Documenting Python Code¶

Modules¶

Module-level docstrings must be placed as close to the top of the Python file as possible: below the boilerplate and any #!/usr/bin/env python, but above the imports. Module-level docstrings should not be indented.

#
# LSST Data Management System
# See COPYRIGHT file at the top of the source tree.
#
# [...]
#
# You should have received a copy of the LSST License Statement and
# the GNU General Public License along with this program. If not,
# see <http://www.lsstcorp.org/LegalNotices/>.
#
"""Summary of MyModule.

Extended discussion of my module.
"""

import lsst.afw.table as afw_table
# [...]

Classes, Methods, and Functions¶

Class/method/function docstrings must be placed directly below the class/method/function declaration, and indented to the level of the scope.

class MyClass(object):
    """Summary of MyClass.

    Additional discussion.
    """

    def __init__(self):
        pass

    def method(self):
        """Summary of method.

        Extended Discussion of my method.
        """
        pass

def my_function():
    """Summary of my_function.

    Extended discussion of my_function.
    """
    pass

Note that the class docstring takes the place of a docstring of the __init__ method; __init__ has no docstring.

No space between headers and paragraphs¶

For docstrings the numpydoc standard is to omit any space between a header and the following paragraph.

For example

"""A summary

A Headline
----------
A paragraph
"""

This deviation from the normal style guide is in keeping with Python community idioms, and to save vertical space in terminal help printouts.

Top level headers are defined with ‘-‘¶

In docstrings, the top level header is marked up with a -, the third level listed in our ReStructuredTextStyle guide. The header hierarchy is thus:

1. Sections -,
2. Subsections ^,
3. Subsubsections ".

This deviation from our reST style guide is in keeping with Numpy community idioms, and required by our Sphinx tooling.

Short Summary¶

A one-line summary that does not use variable names or the function name:

def add(a, b):
    """Sum two numbers."""
    return a + b

The summary should be written as a present-tense action. Do not write something like “Sums two numbers.”

The one line summary can be used alone only in extremely trivial cases, such as Python properties. Keep in mind our style guideline for placing the short summary on the same line as the opening (and closing, if used alone) docstring delimiters. In virtually all cases using a full multi-line docstring is the correct thing to do.

Deprecation Warning¶

A section (where applicable) to warn users that the object is deprecated. Section contents should include:

1. In what stack version the object was deprecated, and when it will be removed.
2. Reason for deprecation if this is useful information (e.g., object is superseded, duplicates functionality found elsewhere, etc.).
3. New recommended way of obtaining the same functionality.

This section should use the note Sphinx directive instead of an underlined section header.

.. note:: Deprecated in 11_0
          `ndobj_old` will be removed in 12_0, it is replaced by
          `ndobj_new` because the latter works also with array subclasses.

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.

Parameters¶

For functions, methods and classes.

Parameters is a description of the function arguments, keywords and their respective types.

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

Notice that the description is indented by four spaces from the {name} : {type} line of each argument. If a description spans more than one line, the continuation lines must be indented to the same level.

Arguments should be listed in the same order as they appear in the function signature.

When describing an argument in the description, enclose the name of the variable in single backticks (the default role in reST, which is Python-aware in docstrings).

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

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

x : int, optional

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

x1, x2 : array-like
    Input arrays, description of `x1`, `x2`.

Methods¶

For classes.

If a class has a very large number of methods, which are hard to discover, an additional Methods section can be provided to list them:

Methods
-------
read(filename)
   Read a table from a file
sort(column, order='ascending')
   Sort by `column`

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

Do not list self as the first parameter of a method.

Attributes¶

For classes.

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

Returns¶

For functions and methods.

Returns is an explanation of the returned values and their types, of the same format as Parameters.

If a sequence of values is returned, each value may be separately listed, in order:

Returns
-------
x : int
    Description of x.
y : int
    Description of y.

If a return type is dict, ensure that the key-value pairs are documented in the description.

Yields¶

For generators.

Yields is used identically to Returns, but for generators.

Other Parameters¶

For classes, methods and functions.

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

Raises¶

For classes, methods and functions.

Raises is an optional section detailing which errors get raised and under what conditions:

Raises
------
IOError
    If the file could not be read.

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

See Also¶

See Also is 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 a function such as numpy.cos, we would have

See Also
--------
sin : Compute an element-wise Sine function.
tan : Compute an element-wise Tangent function.

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

Prefix objects from other sub-modules appropriately by their greatest common namespace. E.g., whilst documenting a lsst.afw.tables module, refer to a class in lsst.afw.detection by

afw.detection.Footprint : Regular detection footprint.

When referring to an entirely different module or package, use the full namespace.

astropy.table.Tables : Flexible table data structures

Functions may be listed without descriptions; 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

Notes¶

Notes is 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:

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.

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.

Note that Web pages should be referenced with regular inline links.

References are meant to augment the docstring, but should not be required to understand it. References are numbered, starting from one, in the order in which they are cited.

Examples¶

Examples is an optional section for examples, using the doctest format. These examples do not replace unit tests, but are intended to be tested to ensure documentation and code is consistent. 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:

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

It is not necessary to use the doctest markup <BLANKLINE> to indicate empty lines in the output.