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Testing

This page describes how to run the test suite and how tests are organized.

Running Tests

pytest

From the project root. The test configuration is in pytest.ini.

With coverage reporting:

pytest --cov

Current Test Coverage

The test suite is currently minimal. Only one test file exists:

tests/test_config.py

Tests for config/logconf.py:

Function What it tests
logger_handles_empty_log_directory Logger creates log dir if missing
logger_does_not_duplicate_handlers Calling setup_logger twice does not duplicate handlers
logger_handles_no_log_directory Logger works without a log dir (stream-only)
logger_respects_custom_formatter Logger uses ColoredFormatter for all handlers

Known issue: These test functions are not prefixed with test_, so pytest does not collect or run them automatically. They must be renamed (e.g. def test_logger_handles_...) before they become active tests. This is a pre-existing gap in the test suite.

Current Limitations

  • Most pipeline modules (kinopt, tfopt, networkmodel, paramest) have no automated tests.
  • The test suite does not cover ODE solving, parameter estimation, optimization, or data I/O.
  • Integration tests (end-to-end pipeline runs) do not exist.

Unit tests

Use pytest with tmp_path fixture for file-I/O tests:

import pytest
from config.logconf import setup_logger

def test_logger_creates_log_dir(tmp_path):
    log_dir = str(tmp_path / "logs")
    setup_logger(name="test", log_dir=log_dir)
    assert (tmp_path / "logs").exists()

What should be unit-tested

  • Configuration loading (config_loader.load()) with a fixture config.toml
  • Parameter bounds validation
  • ODE right-hand side functions with known analytical inputs
  • Loss function values for zero-error inputs
  • Fréchet distance (frechet.frechet_distance) for trivial curves

What should be integration-tested

  • A minimal end-to-end run of processing.cleanup with a synthetic input CSV
  • kinopt.local or tfopt.local with a small synthetic dataset
  • networkmodel.runner with a tiny synthetic 2-gene network

Running with Poetry

If using Poetry:

poetry run pytest
poetry run pytest --cov --cov-report=html

pytest.ini

The project includes a pytest.ini at the root. Check it for any custom markers or configuration that affects test discovery.