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Sciware

Testing and packaging workshop guide

Repo setup and packaging

Fork and clone the repo

Setup your repo

  • cd sciware-testing-python
  • pip3 install -e .
    • Or pip3 install --user -e . without venv/conda
  • pytest

You should see: 12 passed, 2 skipped, 2 xfailed, 1 xpassed

Code overview

  • Code lives in sciware_testing_python/*.py (main module: exercise.py)
  • Tests live in tests/test_*.py
  • Let's look at sciware_testing_python/exercise.py now
    • sum_numbers: what does it do? how do you use it?

Exercise: write tests

Simple tests

  • Open tests/test_exercise.py
  • Write some tests for sum_numbers
    • Fill in test_sum_numbers_yours and test_sum_numbers_empty
    • Change pass to assert sum_numbers(..) == ..
  • Run pytest tests/test_exercise.py

Bonus: commit and push your changes

Exercise: doctests

  • Open sciware_testing_python/exercise.py
  • Add another doctest to the lines in quoted documentation: 
    • Example
-------
>>> sum_numbers([])
0
    • Any >>> line in a docstring will be executed and compared to the expected output on the following line
  • Run pytest --doctest-modules sciware_testing_python/exercise.py

Exercise: test-driven fixes

  • Look at sciware_testing_python/exercise.py add_vectors
    • It has a problem (but don't fix it yet)
  • Add a new test for add_vectors to tests/test_exercise.py
  • pytest tests/test_exercise.py: FAIL!
  • Fix add_vectors and try again
    • Hint: change * to +

Exercise: testing for error cases

  • Update the test_sum_strings test in tests/test_exercise.py to call sum_numbers on a list of strings
  • pytest tests/test_exercise.py: FAIL
  • Tell pytest that this should actually fail:
    • Add (uncomment) @pytest.mark.xfail(strict=True) before the function
  • Run tests again: now it should pass

Exercise: test-driven development (TDD)

  • Open tests/test_tdd.py and look at the tests
    • We wrote a test before writing the code for count_twos
  • Remove the @pytest.mark.skip line for test_count_twos
  • Run pytest tests/test_tdd.py: FAIL!
    • count_twos doesn't exist yet!
  • Add a count_twos function to sciware_testing_python/exercise.py
  • Run the tests again to pass

Bonus: other pytest features

  • See examples in tests/test_examples.py
  • @pytest.mark.parameterize
    • can be used to loop over input arguments for your test
    • @pytest.mark.parameterize("arg1, arg2, ...", [[val1, val2, ...], ...]
  • @pytest.fixture
    • Fixtures are called automatically to generate/load matching arguments

CI: Github Actions

Enable action on your fork

  • Click on "Actions" tab
  • Click "I understand ... enable"

Exercise: improve CI tests

  • Open .github/workflows/exercise.yml
  • Add 3.9 to python-version to add testing for Python 3.9
  • Add a pytest --doctest-modules to the Test step
  • Commit and push (to your repo)

Bonus:

  • Open README.md
  • Fix the badge link to point to your repo

Bonus: Code coverage

  • Run pytest --cov
  • Open .github/workflows/exercise.yml
  • Update the Test step so it runs pytest --doctest-modules --cov

Code Coverage (cont.)

  • Setup your account at codecov.io
    • Link it to sciware-testing-python
    • Go to Settings -> Repository Upload Token and copy the token
  • Uncomment the Codecov step and paste your token
  • Commit and push (to your repo)

Bonus: Typing

  • Run mypy
  • Add type some annotations to sciware_testing_python/exercise.py (see examples.py)