Todo
Testing Guidelines
Writing Command-Line Scripts
C or Cython Extensions
Python Coding Guidelines¶
This section describes requirements and guidelines.
An Example Python Project¶
We have created a skeleton Python project which should provide a full introduction to the various recommendations and requirements for the development of Python. The philosophy behind the development of this template was to demonstrate one way to meet the project guidelines and demonstrate a recommended project layout.
The recommended project layout is as follows:
.
├── CHANGELOG.rst
├── docker-requirements.txt
├── docs
│ ├── Makefile
│ └── src
│ ├── conf.py
│ ├── index.rst
│ ├── package
│ │ └── guide.rst
│ ├── README.md -> ../../README.md
│ ├── _static
│ │ ├── css
│ │ │ └── custom.css
│ │ ├── img
│ │ │ ├── favicon.ico
│ │ │ ├── logo.jpg
│ │ │ └── logo.svg
│ │ └── js
│ │ └── github.js
│ └── _templates
│ ├── footer.html
│ └── layout.html
├── LICENSE
├── Makefile
├── Pipfile
├── README.md
├── setup.cfg
├── setup.py
├── src
│ └── ska
│ └── skeleton
│ ├── example.py
│ └── __init__.py
└── tests
├── __init__.py
└── test_example.py
Interface and Dependencies¶
All code must be compatible with Python 3.7 and later.
The new Python 3 formatting style should be used (i.e.
"{0:s}".format("spam")
instead of"%s" % "spam"
), or use format stringsf"{spam}"
if variablespam="spam"
is in scope.
Documentation and Testing¶
Docstrings must be present for all public classes/methods/functions, and must follow the form outlined by PEP8 Docstring Conventions.
Unit tests should be provided for as many public methods and functions as possible, and should adhere to Pytest best practices.
Data and Configuration¶
All persistent configuration should use python-dotenv. Such configuration
.env
files should be placed at the top of theska_python_skeleton
module and provide a description that is sufficient for users to understand the settings changes.
Standard output, warnings, and errors¶
The built-in print(...)
function should only be used for output that
is explicitly requested by the user, for example print_header(...)
or list_catalogs(...)
. Any other standard output, warnings, and
errors should follow these rules:
For errors/exceptions, one should always use
raise
with one of the built-in exception classes, or a custom exception class. The nondescriptException
class should be avoided as much as possible, in favor of more specific exceptions (IOError, ValueError, etc.).For warnings, one should always use
warnings.warn(message, warning_class)
. These get redirected tolog.warning()
by default.For informational and debugging messages, one should always use
log.info(message)
andlog.debug(message)
.
Logging implementation¶
There is a standard Python logging module for logging in SKA projects. This module ensures that messages are formatted correctly according to our formatting standards.
For details on how to use the logging module with detailed examples, please refer to: https://gitlab.com/ska-telescope/ska-logging/tree/master#ska-logging-configuration-library
Coding Style/Conventions¶
The code will follow the standard PEP8 Style Guide for Python Code. In particular, this includes using only 4 spaces for indentation, and never tabs.
The
import numpy as np
,import matplotlib as mpl
, andimport matplotlib.pyplot as plt
naming conventions should be used wherever relevant.from packagename import *
should never be used, except as a tool to flatten the namespace of a module. An example of the allowed usage is given in Acceptable use of from module import *.Classes should either use direct variable access, or Python’s property mechanism for setting object instance variables.
get_value
/set_value
style methods should be used only when getting and setting the values requires a computationally-expensive operation. Properties vs. get_/set_ below illustrates this guideline.Classes should use the builtin
super()
function when making calls to methods in their super-class(es) unless there are specific reasons not to.super()
should be used consistently in all subclasses since it does not work otherwise. super() vs. Direct Calling illustrates why this is important.Multiple inheritance should be avoided in general without good reason.
__init__.py
files for modules should not contain any significant implementation code.__init__.py
can contain docstrings and code for organizing the module layout, however (e.g.from submodule import *
in accord with the guideline above). If a module is small enough that it fits in one file, it should simply be a single file, rather than a directory with an__init__.py
file.
Unicode guidelines¶
For maximum compatibility, we need to assume that writing non-ASCII characters to the console or to files will not work.
Including C Code¶
When C extensions are used, the Python interface for those extensions must meet the aforementioned Python interface guidelines.
The use of Cython is strongly recommended for C extensions. Cython extensions should store
.pyx
files in the source code repository, but they should be compiled to.c
files that are updated in the repository when important changes are made to the.pyx
file.In cases where C extensions are needed but Cython cannot be used, the PEP 7 Style Guide for C Code is recommended.
Examples¶
This section shows examples in order to illustrate points from the guidelines.
Properties vs. get_/set_¶
This example shows a sample class illustrating the guideline regarding the use of properties as opposed to getter/setter methods.
Let’s assuming you’ve defined a ':class:`Star`'
class and create an instance
like this:
>>> s = Star(B=5.48, V=4.83)
You should always use attribute syntax like this:
>>> s.color = 0.4
>>> print(s.color)
0.4
Using Python properties, attribute syntax can still do anything possible with a get/set method. For lengthy or complex calculations, however, use a method:
>>> print(s.compute_color(5800, age=5e9))
0.4
super() vs. Direct Calling¶
By calling super()
the entire method resolution order for
D
is precomputed, enabling each superclass to cooperatively determine which
class should be handed control in the next super()
call:
# This is safe
class A(object):
def method(self):
print('Doing A')
class B(A):
def method(self):
print('Doing B')
super().method()
class C(A):
def method(self):
print('Doing C')
super().method()
class D(C, B):
def method(self):
print('Doing D')
super().method()
>>> d = D()
>>> d.method()
Doing D
Doing C
Doing B
Doing A
As you can see, each superclass’s method is entered only once. For this to
work it is very important that each method in a class that calls its
superclass’s version of that method use super()
instead of calling the
method directly. In the most common case of single-inheritance, using
super()
is functionally equivalent to calling the superclass’s method
directly. But as soon as a class is used in a multiple-inheritance
hierarchy it must use super()
in order to cooperate with other classes in
the hierarchy.
Note
For more information on the the benefits of super()
, see
https://rhettinger.wordpress.com/2011/05/26/super-considered-super/
Acceptable use of from module import *
¶
from module import *
is discouraged in a module that contains
implementation code, as it impedes clarity and often imports unused variables.
It can, however, be used for a package that is laid out in the following
manner:
packagename
packagename/__init__.py
packagename/submodule1.py
packagename/submodule2.py
In this case, packagename/__init__.py
may be:
"""
A docstring describing the package goes here
"""
from submodule1 import *
from submodule2 import *
This allows functions or classes in the submodules to be used directly as
packagename.foo
rather than packagename.submodule1.foo
. If this is
used, it is strongly recommended that the submodules make use of the __all__
variable to specify which modules should be imported. Thus, submodule2.py
might read:
from numpy import array, linspace
__all__ = ['foo', 'AClass']
def foo(bar):
# the function would be defined here
pass
class AClass(object):
# the class is defined here
pass
This ensures that from submodule import *
only imports ':func:`foo'
and ':class:`AClass'
, but not ':class:`numpy.array'
or
':func:`numpy.linspace'
.
. _python-packaging:
Packaging¶
SKA python packages use setuptools to assemble the packages
Apart from the standard arguments to setup()
, several extra
enhancements are used.
Running tests out of the top-level directory can lead to conflicts when the
package is a direct child. It is best to put the package code in a subdirectory
e.g. src
package_dir={"": "src"}
Package layout:
setup.py
setup.cfg
requirements.txt
requirements-test.txt
src/ska/foo/__init__.py
src/ska/foo/bardevice.py
tests/__init__.py
tests/test_bardevice.py
docs/requirements.txt
docs/source/conf.py
docs/source/index.rst
Namespace¶
It is recommended to use the ska
namespace package for modules developed
in Python which are directly related to SKA.
Namespace packages
in python3 are native and distinguish themselves as directories without __init__.py
files. They have to be declared by using the output of
setuptools.find_namespace_packages()
to supply to the packages
keyword in setup()
Requirements¶
There are many ways to handle the installation of dependencies in python
.
pip
Best practice though is to put direct dependencies into install_requires
usually with a lower compatibility bound, but not explicit, e.g.
install_requires=[
"pytango >= 9.3.2",
"lmcbaseclasses >= 0.5.4"
]
For testing a package there is better to use and explicit requirements.txt file
rather than setup(test_requires=)
.
A typical development scenario could look like:
pip install -e . # pulls in dependencies via install_requires
pip install -r requirements-test.txt
pytest tests
Entry points¶
If your code contains scripts or main functions in your module, these can
automatically wrapped as executables in the deployed package. For example
Tango Device Classes
can be exposed without adding wrapper scripts
entry_points=
Sample setup.py
¶
Here is a sample for the foo module in the ska
namespace package:
setuptools.setup(
name="foo.bar",
description="Foo stuff",
version=0.0.1,
author="Prof Dr Dr Foo",
author_email="foo AT bar DOT org",
license="IP here",
url="https://foo.bar.org",
classifiers=[
"Development Status :: 3 - Alpha",
"Intended Audience :: Developers",
"License :: Other/Proprietary License",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Topic :: Software Development :: Libraries :: Python Modules",
"Topic :: Scientific/Engineering :: Astronomy"],
platforms=["OS Independent"],
package_dir={"": "src"},
packages=setuptools.find_namespace_packages(where="src"),
entry_points={
"console_scripts": [
"FooDevice=ska.foo.bar_device:main",
]
},
include_package_data=True,
install_requires=[
# should be pulled in by lmcbaseclasses but isn't
"pytango >= 9.3.2",
"lmcbaseclasses >= 0.5.4"
],
keywords="foo tango ska",
zip_safe=False
)
Reproducible workflow¶
Todo
This section is still evolving
While testing in a local environment is quick and easy it doesn’t fully guarantee independence of the system. A widely used way to abstract environment handling is tox, which can control your testing workflow through several stages similar to what various continuous integration pipelines do.
Simply install via pip install tox
Here is a SKA pytango package example tox.ini:
[tox]
envlist = py37
[testenv]
setenv = PIP_DISABLE_VERSION_CHECK = 1
install_command = python -m pip install --extra-index-url https://artefact.skao.int/repository/pypi-internal/simple {opts} {packages}
deps =
-rrequirements.txt # runtime requirements
-rrequirements-test.txt # test/development requirements
commands =
# this ugly hack is here because:
# https://github.com/tox-dev/tox/issues/149
python -m pip install -U --extra-index-url https://artefact.skao.int/repository/pypi-internal/simple -r{toxinidir}/requirements.txt
#
python -m pytest {posargs}
# use system site-packages for pytango (and c++ library dependencies)
sitepackages = true
[testenv:docs]
description = build documentation
basepython = python3
sitepackages = false # we want to run docs without pytango, as that isn't available on RTD
skip_install = true
install_command = python -m pip install -U {opts} {packages}
deps = -rdocs/requirements.txt
commands =
sphinx-build -E -W -c docs/source/ -b html docs/source/ docs/build/html
[testenv:lint]
basepython = python3
skip_install = true
description = report linting
whitelist_externals = mkdir
deps = -rrequirements-tst.txt
commands =
- mkdir -p build/reports
- python -m flake8 --max-line-length=88 --format=junit-xml --output-file=build/reports/linting.xml
python -m flake8 --max-line-length=88 --statistics --show-source
To use tox simple invoke as follows:
tox -e py37
tox -e lint
...
Acknowledgements¶
The present document’s coding guidelines are derived from project Astropy’s coding guidelines.