Module 3: Installable package and pytest

In the last module, you introduced modules, classes and a new notebook in you repo. In this module, you will add tests to your code base. But first, you will make your package installable.

• Create new branch “package-test” (Make sure changes from last module have been merged, and that you start from the main branch)
• 3.1 Installable package
  • Organize the files into folders and add setup.py. Call your package tscleaner.
    • subfolders: tscleaner, scripts, notebooks, tests
    • make an init-file __init__.py in the tscleaner folder with the following content:

    from .cleaning import SpikeCleaner, FlatPeriodCleaner, OutOfRangeCleaner
    from .plotting import plot_timeseries

    • create a setup.py in the root with the following content (change with your data):

    from setuptools import setup, find_packages
    setup(
      name='MyPackageName',  
      version='0.0.1',  
      url='https://github.com/mypackage.git',  
      author='Author Name',  
      author_email='author@gmail.com',  
      description='Description of my package',  
      packages=find_packages(),  
      install_requires=['numpy', 'matplotlib'],  
    )  

• Install the package in editable mode, by running the below command from the project root. - > pip install -e .
  • Modify import statements in notebook_A and script main.py and make sure they run.
  • Modify the cleaner tools by raising exceptions for invalid inputs.
  • Move the csv file to /tests/testdata and update notebook with relative path to the file
• 3.2 Pytest
  • Make sure pytest and pytest-cov are installed
  • Write unit tests with pytest in the /tests folder. Create an empty __init__.py file in the folder. Create a file test_cleaning.py and create at least three tests that verify that the cleaning tools work as intended
  • If all your tests are failing, consider if you have given the right requirements in the setup.py…
  • [Optional] Consider to make a fixture that reads the csv file and you can read in all tests
  • Run the tests from the commandline by writting >pytest in the project root (can you also run the tests from VSCode?)
  • Assess the test coverage with >pytest --cov=tscleaner tests
  • [Optional] Get coverage as html with >pytest --cov=tscleaner --cov-report html (check the index.html in the htmlcov subfolder afterwards)
• Create pull request in GitHub and “request review” from your reviewers
• Get feedback, Adjust code until approval, then merge (and delete branch)

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