Coverage Guide¶

To measure test coverage in the Biofilter project, we use Coverage.py. This guide outlines the steps to install, run, and generate coverage reports while considering the integration with Poetry and the CI/CD pipeline.

1. Install Coverage.py¶

Coverage.py is already included in the project’s development dependencies via Poetry. To ensure it is installed, simply run:

poetry install

This command installs all development dependencies, including Coverage.py.

Note

There is no need to install coverage manually using pip, as it is managed through Poetry.

2. Run Tests with Coverage¶

In the Biofilter project directory, use coverage to run the tests and collect coverage data. Since we are using Poetry, the command is:

poetry run coverage run -m pytest

This command uses coverage to execute pytest, running all tests and collecting information on which parts of the code are covered.

3. Generate a Coverage Report in the Terminal¶

After running the tests, generate a coverage report in the terminal:

poetry run coverage report -m

The -m option displays which lines were not covered.

4. Generate an HTML Report¶

For a more detailed view, generate an HTML report:

poetry run coverage html

This creates a directory called htmlcov with an index.html file. Open this file in a browser for a detailed view of the coverage.

5. Exclude Files or Lines from the Report (Optional)¶

To exclude specific files or certain lines (e.g., docstrings or debugging instructions), create a .coveragerc file in the root directory of the Biofilter project. Use the following example:

[run]
omit =
   tests/*
   setup.py

[report]
exclude_lines =
   # Exclude debug lines
   if __name__ == "__main__":
   pragma: no cover

This configuration ensures that coverage focuses only on the relevant parts of the codebase.

Integration with CI/CD¶

Test coverage is also verified automatically in the CI/CD pipeline through GitHub Actions. This ensures that every change to the codebase maintains or improves test coverage. Before pushing changes, it is recommended to check the coverage locally using the commands outlined above.

Important

Always verify coverage locally before committing to avoid failures during the CI/CD process.

Summary of Commands¶

Install dependencies: (if not already installed)
```
poetry install
```
Run tests with coverage:
```
poetry run coverage run -m pytest
```
Generate terminal report:
```
poetry run coverage report -m
```
Generate HTML report:
```
poetry run coverage html
```