testbed/astropy__astropy/docs/development/docrules.rst

.. doctest-skip-all
.. _doc-rules:

***********************
Astropy Docstring Rules
***********************

The original source for these docstring standards is the NumPy_ project, and
the associated numpydoc_ tools. The most up-to-date version of these standards
can be found at `numpy's github site
<https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt>`_. The
guidelines below have been adapted to the Astropy package.


Overview
========

In general, we follow the standard Python style conventions as described here:

 * `Style Guide for C Code <https://www.python.org/dev/peps/pep-0007/>`_
 * `Style Guide for Python Code <https://www.python.org/dev/peps/pep-0008/>`_
 * `Docstring Conventions <https://www.python.org/dev/peps/pep-0257/>`_

Additional PEPs of interest regarding documentation of code:

 * `Docstring Processing Framework <https://www.python.org/dev/peps/pep-0256/>`_
 * `Docutils Design Specification <https://www.python.org/dev/peps/pep-0258/>`_

Use a code checker:

 * `pylint <https://www.logilab.org/857>`_
 * `pyflakes <https://pypi.python.org/pypi/pyflakes>`_
 * `pycodestyle <https://github.com/PyCQA/pycodestyle>`_

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

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

Do not abbreviate ``scipy``. There is no motivating use case to abbreviate
it in the real world, so we avoid it in the documentation to avoid
confusion.

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_ and SciPy_ have defined a common convention for docstrings that
provides for consistency, while also allowing our toolchain to produce
well-formatted reference guides. This format should be used for Astropy
docstrings.

This docstring standard uses `re-structured text (reST)
<http://docutils.sourceforge.net/rst.html>`_ 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.

.. _numpydoc-sections:

Sections
========

.. highlight:: rst

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. **Deprecation warning**

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

   * In what Astropy version the object was deprecated, and when it will
     be removed.

   * Reason for deprecation if this is useful information (e.g., object
     is superseded, duplicates functionality found elsewhere, etc.).

   * 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 Astropy 1.2
               `ndobj_old` will be removed in Astropy 2.0, it is replaced by
               `ndobj_new` because the latter works also with array subclasses.

3. **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.

   At the end of the extended summary one may optionally include one or more
   links to section(s) in the narrative documentation which provide additional
   usage information.  This is most commonly the case for major classes
   or functions which have complex behavior that is not fully described
   by the docstring itself.  The format is shown in the two examples
   below.

   One link::

      See also: http://docs.astropy.org/en/stable/table/

   Two or more links::

      See also:

      - http://docs.astropy.org/en/stable/table/
      - http://docs.astropy.org/en/stable/table/mixin_columns.html

4. **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 precise 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`.

5. **Returns**

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

6. **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 parameters,
   to prevent cluttering the **parameters** section.

7. **Raises**

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

     Raises
     ------
     InvalidWCSException
         If the WCS information is invalid.

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

8. **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 a hypothetical function ``astropy.wcs.world2pix``
   converting sky to pixel coordinates, we would have::

     See Also
     --------
     pix2world : Convert pixel to sky coordinates

   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 a hypothetical ``astropy.vo`` module, refer to a function in
   ``table`` by

   ::

     table.read : Read in a VO table

   When referring to an entirely different module::

     astropy.coords : Coordinate handling routines

   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

9. **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 <http://www.latex-project.org/>`_
   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.

10. **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
        modeling 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]_

   .. [1] O. McNoleg, "The integration of GIS, remote sensing,
      expert systems and adaptive co-kriging for environmental habitat
      modeling 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. References are numbered, starting from one, in the order
   in which they are cited.

11. **Examples**

   An optional section for examples, using the `doctest
   <https://docs.python.org/3/library/doctest.html>`_ 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::

     >>> astropy.wcs.world2pix(233.2, -12.3)
     (134.5, 233.1)

     Comment explaining the second example

     >>> astropy.coords.fk5_to_gal("00:42:44.33 +41:16:07.5")
     (121.1743, -21.5733)

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

     >>> astropy.coords.randomize_position(244.9, 44.2, radius=0.1)
     (244.855, 44.13)  # random

   It is not necessary to use the doctest markup ``<BLANKLINE>`` to indicate
   empty lines in the output. The examples may assume that ``import numpy as
   np`` is executed before the example code.

.. We need to consider whether to add a doctest= option to astropy.test to
.. enable automated testing of the examples as in Numpy.

Documenting classes
===================

Class docstrings
----------------

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


.. highlight:: python

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 Table(ndarray):
      """
      A class to represent tables of data

      ...

      Attributes
      ----------
      columns : list
          List of columns

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

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.

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

Method docstrings
-----------------

Document these as you would any other function. Do not include ``self`` in
the list of parameters. If a method has an equivalent function, the function
docstring should contain the detailed documentation, and the method
docstring should refer to it. Only put brief ``Summary`` and ``See Also``
sections in the method docstring.

Documenting class instances
===========================

Instances of classes that are part of the Astropy API 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.

Documenting modules
===================

Each module should have a docstring with at least a summary line. Other
sections are optional, and should be used in the same order as for documenting
functions when they are appropriate::

    1. summary
    2. extended summary
    3. routine listings
    4. see also
    5. notes
    6. references
    7. examples

Routine listings are encouraged, especially for large modules, for which it is
hard to get a good overview of all functionality provided by looking at the
source file(s) or the ``__all__`` dict.

Note that license and author info, while often included in source files, do not
belong in docstrings.

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:

  .. code-block:: rst

    .. 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.

* ``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 back-ticks (```astropy```).

A more extensive example of reST markup can be found in `this example document
<http://docutils.sourceforge.net/docs/user/rst/demo.txt>`_; the `quick
reference <http://docutils.sourceforge.net/docs/user/rst/quickref.html>`_ is
useful while editing.

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

Conclusion
==========

`An example <https://github.com/numpy/numpy/blob/master/doc/example.py>`_ of the
format shown here is available.
Refer to How to Build API/Reference
Documentation :ref:`astropy-doc-building`
on how to use Sphinx_ to build the manual.


.. _NumPy: http://www.numpy.org/
.. _numpydoc: https://pypi.python.org/pypi/numpydoc/0.3.1
.. _Matplotlib: http://matplotlib.sourceforge.net/
.. _SciPy: https://www.scipy.org/
.. _Sphinx: http://sphinx.pocoo.org