├── .flake8 ├── .gitignore ├── .travis.yml ├── CONTRIBUTING.rst ├── LICENSE.txt ├── README.rst ├── docs ├── Makefile ├── make.bat └── source │ ├── api │ ├── annodoc.rst │ ├── annospan.rst │ ├── annotier.rst │ └── index.rst │ ├── conf.py │ ├── index.rst │ └── readme.rst ├── epitator ├── __init__.py ├── annodoc.py ├── annospan.py ├── annotator.py ├── annotier.py ├── count_annotator.py ├── database_interface.py ├── date_annotator.py ├── disease_annotator.py ├── geoname_annotator.py ├── geoname_classifier.py ├── get_database_connection.py ├── importers │ ├── __init__.py │ ├── doid_extension.ttl │ ├── import_all.py │ ├── import_disease_ontology.py │ ├── import_geonames.py │ ├── import_species.py │ └── import_wikidata.py ├── incident_annotator.py ├── infection_annotator.py ├── maximum_weight_interval_set.py ├── metaspan.py ├── ne_annotator.py ├── ngram_annotator.py ├── pos_annotator.py ├── raw_number_annotator.py ├── resolved_keyword_annotator.py ├── spacy_annotator.py ├── spacy_nlp.py ├── species_annotator.py ├── structured_data_annotator.py ├── structured_incident_annotator.py ├── token_annotator.py ├── utils.py └── version.py ├── requirements.readthedocs.txt ├── requirements.txt ├── run_doctests.py ├── runtests.py ├── setup.py └── tests ├── __init__.py └── annotator ├── __init__.py ├── resources ├── WhereToItaly.anc ├── WhereToItaly.txt └── adenoviruses.txt ├── test_count_annotator.py ├── test_date_annotator.py ├── test_db_interface.py ├── test_geoname_annotator.py ├── test_incident_annotator.py ├── test_infection_annotator.py ├── test_ne_annotator.py ├── test_ngram_annotator.py ├── test_pos_annotator.py ├── test_resolved_keyword_annotator.py ├── test_species_annotator.py ├── test_structured_data_annotator.py ├── test_structured_incident_annotator.py ├── test_token_annotator.py └── test_utils.py /.flake8: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ecohealthalliance/EpiTator/HEAD/.flake8 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