Some small refactoring

.gitlab-ci.yml

.pre-commit-config.yaml

MANIFEST.in

nerval/__init__.py

nerval/cli.py

nerval/evaluate.py

nerval/parse.py

nerval/utils.py

setup.py

tests/__init__.py

tests/conftest.py

tests/fixtures/bioeslu.bio

tests/fixtures/end_of_file.bio

tests/fixtures/test_annot.bio

tests/fixtures/test_bad.bio

tests/fixtures/test_empty.bio

tests/fixtures/test_nested.bio

tests/fixtures/test_predict.bio

tests/test_align.py

tests/test_compute_matches.py