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Chapter 3

The document discusses testing Python packages with different environments. It recommends using tox to test packages against multiple Python versions. Tox reads a tox.ini configuration file to determine which Python versions to test against. It installs dependencies and runs commands like pytest to test the package in each specified Python environment.

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36 views

Chapter 3

The document discusses testing Python packages with different environments. It recommends using tox to test packages against multiple Python versions. Tox reads a tox.ini configuration file to determine which Python versions to test against. It installs dependencies and runs commands like pytest to test the package in each specified Python environment.

Uploaded by

2022ac05722
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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Testing your

package
D E V E L O P I N G P Y T H O N PA C K A G E S

James Fulton
Climate informatics researcher
The art and discipline of testing
Imagine you are working on this function

def get_ends(x):
"""Get the first and last element in a list"""
return x[0], x[-1]

You might test it to make sure it works

# Check the function


get_ends([1,1,5,39,0])

(1, 0)

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The art and discipline of testing
Good packages brag about how many tests they have

91% of the pandas package code has tests

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Writing tests
def get_ends(x):
"""Get the first and last element in a list"""
return x[0], x[-1]

def test_get_ends():
assert get_ends([1,5,39,0]) == (1,0)

test_get_ends()

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Writing tests
def get_ends(x):
"""Get the first and last element in a list"""
return x[0], x[1]

def test_get_ends():
assert get_ends([1,5,39,0]) == (1,0)

test_get_ends()

AssertionError:
...

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Writing tests
def get_ends(x):
"""Get the first and last element in a list"""
return x[0], x[-1]

def test_get_ends():
assert get_ends([1,5,39,0]) == (1,0)
assert get_ends(['n','e','r','d']) == ('n','d')

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Organizing tests inside your package
mysklearn/
|-- mysklearn <-- package
|-- tests <-- tests directory
|-- setup.py
|-- LICENSE
|-- MANIFEST.in

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Organizing tests inside your package
Test directory layout Code directory layout

mysklearn/tests/ mysklearn/mysklearn/
|-- __init__.py |-- __init__.py
|-- preprocessing |-- preprocessing
| |-- __init__.py | |-- __init__.py
| |-- test_normalize.py | |-- normalize.py
| |-- test_standardize.py | |-- standardize.py
|-- regression |-- regression
| |-- __init__.py | |-- __init__.py
| |-- test_regression.py | |-- regression.py
|-- test_utils.py |-- utils.py

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Organizing a test module
Inside test_normalize.py Inside normalize.py

from mysklearn.preprocessing.normalize import ( def find_max(x):


find_max, find_min, normalize_data ...
) return x_max

def test_find_max(x): def find_min(x):


assert find_max([1,4,7,1])==7 ...
return x_min
def test_find_min(x):
assert ... def normalize_data(x):
...
def test_normalize_data(x): return x_norm
assert ...

DataCamp: Unit testing for data science

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Running tests with pytest
pytest mysklearn/ <-- navigate to here
|-- mysklearn
pytest looks inside the test directory |-- tests
It looks for modules like |-- setup.py
test_modulename.py |-- LICENSE
|-- MANIFEST.in
It looks for functions like
test_functionname()

It runs these functions and shows output

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Running tests with pytest
pytest

======================== test session starts ========================


platform linux -- Python 3.7.9, pytest-6.1.2, py-1.9.0, pluggy-0.13.1
rootdir: /home/workspace/mypackages/mysklearn
collected 6 items

tests/preprocessing/test_normalize.py ... [ 50%]


tests/preprocessing/test_standardize.py ... [100%]

========================= 6 passed in 0.23s =========================

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Running tests with pytest
pytest

======================== test session starts ========================


platform linux -- Python 3.7.9, pytest-6.1.2, py-1.9.0, pluggy-0.13.1
rootdir: /home/workspace/mypackages/mysklearn <-- ran in this directory
collected 6 items <-- found 6 test functions

tests/preprocessing/test_normalize.py ... [ 50%]


tests/preprocessing/test_standardize.py ... [100%]

========================= 6 passed in 0.23s =========================

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Running tests with pytest
pytest

======================== test session starts ========================


platform linux -- Python 3.7.9, pytest-6.1.2, py-1.9.0, pluggy-0.13.1
rootdir: /home/workspace/mypackages/mysklearn
collected 6 items

tests/preprocessing/test_normalize.py ... [ 50%] <--


tests/preprocessing/test_standardize.py ... [100%] <--

========================= 6 passed in 0.23s =========================

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Running tests with pytest
pytest

======================== test session starts ========================


platform linux -- Python 3.7.9, pytest-6.1.2, py-1.9.0, pluggy-0.13.1
rootdir: /home/workspace/mypackages/mysklearn
collected 6 items

tests/preprocessing/test_normalize.py ... [ 50%]


tests/preprocessing/test_standardize.py ... [100%]

========================= 6 passed in 0.23s =========================

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Running tests with pytest
pytest

==================================== test session starts ====================================


...
tests/preprocessing/test_normalize.py .F. [ 50%]
tests/preprocessing/test_standardize.py ... [100%]

========================================= FAILURES ==========================================


________________________________________ test_mymax _________________________________________
...

tests/preprocessing/test_normalize.py:10: AssertionError
================================== short test summary info ==================================
FAILED tests/preprocessing/test_normalize.py::test_mymax - assert -100 == 100 <-- test_mymax
================================ 1 failed, 5 passed in 0.17s ================================

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Let's practice!
D E V E L O P I N G P Y T H O N PA C K A G E S
Testing your
package with
different
environments
D E V E L O P I N G P Y T H O N PA C K A G E S

James Fulton
Climate informatics researcher
Testing multiple versions of Python
This setup.py allows any version of Python from version 2.7 upwards.

from setuptools import setup, find_packages

setup(
...
python_requires='>=2.7',
)

To test these Python versions you must:

Install all these Python versions

Install your package and all dependencies into each Python


Run pytest

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Testing multiple versions of Python
This setup.py allows any version of Python from version 2.7 upwards.

from setuptools import setup, find_packages

setup(
...
python_requires='>=2.7',
)

To test these Python versions you must:

Install all these Python versions

Run tox

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What is tox?
Designed to run tests with multiple versions of Python

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Configure tox
Configuration file - tox.ini mysklearn/
|-- mysklearn
| |-- ...
|-- tests
| |-- ...
|-- setup.py
|-- LICENSE
|-- MANIFEST.in
|-- tox.ini <--- configuration file

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Configure tox
Configuration file - tox.ini Headings are surrounded by square
brackets [...] .
[tox]
To test Python version X.Y add pyXY to
envlist = py27, py35, py36, py37
envlist .

The versions of Python you test need to be


[testenv]
installed already.
deps = pytest
commands = The commands parameter lists the terminal
pytest commands tox will run.
echo "run more commands"
The commands list can be any commands
...
which will run from the terminal, like ls ,
cd , echo etc.

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Running tox
tox mysklearn/ <-- navigate to here
|-- mysklearn
| |-- ...
|-- tests
| |-- ...
|-- setup.py
|-- LICENSE
|-- MANIFEST.in
|-- tox.ini

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tox output
py27 create: /mypackages/mysklearn/.tox/py27
py27 installdeps: pytest
py27 inst: /mypackages/mysklearn/.tox/.tmp/package/1/mysklearn-0.1.0.zip
py27 installed: mysklearn==0.1.0,numpy==1.16.6,pandas==0.24.2,pytest==4.6.11,...
py27 run-test-pre: PYTHONHASHSEED='2837498672'
...

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tox output
py27 run-test: commands[0] | pytest
======================== test session starts ========================
platform linux2 -- Python 2.7.17, ...
rootdir: /home/workspace/mypackages/mysklearn
collected 6 items

tests/preprocessing/test_normalize.py ... [ 50%]


tests/preprocessing/test_standardize.py ... [100%]

========================= 6 passed in 0.23s =========================

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tox output
...
__________________________ summary __________________________
py27: commands succeeded
py35: commands succeeded
py36: commands succeeded
py37: commands succeeded

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tox output
...
__________________________ summary __________________________
py27: commands succeeded
py35: commands succeeded
py36: commands succeeded
ERROR: py37: commands failed

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Let's practice!
D E V E L O P I N G P Y T H O N PA C K A G E S
Keeping your
package stylish
D E V E L O P I N G P Y T H O N PA C K A G E S

James Fulton
Climate informatics researcher
Introducing flake8
Standard Python style is described in PEP8
A style guide dictates how code should be laid out

pytest is used to find bugs

flake8 is used to find styling mistakes

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Running flake8
Static code checker - reads code but doesn't run

flake8 features.py

features.py:2:1: F401 'math' imported but unused


..

<filename>:<line number>:<charcter number>:<error code> <desciption>

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Using the output for quality code
1. import numpy as np flake8 features.py
2. import math
3.
2:1: F401 'math' imported but unused
4. def mean(x):
4:1: E302 expected 2 blank lines, found 1
5. """Calculate the mean"""
7:1: E302 expected 2 blank lines, found 0
6. return np.mean(x)
5:4: E111 indentation is not a multiple
7. def std(x):
of four
8. """Calculate the standard deviation"""
6:4: E111 indentation is not a multiple
9. mean_x = mean(x)
of four
10. std = mean((x-mean(x))**2)
9:5: F841 local variable 'mean_x' is
11. return std
assigned to but never used
12.

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Using the output for quality code
1. import numpy as np flake8 features.py
2.
3.
4. def mean(x):
5. """Calculate the mean"""
6. return np.mean(x)
7.
8.
9. def std(x):
10. """Calculate the standard deviation"""
11. mean_x = mean(x)
12. std = mean((x - mean_x)**2)
13. return std
14.

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Breaking the rules on purpose
quadratic.py

4. ...
5. quadratic_1 = 6 * x**2 + 2 * x + 4;
6. quadratic_2 = 12 * x**2 + 2 * x + 8
7. ...

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Breaking the rules on purpose
quadratic.py

4. ...
5. quadratic_1 = 6 * x**2 + 2 * x + 4;
6. quadratic_2 = 12 * x**2 + 2 * x + 8
7. ...

flake8 quadratic.py

quadratic.py:5:14: E222 multiple spaces after operator


quadratic.py:5:35: E703 statement ends with a semicolon

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Breaking the rules on purpose
quadratic.py

4. ...
5. quadratic_1 = 6 * x**2 + 2 * x + 4; # noqa
6. quadratic_2 = 12 * x**2 + 2 * x + 8
7. ...

flake8 quadratic.py

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Breaking the rules on purpose
quadratic.py

4. ...
5. quadratic_1 = 6 * x**2 + 2 * x + 4; # noqa: E222
6. quadratic_2 = 12 * x**2 + 2 * x + 8
7. ...

flake8 quadratic.py

quadratic.py:5:35: E703 statement ends with a semicolon

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flake8 settings
Ignoring style violations without using comments

flake8 --ignore E222 quadratic.py

quadratic.py:5:35: E703 statement ends with a semicolon

flake8 --select F401,F841 features.py

2:1: F401 'math' imported but unused


9:5: F841 local variable 'mean_x' is assigned
to but never used

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Choosing package settings using setup.cfg
Create a setup.cfg to store settings Package file tree

.
|-- example_package
| |-- __init__.py
| `-- example_package.py
|-- tests
| |-- __init__.py
| `-- test_example_package.py
|-- README.rst
|-- LICENSE
|-- MANIFEST.in
`-- setup.py

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Choosing package settings using setup.cfg
Create a setup.cfg to store settings Package file tree

[flake8] .
|-- example_package
ignore = E302 | |-- __init__.py
exclude = setup.py | `-- example_package.py
|-- tests
per-file-ignores = | |-- __init__.py
example_package/example_package.py: E222 | `-- test_example_package.py
|-- README.rst
|-- LICENSE
|-- MANIFEST.in
|-- setup.py
`-- setup.cfg

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The whole package
$ flake8 Package file tree

.
|-- example_package
| |-- __init__.py
| `-- example_package.py
|-- tests
| |-- __init__.py
| `-- test_example_package.py
|-- README.rst
|-- LICENSE
|-- MANIFEST.in
|-- setup.py
`-- setup.cfg

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Use the least filtering possible
Least filtering

1. # noqa : <code>

2. # noqa
3. setup.py → per-file-ignores

4. setup.py → exclude , ignore

Most filtering

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Let's practice!
D E V E L O P I N G P Y T H O N PA C K A G E S

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