This directory contains tests for the gfftk package.

To run the tests, use pytest:

cd /Users/jon/software/gfftk
python -m pytest

To run tests with verbose output:

python -m pytest -v

To run a specific test file:

python -m pytest tests/unit/test_gff.py

To run a specific test:

python -m pytest tests/unit/test_gff.py::TestGFFParsing::test_detect_format

• unit/: Unit tests for individual functions and classes

  • test_basic.py: Basic tests to verify pytest is working
  • test_gff.py: Tests for the gff module
  • test_consensus.py: Tests for the consensus module
  • test_convert.py: Tests for the convert module

• data/: Test data files

  • sample.gff3: Sample GFF3 file for testing
  • sample.fasta: Sample FASTA file for testing

When adding new tests, follow these guidelines:

1. Create a new test file in the appropriate directory (e.g., tests/unit/test_new_module.py)
2. Use the pytest framework for writing tests
3. Use descriptive test names that indicate what is being tested
4. Use fixtures for common test data
5. Clean up any temporary files created during tests

To run tests with coverage reporting:

python -m pytest --cov=gfftk

To generate a detailed HTML coverage report:

python -m pytest --cov=gfftk --cov-report=html

This will create a htmlcov directory with the coverage report.