Setup ruff for lintint/formatting

.flake8

.isort.cfg

.pre-commit-config.yaml

nerval/__init__.py

nerval/cli.py

nerval/evaluate.py

nerval/parse.py

nerval/utils.py

pyproject.toml

setup.py

tests/conftest.py

tests/test_align.py

tests/test_compute_matches.py

tests/test_compute_scores.py

tests/test_get_labels_aligned.py

tests/test_parse_bio.py

tests/test_run.py