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 an empty pyproject.toml. Call your package tscleaner.
    • subfolders: src/tscleaner, scripts, notebooks, tests
    • make an init-file __init__.py in the src/tscleaner folder with the following content:

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

  Project structure:

  ├── notebooks/
  ├── scripts/
  ├── src/
  │   └── tscleaner/
  │       └── __init__.py
  ├── tests/
  └── pyproject.toml

  • edit the pyproject.toml in the root with the following content (change with your data):

  [project]
  name = "tscleaner"
  version = "0.1.0"
  description = "Add your description here"
  authors = [
      { name = "Mike Water", email = "xyz@dhigroup.com" }
  ]
  requires-python = ">=3.13"
  dependencies = [
      "matplotlib",
      "numpy",
  ]
  
  [dependency-groups]
  dev = ["pytest", "pytest-cov"]
  
  [tool.pytest.ini_options]
  pythonpath = ["src"]

  • 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

  • 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 pyproject.toml…
  • [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 > uv run pytest in the project root (can you also run the tests from VSCode?)
  • Assess the test coverage with > uv run pytest --cov=tscleaner tests
  • [Optional] Get coverage as html with > uv run 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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