.coveragerc .github/workflows/run_tests.yaml .gitignore LICENSE.md Makefile Pipfile Pipfile.lock README.md delta_load_algorithm.md delta_load_atomicity.md docker-compose.yaml relation_engine/batchload/delta_load.py relation_engine/batchload/rollback_delta_load.py relation_engine/batchload/test/delta_load_integration_test.py relation_engine/batchload/test/test_helpers.py relation_engine/batchload/test/time_travelling_database_test.py relation_engine/batchload/time_travelling_database.py relation_engine/ontologies/obograph/helper_scripts/envo_obograph_download_archive.py relation_engine/ontologies/obograph/helper_scripts/go_obograph_download_archive.py relation_engine/ontologies/obograph/loaders/obograph_delta_loader.py relation_engine/ontologies/obograph/parsers.py relation_engine/taxa/gtdb/loaders/gtdb_taxa_delta_loader.py relation_engine/taxa/gtdb/parsers.py relation_engine/taxa/ncbi/helper_scripts/ncbi_taxa_download_archive.py relation_engine/taxa/ncbi/loaders/ncbi_taxa_delta_loader.py relation_engine/taxa/ncbi/parsers.py relation_engine/taxa/ncbi/test/parsers_test.py relation_engine/taxa/rdp/loaders/rdp_taxa_delta_loader.py relation_engine/taxa/rdp/parsers.py relation_engine/taxa/silva/loaders/silva_taxa_delta_loader.py relation_engine/taxa/silva/parsers.py relation_engine/taxa/silva/test/test.py relation_engine/taxa/silva/util/dprint.py relation_engine/test/testing_helpers.py scripts/run_tests.sh snippets/README.md snippets/ncbi_taxa_rank_changes.md snippets/ncbi_taxa_rank_counts.md snippets/ncbi_taxa_ranks_ordered.txt snippets/performance_ncbi_bulk_vs_delta_loader.md src/GO/GO_parser.py src/GO/obo_parser.py src/GO/tests/data/GO_edges_consider.json src/GO/tests/data/GO_edges_disjoint_from.json src/GO/tests/data/GO_edges_intersection_of.json src/GO/tests/data/GO_edges_isa.json src/GO/tests/data/GO_edges_relationship.json src/GO/tests/data/GO_edges_replaced_by.json src/GO/tests/data/GO_term.json src/GO/tests/data/go.obo src/GO/tests/test_edges.py src/GO/tests/test_obo_parser.py src/GO/tests/test_terms.py src/KEGG/generate_kegg_complexes.py src/__init__.py src/gtdb/__init__.py src/gtdb/main.py src/jacobson_ornl/main.py src/modelseed/README.md src/modelseed/__init__.py src/modelseed/create_reaction_similarity_matrix.py src/modelseed/download_genbank_file.py src/modelseed/download_many_genbanks.py src/modelseed/generate_complexes.py src/modelseed/generate_genome_helpers.py src/modelseed/generate_genomes.py src/modelseed/generate_import_data_test.sh src/modelseed/generate_reaction_similarities_json.py src/modelseed/generate_reactions.py src/modelseed/import_compounds.py src/modelseed/import_json_data.py src/modelseed/import_reaction_similarities.py src/modelseed/test/__init__.py src/modelseed/test/test_flatten_boolean_expr.py src/modelseed/test/test_import_genome.py src/modelseed/utils/__init__.py src/modelseed/utils/flatten_boolean_expr.py src/modelseed/utils/init_db.py src/modelseed/utils/parse_gpr.py src/modelseed/utils/write_import_file.py src/ncbi/NCBI_tax_loader.py src/utils/__init__.py src/utils/import_directory.py src/utils/import_json_file.py src/utils/shell_load_directory.sh tox.ini <<<<<< network # path=./cov.xml /home/runner/work/relation_engine_importers/relation_engine_importers <<<<<< EOF