X(e^{j\omega } ) = x(n)e^{ - j\omega n}
    

    Equations can also be typeset underneath the math directive:

    The discrete-time Fourier time-convolution property states that
    
    .. math::
    
         x(n) * y(n) \Leftrightarrow X(e^{j\omega } )Y(e^{j\omega } )\\
         another equation here
    

    Math can furthermore be used inline, i.e.

    The value of :math:`\omega` is larger than 5.
    

    Variable names are displayed in typewriter font, obtained by using \mathtt{var}:

    We square the input parameter `alpha` to obtain
    :math:`\mathtt{alpha}^2`.
    

    Note that LaTeX is not particularly easy to read, so use equations sparingly.

    Images are allowed, but should not be central to the explanation; users viewing the docstring as text must be able to comprehend its meaning without resorting to an image viewer. These additional illustrations are included using:

    .. image:: filename
    

    where filename is a path relative to the reference guide source directory.

  9. References

    References cited in the notes section may be listed here, e.g. if you cited the article below using the text [1]_, include it as in the list as follows:

    .. [1] O. McNoleg, "The integration of GIS, remote sensing,
       expert systems and adaptive co-kriging for environmental habitat
       modelling of the Highland Haggis using object-oriented, fuzzy-logic
       and neural-network techniques," Computers & Geosciences, vol. 22,
       pp. 585-588, 1996.
    

    which renders as

    [1]

    O. McNoleg, "The integration of GIS, remote sensing, expert systems and adaptive co-kriging for environmental habitat modelling of the Highland Haggis using object-oriented, fuzzy-logic and neural-network techniques," Computers & Geosciences, vol. 22, pp. 585-588, 1996.

    Referencing sources of a temporary nature, like web pages, is discouraged. References are meant to augment the docstring, but should not be required to understand it. Follow the citation format of the IEEE, which states that references are numbered, starting from one, in the order in which they are cited.

  10. Examples

An optional section for examples, using the doctest format. This section is meant to illustrate usage, not to provide a testing framework -- for that, use the tests/ directory. While optional, this section is very strongly encouraged.

When multiple examples are provided, they should be separated by blank lines. Comments explaining the examples should have blank lines both above and below them:

>>> np.add(1, 2)
3

Comment explaining the second example

>>> np.add([1, 2], [3, 4])
array([4, 6])

For tests with a result that is random or platform-dependent, mark the output as such:

>>> import numpy.random
>>> np.random.rand(2)
array([ 0.35773152,  0.38568979])  #random

You can run examples using:

>>> np.test(doctests=True)

It is not necessary to use the doctest markup <BLANKLINE> to indicate empty lines in the output. Note that the option to run the examples through numpy.test is provided for checking if the examples work, not for making the examples part of the testing framework.

The examples may assume that import numpy as np is executed before the example code in numpy, and import scipy as sp in scipy. Additional examples may make use of matplotlib for plotting, but should import it explicitly, e.g., import matplotlib.pyplot as plt.

Documenting classes

Class docstring

Use the same sections as outlined above (all except Returns are applicable). The constructor (__init__) should also be documented here, the parameters section of the docstring details the constructors parameters.

An Attributes section, located below the parameters section, may be used to describe class variables:

Attributes
----------
x : float
    The X coordinate.
y : float
    The Y coordinate.

Attributes that are properties and have their own docstrings can be simply listed by name:

Attributes
----------
real
imag
x : float
    The X coordinate
y : float
    The Y coordinate

In general, it is not necessary to list class methods. Those that are not part of the public API have names that start with an underscore. In some cases, however, a class may have a great many methods, of which only a few are relevant (e.g., subclasses of ndarray). Then, it becomes useful to have an additional Methods section:

class Photo(ndarray):
    """
    Array with associated photographic information.

    ...

    Attributes
    ----------
    exposure : float
        Exposure in seconds.

    Methods
    -------
    colorspace(c='rgb')
        Represent the photo in the given colorspace.
    gamma(n=1.0)
        Change the photo's gamma exposure.

    """

If it is necessary to explain a private method (use with care!), it can be referred to in the extended summary or the notes. Do not list private methods in the Methods section.

Note that self is not listed as the first parameter of methods.

Method docstrings

Document these as you would any other function. Do not include self in the list of parameters.

Documenting class instances

Instances of classes that are part of the Numpy API (for example np.r_ np,c_, np.index_exp, etc.) may require some care. To give these instances a useful docstring, we do the following:

  • Single instance: If only a single instance of a class is exposed, document the class. Examples can use the instance name.
  • Multiple instances: If multiple instances are exposed, docstrings for each instance are written and assigned to the instances' __doc__ attributes at run time. The class is documented as usual, and the exposed instances can be mentioned in the Notes and See Also sections.

Documenting constants

Use the same sections as outlined for functions where applicable:

1. summary
2. extended summary (optional)
3. see also (optional)
4. references (optional)
5. examples (optional)

Docstrings for constants will not be visible in text terminals (constants are of immutable type, so docstrings can not be assigned to them like for for class instances), but will appear in the documentation built with Sphinx.

Other points to keep in mind

  • Notes and Warnings : If there are points in the docstring that deserve special emphasis, the reST directives for a note or warning can be used in the vicinity of the context of the warning (inside a section). Syntax:

    .. warning:: Warning text.
    
    .. note:: Note text.
    

    Use these sparingly, as they do not look very good in text terminals and are not often necessary. One situation in which a warning can be useful is for marking a known bug that is not yet fixed.

  • Questions and Answers : For general questions on how to write docstrings that are not answered in this document, refer to http://docs.scipy.org/numpy/Questions+Answers/.

  • array_like : For functions that take arguments which can have not only a type ndarray, but also types that can be converted to an ndarray (i.e. scalar types, sequence types), those arguments can be documented with type array_like.

Common reST concepts

For paragraphs, indentation is significant and indicates indentation in the output. New paragraphs are marked with a blank line.

Use italics, bold, and courier if needed in any explanations (but not for variable names and doctest code or multi-line code). Variable, module and class names should be written between single backticks (`numpy`).

A more extensive example of reST markup can be found in this example document; the quick reference is useful while editing.

Line spacing and indentation are significant and should be carefully followed.

Conclusion

An example of the format shown here is available. Refer to How to Build API/Reference Documentation on how to use Sphinx to build the manual.

This document itself was written in ReStructuredText, and may be converted to HTML using:

$ rst2html HOWTO_DOCUMENT.txt HOWTO_DOCUMENT.html
Something went wrong with that request. Please try again.