Specific installations

When cloning the repository, you may want to run tests on the source code. From the repository directory, you can add install options to the pip install -e . command to install specific dependencies for PhysioBlocks.

test: Install dependencies to run tests and code coverage.
doc: Install dependencies to build the documentation.
quality: Install dependencies to check code quality.
tox: Install tox to automatize package tests.

After installing PhysioBlocks with any of those options, you will be able to run the corresponding tests on the package.

Run tests and coverage

With a test option installation, from the repository directory:

coverage run -m pytest
coverage html

The coverage report will be available in html in the htmlcov folder.

Log messages while running tests

To log information or debug messages when running the tests:

1. Always log while running the tests: locally change the pyproject.toml

Add the lines defining the log_cli and log_cli_level under the [tool.pytest.ini_options] of the pyproject.toml file like in the following example:

[tool.pytest.ini_options]
addopts = "-ra -q"
testpaths = [ "tests", ]
log_cli = true
log_cli_level = "DEBUG"

2. Occasionally log while running the tests: overwrite pytest arguments in the command line

Overwrite the log_cli and log_cli_level in the command line when running a test. From the repository directory:

# Example 1: Run all test with debug level logs:
pytest -o log_cli=true -o log_cli_level=DEBUG

# Example 2: Run a single test with debug level logs:
# $TEST_FILE_PATH: the path of the file contening the test
# $TEST_NAME: the test to run
pytest $TEST_FILE_PATH -k $TEST_NAME -o log_cli=true -o log_cli_level=DEBUG

Build the documentation

With a doc option installation, from the repository directory:

cd doc
make html

The documentation will be available in the doc/build folder.

Check quality

With a quality option installation, from the repository directory:

# Format code with ruff:
ruff format

# Check code with ruff:
ruff check

# Check typing with mypy:
mypy PhysioBlocks --strict --ignore-missing-imports

Run the automated package tests

With a tox option installation, from the repository directory:

# Runs formater, linter, type checker and tests for several python versions
tox