Unit Tests

Disclaimer: this course is adapted from the following sources:

Tests

Tests are small pieces of code ensuring that a part of a program is working as expected.

Why tests are useful

This is why we place the uttermost importance on implementing tests along the development steps. It will help you to ensure:

  • that code works correctly.
  • that changes do not break anything.
  • that bugs are not reintroduced.
  • robustness to user errors.
  • code is reachable (i.e., it will actually be executed)
  • etc.

Types of tests

There are different kinds of tests, with the more important ones being:

  1. Unit tests: test whether a simple unit element (function, class, etc.) does the right thing.
  2. Integration tests: test whether the different parts used by your software work well together.
  3. Non-regression tests: test whether a new or modified functionality works correctly and that previous functionalities were not affected (e.g., removing a bug does not alter the rest of the code).

How to test?

Many coding languages come with their own test framework. In python, we will focus on pytest. It is simple though powerful. pytest searches for all test*.py files and runs all test* methods found. It outputs a nice error report.

EXERCISE: pytest
  1. Install pytest with pip using the user scheme (--user option)
  2. Test if the command pytest is in your PATH (depending on your configuration you will have to add ~/.local/bin in PATH)

Get the path to pytest binary as follows with python:

import pytest
pytest.__path__

This outputs a directory containing the pytest binary, say /path/to/pytest. Then, to add the path containing pytest in your (Linux) system, you have to type the following command in your terminal:

$ export PATH=$PATH:/path/to/pytest
$ pytest --help

Example

Let us assume we have a file inc.py containing

def inc1(x):
    return x + 1

def inc2(x):
    return x + 2

Thence, the content of test_inc.py is

from inc import inc1, inc2

# This test will work
def test_inc1():
    assert inc1(3) == 4

# This test will fail
def test_inc2():
    assert inc2(-1) == 4

To run these tests:

$ pytest test_inc.py
EXERCISE: documentation
  1. Correct the test_inc2 test.
  2. Determine the syntax to run any test in a directory.
  3. Determine the syntax to run only the test called test_inc1.

Code coverage

pytest comes with some useful plugins. In particular, we will use the coverage report plugin.

A test coverage is a measure used to describe the degree to which the source code of a program is executed when a particular test suite runs. A program with high test coverage, measured as a percentage, has had more of its source code executed during testing: this suggests it has a lower chance of containing undetected software bugs compared to a program with low test coverage.

To install the coverage plugin simply run the pip command:

$ pip install pytest-cov

Assuming the inc_cov.py contains:

def inc(x):
    if x < 0:
        return 0
    return x + 1

def dec(x):
     return x - 1

and a single test is performed through the file test_inc_cov.py

from inc_cov import inc

def test_inc():
     assert inc(3) == 4

then

pytest test_inc_cov.py --cov
============================= test session starts =============================
platform linux -- Python 3.10.10, pytest-7.4.2, pluggy-1.0.0
rootdir: /home/jsalmon/Documents/Mes_cours/Montpellier/HAX712X/Courses/Test
plugins: dash-2.9.3, cov-4.1.0, anyio-3.6.2
collected 1 item

test_inc_cov.py                                                          [100%]

---------- coverage: platform linux, python 3.10.10-final-0 ----------
Name              Stmts   Miss  Cover
-------------------------------------
inc_cov.py            6      2    67%
test_inc_cov.py       3      0   100%
-------------------------------------
TOTAL                 9      2    78%


===============================================================================
1 passed in 0.02s
===============================================================================

Two lines in inc_cov module were not used. See

pytest --cov --cov-report=html test_inc_cov.py

============================= test session starts =============================
platform linux -- Python 3.10.10, pytest-7.4.2, pluggy-1.0.0
rootdir: /home/jsalmon/Documents/Mes_cours/Montpellier/HAX712X/Courses/Test
plugins: dash-2.9.3, cov-4.1.0, anyio-3.6.2
collected 1 item

test_inc_cov.py                                                          [100%]

---------- coverage: platform linux, python 3.10.10-final-0 ----------
Coverage HTML written to dir htmlcov

for details.

EXERCISE:
  1. Install the pytest’s coverage plugin.
  2. Load the biketrauma package you can download at https://github.com/HMMA238-2020/biketrauma/
  3. Add some unit tests to biketrauma in a new sub-directory ./biketrauma/tests/:

    • Create a first test_df() that test if the Côtes-d’or département has 152 accidents. Add a second test_df_log() testing that the log of the number of accidents in the département 92 is close to 7.161622002.

    • Create a test_dl() function that tests the md5sum hash of the downloaded file (a.k.a. bicycle_db.csv). You may use the pooch package or you can use this piece of code to compute the md5sum:

import hashlib
def md5(fname):
    hash_md5 = hashlib.md5()
    with open(fname, "rb") as f:
        for chunk in iter(lambda: f.read(4096), b""):
            hash_md5.update(chunk)
    return hash_md5.hexdigest()

By running the following line in the biketrauma/biketrauma location:

pytest --cov-report=html --cov=biketrauma tests/

you should reach 79% of code coverage, and the report should look like this (see the htmlcov/index.html file for an interactive report):

---------- coverage: platform linux, python 3.10.10-final-0 ----------
Name                                    Stmts   Miss  Cover
----------------------------------------------------------------------
biketrauma/__init__.py                      4      0   100%
biketrauma/io/Load_db.py                   22      5    77%
biketrauma/io/__init__.py                   3      0   100%
biketrauma/preprocess/__init__.py           0      0   100%
biketrauma/preprocess/get_accident.py       7      0   100%
biketrauma/vis/__init__.py                  0      0   100%
biketrauma/vis/plot_location.py             6      4    33%
----------------------------------------------------------------------
TOTAL                                      42      9    79%

References

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