Developer documentation
Coding Style
Overall code formatting should adhere to the Google Python Style Rules. Most notably, use 4 spaces for indentation (no tabs!) and try to keep maximum line length to 80 characters.
Testing
It is good practice to write tests for all your functions and classes. Those tests may not be too extensive but should cover the basic use cases to ensure correct behavior through further development of the package.
The Typhon testing framework is using pytest. You can run the tests from the command line using:
pytest --pyargs typhon
Documentation Style
General
All code documentation in Typhon should follow the Google Style Python Docstrings format. Below you can find various example on how the docstrings should look like. The example is taken from http://sphinxcontrib-napoleon.readthedocs.org/en/latest/example_google.html
Download: example_google.py
# -*- coding: utf-8 -*-
"""Example Google style docstrings.
This module demonstrates documentation as specified by the `Google Python
Style Guide`_. Docstrings may extend over multiple lines. Sections are created
with a section header and a colon followed by a block of indented text.
Example:
Examples can be given using either the ``Example`` or ``Examples``
sections. Sections support any reStructuredText formatting, including
literal blocks::
$ python example_google.py
Section breaks are created by resuming unindented text. Section breaks
are also implicitly created anytime a new section starts.
Attributes:
module_level_variable1 (int): Module level variables may be documented in
either the ``Attributes`` section of the module docstring, or in an
inline docstring immediately following the variable.
Either form is acceptable, but the two should not be mixed. Choose
one convention to document module level variables and be consistent
with it.
.. _Google Python Style Guide:
http://google.github.io/styleguide/pyguide.html
"""
module_level_variable1 = 12345
module_level_variable2 = 98765
"""int: Module level variable documented inline.
The docstring may span multiple lines. The type may optionally be specified
on the first line, separated by a colon.
"""
def module_level_function(param1, param2=None, *args, **kwargs):
"""This is an example of a module level function.
Function parameters should be documented in the ``Args`` section. The name
of each parameter is required. The type and description of each parameter
is optional, but should be included if not obvious.
Parameter types -- if given -- should be specified according to
`PEP 484`_, though `PEP 484`_ conformance isn't required or enforced.
If \*args or \*\*kwargs are accepted,
they should be listed as ``*args`` and ``**kwargs``.
The format for a parameter is::
name (type): description
The description may span multiple lines. Following
lines should be indented. The "(type)" is optional.
Multiple paragraphs are supported in parameter
descriptions.
Args:
param1 (int): The first parameter.
param2 (Optional[str]): The second parameter. Defaults to None.
Second line of description should be indented.
*args: Variable length argument list.
**kwargs: Arbitrary keyword arguments.
Returns:
bool: True if successful, False otherwise.
The return type is optional and may be specified at the beginning of
the ``Returns`` section followed by a colon.
The ``Returns`` section may span multiple lines and paragraphs.
Following lines should be indented to match the first line.
The ``Returns`` section supports any reStructuredText formatting,
including literal blocks::
{
'param1': param1,
'param2': param2
}
Raises:
AttributeError: The ``Raises`` section is a list of all exceptions
that are relevant to the interface.
ValueError: If `param2` is equal to `param1`.
.. _PEP 484:
https://www.python.org/dev/peps/pep-0484/
"""
if param1 == param2:
raise ValueError('param1 may not be equal to param2')
return True
def example_generator(n):
"""Generators have a ``Yields`` section instead of a ``Returns`` section.
Args:
n (int): The upper limit of the range to generate, from 0 to `n` - 1.
Yields:
int: The next number in the range of 0 to `n` - 1.
Examples:
Examples should be written in doctest format, and should illustrate how
to use the function.
>>> print([i for i in example_generator(4)])
[0, 1, 2, 3]
"""
for i in range(n):
yield i
class ExampleError(Exception):
"""Exceptions are documented in the same way as classes.
The __init__ method may be documented in either the class level
docstring, or as a docstring on the __init__ method itself.
Either form is acceptable, but the two should not be mixed. Choose one
convention to document the __init__ method and be consistent with it.
Note:
Do not include the `self` parameter in the ``Args`` section.
Args:
msg (str): Human readable string describing the exception.
code (Optional[int]): Error code.
Attributes:
msg (str): Human readable string describing the exception.
code (int): Exception error code.
"""
def __init__(self, msg, code):
self.msg = msg
self.code = code
class ExampleClass(object):
"""The summary line for a class docstring should fit on one line.
If the class has public attributes, they may be documented here
in an ``Attributes`` section and follow the same formatting as a
function's ``Args`` section. Alternatively, attributes may be documented
inline with the attribute's declaration (see __init__ method below).
Properties created with the ``@property`` decorator should be documented
in the property's getter method.
Attribute and property types -- if given -- should be specified according
to `PEP 484`_, though `PEP 484`_ conformance isn't required or enforced.
Attributes:
attr1 (str): Description of `attr1`.
attr2 (Optional[int]): Description of `attr2`.
.. _PEP 484:
https://www.python.org/dev/peps/pep-0484/
"""
def __init__(self, param1, param2, param3):
"""Example of docstring on the __init__ method.
The __init__ method may be documented in either the class level
docstring, or as a docstring on the __init__ method itself.
Either form is acceptable, but the two should not be mixed. Choose one
convention to document the __init__ method and be consistent with it.
Note:
Do not include the `self` parameter in the ``Args`` section.
Args:
param1 (str): Description of `param1`.
param2 (Optional[int]): Description of `param2`. Multiple
lines are supported.
param3 (List[str]): Description of `param3`.
"""
self.attr1 = param1
self.attr2 = param2
self.attr3 = param3 #: Doc comment *inline* with attribute
#: List[str]: Doc comment *before* attribute, with type specified
self.attr4 = ['attr4']
self.attr5 = None
"""Optional[str]: Docstring *after* attribute, with type specified."""
@property
def readonly_property(self):
"""str: Properties should be documented in their getter method."""
return 'readonly_property'
@property
def readwrite_property(self):
"""List[str]: Properties with both a getter and setter should only
be documented in their getter method.
If the setter method contains notable behavior, it should be
mentioned here.
"""
return ['readwrite_property']
@readwrite_property.setter
def readwrite_property(self, value):
value
def example_method(self, param1, param2):
"""Class methods are similar to regular functions.
Note:
Do not include the `self` parameter in the ``Args`` section.
Args:
param1: The first parameter.
param2: The second parameter.
Returns:
True if successful, False otherwise.
"""
return True
def __special__(self):
"""By default special members with docstrings are included.
Special members are any methods or attributes that start with and
end with a double underscore. Any special member with a docstring
will be included in the output.
This behavior can be disabled by changing the following setting in
Sphinx's conf.py::
napoleon_include_special_with_doc = False
"""
pass
def __special_without_docstring__(self):
pass
def _private(self):
"""By default private members are not included.
Private members are any methods or attributes that start with an
underscore and are *not* special. By default they are not included
in the output.
This behavior can be changed such that private members *are* included
by changing the following setting in Sphinx's conf.py::
napoleon_include_private_with_doc = True
"""
pass
def _private_without_docstring(self):
pass
Properties
All documentation for properties should be attached to the getter function (@property). No information should be put in the setter function of the property. Because all access occurs through the property name and never by calling the setter function explicitly, documentation put there will never be visible. Neither in the ipython interactive help nor in Sphinx.
Adding functions / classes
When you add a new function or class, you also have to add its name the corresponding rst file in the doc/ folder.
Common module names
This is a list of short names that should be used consistently for importing external modules:
import numpy as np
import scipy as sp
import matplotlib as mpl
import matplotlib.pyplot as plt
Logging
The standard logging module is used to create log messages. Make sure
to use an appropriate log level for your message. The default level,
comparable to a print, should be logging.INFO:
logger = logging.getLogger(__name__)
logger.info('Common log message.')
In rare occasions, the print function may be used, if the output gives
additional information to the user that exceeds the scope of a log. In those
cases, the additional output has to be guarded by a verbose keyword
which defaults to False:
def function(verbose=False):
if verbose:
print('Message to stdout'.)
Comments
All code should be properly commented. To quote a blog post on dev.to:
While clean code shows what is done, comments should explain why a feature is implemented in a certain way. This approach is often called Commenting Showing Intent (CSI). It helps other developers and your future self to comprehend why a certain implementation has been chosen. In addition, possible implications with other parts of the project should be addressed.