Pytest results (Python 3.14) - 2026-06-28T22:59:07Z

============================= test session starts ==============================
platform linux -- Python 3.14.6, pytest-9.1.1, pluggy-1.6.0 -- /home/runner/.local/share/hatch/env/virtual/gget/dY-b3nRT/hatch-test.py3.14/bin/python3
cachedir: .pytest_cache
Using --randomly-seed=495051567
rootdir: /home/runner/work/gget/gget
configfile: pyproject.toml
testpaths: tests
plugins: randomly-3.16.0, rerunfailures-14.0, mock-3.15.1, cov-7.1.0, xdist-3.8.0
collecting ... collected 422 items

tests/test_elm.py::TestELM::test_elm_uniprot_id_in_elm PASSED            [  0%]
tests/test_elm.py::TestELM::test_elm_uniprot_aminoacidseq PASSED         [  0%]
tests/test_elm.py::TestELM::test_elm_uniprot_id_new PASSED               [  0%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_combined_filters PASSED [  0%]
tests/test_virus.py::TestVirus::test_batch_accessions_for_url PASSED     [  1%]
tests/test_virus.py::TestVirus::test_save_partial_metadata_empty PASSED  [  1%]
tests/test_virus.py::TestVirus::test_virus_min_greater_than_max_collection_date PASSED [  1%]
tests/test_virus.py::TestVirus::test_virus_invalid_keep_temp_type PASSED [  1%]
tests/test_virus.py::TestVirus::test_filter_genbank_metadata_no_filters PASSED [  2%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_vaccine_strain_true PASSED [  2%]
tests/test_virus.py::TestVirus::test_virus_invalid_lab_passaged_type PASSED [  2%]
tests/test_virus.py::TestVirus::test_virus_with_genbank_metadata_retrieval PASSED [  2%]
tests/test_virus.py::TestVirus::test_validate_datasets_binary_nonexistent PASSED [  3%]
tests/test_virus.py::TestVirus::test_virus_with_multiple_filters PASSED  [  3%]
tests/test_virus.py::TestVirus::test_get_modified_virus_name_empty_returns_none PASSED [  3%]
tests/test_virus.py::TestVirus::test_filter_cached_host_not_in_strategy PASSED [  3%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_max_seq_length PASSED [  4%]
tests/test_virus.py::TestVirus::test_parse_genbank_xml_invalid_raises PASSED [  4%]
tests/test_virus.py::TestVirus::test_local_name_without_namespace PASSED [  4%]
tests/test_virus.py::TestVirus::test_parse_partial_date_year_month_min PASSED [  4%]
tests/test_virus.py::TestVirus::test_virus_min_greater_than_max_gene_count PASSED [  4%]
tests/test_virus.py::TestVirus::test_retry_helper_exponential_backoff_timing PASSED [  5%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_submitter_institution PASSED [  5%]
tests/test_virus.py::TestVirus::test_merge_metadata_csvs_missing_standard_file PASSED [  5%]
tests/test_virus.py::TestVirus::test_filter_genbank_metadata_empty PASSED [  5%]
tests/test_virus.py::TestVirus::test_virus_empty_virus_name PASSED       [  6%]
tests/test_virus.py::TestVirus::test_clean_xml_declarations_no_declarations PASSED [  6%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_geographic_location PASSED [  6%]
tests/test_virus.py::TestVirus::test_retry_helper_successful_operation PASSED [  6%]
tests/test_virus.py::TestVirus::test_write_fasta_record_with_description PASSED [  7%]
tests/test_virus.py::TestVirus::test_filter_cached_annotated PASSED      [  7%]
tests/test_virus.py::TestVirus::test_virus_completeness_filter_verification PASSED [  7%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_submitter_country PASSED [  7%]
tests/test_virus.py::TestVirus::test_parse_genbank_xml_empty_set PASSED  [  8%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_protein_count PASSED [  8%]
tests/test_virus.py::TestVirus::test_virus_with_collection_date_filters PASSED [  8%]
tests/test_virus.py::TestVirus::test_write_fasta_record_long_sequence_wraps PASSED [  8%]
tests/test_virus.py::TestVirus::test_virus_invalid_completeness PASSED   [  9%]
tests/test_virus.py::TestVirus::test_virus_none_virus_name PASSED        [  9%]
tests/test_virus.py::TestVirus::test_load_metadata_from_api_reports_basic PASSED [  9%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_no_filters PASSED [  9%]
tests/test_virus.py::TestVirus::test_virus_multi_accession_file_input PASSED [  9%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_submitter_name PASSED [ 10%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_vaccine_strain_false PASSED [ 10%]
tests/test_virus.py::TestVirus::test_save_genbank_metadata_to_csv_empty PASSED [ 10%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_segment PASSED [ 10%]
tests/test_virus.py::TestVirus::test_virus_with_length_filters PASSED    [ 11%]
tests/test_virus.py::TestVirus::test_retry_helper_success_after_retry PASSED [ 11%]
tests/test_virus.py::TestVirus::test_save_metadata_to_csv_empty_metadata PASSED [ 11%]
tests/test_virus.py::TestVirus::test_virus_with_source_database_filter PASSED [ 11%]
tests/test_virus.py::TestVirus::test_virus_invalid_genbank_batch_size_zero PASSED [ 12%]
tests/test_virus.py::TestVirus::test_virus_invalid_genbank_metadata_type PASSED [ 12%]
tests/test_virus.py::TestVirus::test_clean_xml_declarations PASSED       [ 12%]
tests/test_virus.py::TestVirus::test_unzip_file_valid PASSED             [ 12%]
tests/test_virus.py::TestVirus::test_get_datasets_path_uses_bundled_binary PASSED [ 13%]
tests/test_virus.py::TestVirus::test_filter_genbank_metadata_has_proteins PASSED [ 13%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_source_database PASSED [ 13%]
tests/test_virus.py::TestVirus::test_parse_partial_date_year_only_max_comparison PASSED [ 13%]
tests/test_virus.py::TestVirus::test_unzip_file_nonexistent_raises PASSED [ 13%]
tests/test_virus.py::TestVirus::test_virus_min_greater_than_max_seq_length PASSED [ 14%]
tests/test_virus.py::TestVirus::test_parse_accession_input_from_file PASSED [ 14%]
tests/test_virus.py::TestVirus::test_virus_invalid_genbank_batch_size_type PASSED [ 14%]
tests/test_virus.py::TestVirus::test_virus_with_protein_count_filters PASSED [ 14%]
tests/test_virus.py::TestVirus::test_parse_baseline_file_none_raises PASSED [ 15%]
tests/test_virus.py::TestVirus::test_is_sars_cov2_query_accession_mode PASSED [ 15%]
tests/test_virus.py::TestVirus::test_filter_genbank_metadata_genotype PASSED [ 15%]
tests/test_virus.py::TestVirus::test_virus_min_greater_than_max_release_date PASSED [ 15%]
tests/test_virus.py::TestVirus::test_retry_helper_non_retryable_exception PASSED [ 16%]
tests/test_virus.py::TestVirus::test_filter_genbank_metadata_provirus_false PASSED [ 16%]
tests/test_virus.py::TestVirus::test_is_alphainfluenza_query_negative PASSED [ 16%]
tests/test_virus.py::TestVirus::test_is_alphainfluenza_query_common_names PASSED [ 16%]
tests/test_virus.py::TestVirus::test_get_modified_virus_name_add_virus_suffix PASSED [ 17%]
tests/test_virus.py::TestVirus::test_filter_genbank_metadata_gen_mol_type PASSED [ 17%]
tests/test_virus.py::TestVirus::test_get_memory_usage_returns_dict PASSED [ 17%]
tests/test_virus.py::TestVirus::test_filter_genbank_metadata_genotype_list PASSED [ 17%]
tests/test_virus.py::TestVirus::test_get_modified_virus_name_already_correct_returns_none PASSED [ 18%]
tests/test_virus.py::TestVirus::test_local_name_with_namespace PASSED    [ 18%]
tests/test_virus.py::TestVirus::test_parse_date_invalid_raises PASSED    [ 18%]
tests/test_virus.py::TestVirus::test_parse_accession_input_empty_file_raises_error PASSED [ 18%]
tests/test_virus.py::TestVirus::test_virus_with_annotated_filter PASSED  [ 18%]
tests/test_virus.py::TestVirus::test_merge_baseline_with_new_empty_new PASSED [ 19%]
tests/test_virus.py::TestVirus::test_merge_baseline_with_new_deduplicates PASSED [ 19%]
tests/test_virus.py::TestVirus::test_parse_date_full PASSED              [ 19%]
tests/test_virus.py::TestVirus::test_filter_cached_min_release_date PASSED [ 19%]
tests/test_virus.py::TestVirus::test_filter_genbank_metadata_combined PASSED [ 20%]
tests/test_virus.py::TestVirus::test_filter_cached_geographic_location PASSED [ 20%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_collection_date_range PASSED [ 20%]
tests/test_virus.py::TestVirus::test_unzip_file_bad_zip_raises PASSED    [ 20%]
tests/test_virus.py::TestVirus::test_parse_genbank_xml_basic PASSED      [ 21%]
tests/test_virus.py::TestVirus::test_parse_baseline_file_empty_raises PASSED [ 21%]
tests/test_virus.py::TestVirus::test_parse_baseline_file_nonexistent_raises PASSED [ 21%]
tests/test_virus.py::TestVirus::test_parse_baseline_file_jsonl PASSED    [ 21%]
tests/test_virus.py::TestVirus::test_parse_partial_date_year_only_min_comparison PASSED [ 22%]
tests/test_virus.py::TestVirus::test_merge_metadata_csvs_fills_missing PASSED [ 22%]
tests/test_virus.py::TestVirus::test_virus_relationship_check_counts_match PASSED [ 22%]
tests/test_virus.py::TestVirus::test_datasets_cli_version_output PASSED  [ 22%]
tests/test_virus.py::TestVirus::test_get_modified_virus_name_invalid_attempt_returns_none PASSED [ 22%]
tests/test_virus.py::TestVirus::test_parse_baseline_file_json PASSED     [ 23%]
tests/test_virus.py::TestVirus::test_virus_multi_accession_space_separated PASSED [ 23%]
tests/test_virus.py::TestVirus::test_save_genbank_metadata_to_csv_basic PASSED [ 23%]
tests/test_virus.py::TestVirus::test_virus_invalid_genbank_batch_size_negative PASSED [ 23%]
tests/test_virus.py::TestVirus::test_deduplicate_all_existing PASSED     [ 24%]
tests/test_virus.py::TestVirus::test_load_metadata_from_api_reports_empty PASSED [ 24%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_annotated_true PASSED [ 24%]
tests/test_virus.py::TestVirus::test_merge_baseline_with_new_csv PASSED  [ 24%]
tests/test_virus.py::TestVirus::test_force_garbage_collection_runs PASSED [ 25%]
tests/test_virus.py::TestVirus::test_virus_invalid_is_accession_type PASSED [ 25%]
tests/test_virus.py::TestVirus::test_stream_copy_fasta_with_accession_filter PASSED [ 25%]
tests/test_virus.py::TestVirus::test_virus_metadata_schema_validation PASSED [ 25%]
tests/test_virus.py::TestVirus::test_virus_integer_virus_id PASSED       [ 26%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_host PASSED    [ 26%]
tests/test_virus.py::TestVirus::test_validate_datasets_binary_valid PASSED [ 26%]
tests/test_virus.py::TestVirus::test_merge_metadata_csvs_no_overwrite PASSED [ 26%]
tests/test_virus.py::TestVirus::test_stream_copy_fasta_all_records PASSED [ 27%]
tests/test_virus.py::TestVirus::test_genbank_xml_to_csv_basic PASSED     [ 27%]
tests/test_virus.py::TestVirus::test_save_command_summary_with_error PASSED [ 27%]
tests/test_virus.py::TestVirus::test_is_sars_cov2_query_negative PASSED  [ 27%]
tests/test_virus.py::TestVirus::test_check_min_max_date_invalid_raises PASSED [ 27%]
tests/test_virus.py::TestVirus::test_virus_with_max_ambiguous_chars_filter PASSED [ 28%]
tests/test_virus.py::TestVirus::test_parse_baseline_file_text PASSED     [ 28%]
tests/test_virus.py::TestVirus::test_filter_genbank_metadata_provirus_true PASSED [ 28%]
tests/test_virus.py::TestVirus::test_check_min_max_none_values PASSED    [ 28%]
tests/test_virus.py::TestVirus::test_virus_min_greater_than_max_protein_count PASSED [ 29%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_min_seq_length PASSED [ 29%]
tests/test_virus.py::TestVirus::test_get_modified_virus_name_remove_parentheses PASSED [ 29%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_max_release_date PASSED [ 29%]
tests/test_virus.py::TestVirus::test_filter_genbank_metadata_mature_peptide_count PASSED [ 30%]
tests/test_virus.py::TestVirus::test_save_metadata_to_csv_basic PASSED   [ 30%]
tests/test_virus.py::TestVirus::test_filter_genbank_metadata_min_gene_count PASSED [ 30%]
tests/test_virus.py::TestVirus::test_check_min_max_invalid_raises PASSED [ 30%]
tests/test_virus.py::TestVirus::test_write_fasta_record_without_description PASSED [ 31%]
tests/test_virus.py::TestVirus::test_load_metadata_from_api_reports_multiple PASSED [ 31%]
tests/test_virus.py::TestVirus::test_virus_with_geographic_location_filter PASSED [ 31%]
tests/test_virus.py::TestVirus::test_check_min_max_equal PASSED          [ 31%]
tests/test_virus.py::TestVirus::test_check_min_max_valid PASSED          [ 31%]
tests/test_virus.py::TestVirus::test_virus_with_completeness_filter PASSED [ 32%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_annotated_false PASSED [ 32%]
tests/test_virus.py::TestVirus::test_virus_with_lab_passaged_filter PASSED [ 32%]
tests/test_virus.py::TestVirus::test_virus_release_date_filter_verification PASSED [ 32%]
tests/test_virus.py::TestVirus::test_get_gget_version_returns_string PASSED [ 33%]
tests/test_virus.py::TestVirus::test_virus_host_filter_verification PASSED [ 33%]
tests/test_virus.py::TestVirus::test_virus_with_host_filter PASSED       [ 33%]
tests/test_virus.py::TestVirus::test_virus_invalid_proteins_complete_type PASSED [ 33%]
tests/test_virus.py::TestVirus::test_filter_sequences_no_filters PASSED  [ 34%]
tests/test_virus.py::TestVirus::test_virus_invalid_annotated_type PASSED [ 34%]
tests/test_virus.py::TestVirus::test_is_alphainfluenza_query_accession_mode PASSED [ 34%]
tests/test_virus.py::TestVirus::test_load_metadata_from_api_reports_missing_accession PASSED [ 34%]
tests/test_virus.py::TestVirus::test_deduplicate_empty_baseline PASSED   [ 35%]
tests/test_virus.py::TestVirus::test_parse_date_various_formats PASSED   [ 35%]
tests/test_virus.py::TestVirus::test_parse_partial_date_empty_raises PASSED [ 35%]
tests/test_virus.py::TestVirus::test_filter_genbank_metadata_env_source PASSED [ 35%]
tests/test_virus.py::TestVirus::test_is_sars_cov2_query_common_names PASSED [ 36%]
tests/test_virus.py::TestVirus::test_parse_accession_input_space_separated PASSED [ 36%]
tests/test_virus.py::TestVirus::test_save_partial_metadata PASSED        [ 36%]
tests/test_virus.py::TestVirus::test_retry_helper_failed_commands_tracking PASSED [ 36%]
tests/test_virus.py::TestVirus::test_get_datasets_version_returns_string_or_none PASSED [ 36%]
tests/test_virus.py::TestVirus::test_filter_sequences_proteins_complete PASSED [ 37%]
tests/test_virus.py::TestVirus::test_parse_partial_date_full_date PASSED [ 37%]
tests/test_virus.py::TestVirus::test_parse_accession_input_nonexistent_file_raises_error PASSED [ 37%]
tests/test_virus.py::TestVirus::test_parse_partial_date_year_month_max PASSED [ 37%]
tests/test_virus.py::TestVirus::test_check_min_max_date_valid PASSED     [ 38%]
tests/test_virus.py::TestVirus::test_filter_genbank_metadata_max_gene_count PASSED [ 38%]
tests/test_virus.py::TestVirus::test_filter_cached_no_filters PASSED     [ 38%]
tests/test_virus.py::TestVirus::test_parse_accession_input_single PASSED [ 38%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_lab_passaged_false PASSED [ 39%]
tests/test_virus.py::TestVirus::test_track_failed_operation_none_dict PASSED [ 39%]
tests/test_virus.py::TestVirus::test_virus_min_greater_than_max_peptide_count PASSED [ 39%]
tests/test_virus.py::TestVirus::test_get_modified_virus_name_add_space_before_virus PASSED [ 39%]
tests/test_virus.py::TestVirus::test_virus_specific_accession_file_creation PASSED [ 40%]
tests/test_virus.py::TestVirus::test_track_failed_operation_creates_key PASSED [ 40%]
tests/test_virus.py::TestVirus::test_filter_cached_complete_only PASSED  [ 40%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_nuc_completeness_partial PASSED [ 40%]
tests/test_virus.py::TestVirus::test_get_modified_virus_name_no_parentheses_returns_none PASSED [ 40%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_isolation_source PASSED [ 41%]
tests/test_virus.py::TestVirus::test_filter_cached_refseq_only PASSED    [ 41%]
tests/test_virus.py::TestVirus::test_filter_cached_host_in_strategy_skipped PASSED [ 41%]
tests/test_virus.py::TestVirus::test_track_failed_operation_appends PASSED [ 41%]
tests/test_virus.py::TestVirus::test_deduplicate_metadata_against_baseline PASSED [ 42%]
tests/test_virus.py::TestVirus::test_save_command_summary_creates_file PASSED [ 42%]
tests/test_virus.py::TestVirus::test_get_datasets_path_returns_valid_path PASSED [ 42%]
tests/test_virus.py::TestVirus::test_parse_baseline_file_csv PASSED      [ 42%]
tests/test_virus.py::TestVirus::test_virus_with_has_proteins_filter PASSED [ 43%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_isolate PASSED [ 43%]
tests/test_virus.py::TestVirus::test_filter_metadata_only_lab_passaged_true PASSED [ 43%]
tests/test_virus.py::TestVirus::test_calculate_max_accessions_per_batch PASSED [ 43%]
tests/test_virus.py::TestVirus::test_validate_datasets_binary_empty_path PASSED [ 44%]
tests/test_virus.py::TestVirus::test_virus_multiple_filters_relationship_check PASSED [ 44%]
tests/test_virus.py::TestVirus::test_filter_sequences_max_ambiguous_chars PASSED [ 44%]
tests/test_virus.py::TestVirus::test_retry_helper_custom_retryable_exceptions PASSED [ 44%]
tests/test_blast.py::TestBlast::test_blast_bad_program PASSED            [ 45%]
tests/test_blast.py::TestBlast::test_blast_db_missing PASSED             [ 45%]
tests/test_blast.py::TestBlast::test_blast_nt PASSED                     [ 45%]
tests/test_blast.py::TestBlast::test_blast_bad_seq PASSED                [ 45%]
tests/test_blast.py::TestBlast::test_blast_bad_db1 PASSED                [ 45%]
tests/test_blast.py::TestBlast::test_blast_bad_fasta PASSED              [ 46%]
tests/test_blast.py::TestBlast::test_blast_bad_db2 PASSED                [ 46%]
tests/test_ref.py::TestRef::test_ref_ftp PASSED                          [ 46%]
tests/test_ref.py::TestRef::test_ref_rel_protist PASSED                  [ 46%]
tests/test_ref.py::TestRef::test_ref_which PASSED                        [ 47%]
tests/test_ref.py::TestRef::test_ref_list PASSED                         [ 47%]
tests/test_ref.py::TestRef::test_ref_rel PASSED                          [ 47%]
tests/test_ref.py::TestRef::test_ref_rel_ftp_octopus PASSED              [ 47%]
tests/test_ref.py::TestRef::test_ref_plant PASSED                        [ 48%]
tests/test_ref.py::TestRef::test_ref_bad_species PASSED                  [ 48%]
tests/test_ref.py::TestRef::test_ref_bad_which PASSED                    [ 48%]
tests/test_ref.py::TestRef::test_ref PASSED                              [ 48%]
tests/test_ref.py::TestRef::test_ref_bad_rel PASSED                      [ 49%]
tests/test_ref.py::TestRef::test_ref_rel_ftp PASSED                      [ 49%]
tests/test_ref.py::TestRef::test_ref_which_plant PASSED                  [ 49%]
tests/test_g2p.py::TestG2P::test_g2p_invalid_pair_returns_none PASSED    [ 49%]
tests/test_g2p.py::TestG2P::test_g2p_schema_invariant_across_input_modes PASSED [ 50%]
tests/test_g2p.py::TestG2P::test_g2p_map_has_pdb_list_column PASSED      [ 50%]
tests/test_g2p.py::TestG2P::test_g2p_gene_auto_resolved PASSED           [ 50%]
tests/test_g2p.py::TestG2P::test_g2p_uniprot_auto_resolved PASSED        [ 50%]
tests/test_g2p.py::TestG2P::test_g2p_features PASSED                     [ 50%]
tests/test_g2p.py::TestG2P::test_g2p_residues_single_int PASSED          [ 51%]
tests/test_g2p.py::TestG2P::test_g2p_alignment PASSED                    [ 51%]
tests/test_g2p.py::TestG2P::test_g2p_out_writes_to_explicit_path PASSED  [ 51%]
tests/test_g2p.py::TestG2P::test_g2p_residues_filter PASSED              [ 51%]
tests/test_g2p.py::TestG2P::test_g2p_map PASSED                          [ 52%]
tests/test_g2p.py::TestG2PValidation::test_alignment_requires_explicit_uniprot PASSED [ 52%]
tests/test_g2p.py::TestG2PValidation::test_missing_both_raises PASSED    [ 52%]
tests/test_g2p.py::TestG2PValidation::test_residues_wrong_type_raises PASSED [ 52%]
tests/test_g2p.py::TestG2PValidation::test_residues_on_map_raises PASSED [ 53%]
tests/test_g2p.py::TestG2PValidation::test_invalid_resource_raises PASSED [ 53%]
tests/test_g2p.py::TestG2PValidation::test_alignment_requires_isoform PASSED [ 53%]
tests/test_opentargets.py::TestOpenTargets::test_error_opentargets_diseases_filter PASSED [ 53%]
tests/test_opentargets.py::TestOpenTargets::test_opentargets PASSED      [ 54%]
tests/test_opentargets.py::TestOpenTargets::test_opentargets_depmap PASSED [ 54%]
tests/test_opentargets.py::TestOpenTargets::test_opentargets_depmap_filter PASSED [ 54%]
tests/test_opentargets.py::TestOpenTargets::test_opentargets_interactions_no_limit PASSED [ 54%]
tests/test_opentargets.py::TestOpenTargets::test_opentargets_drugs PASSED [ 54%]
tests/test_opentargets.py::TestOpenTargets::test_opentargets_interactions PASSED [ 55%]
tests/test_opentargets.py::TestOpenTargets::test_error_opentargets_drugs_invalid_filter PASSED [ 55%]
tests/test_opentargets.py::TestOpenTargets::test_error_opentargets_nonexistent_id PASSED [ 55%]
tests/test_opentargets.py::TestOpenTargets::test_error_opentargets_bad_limit PASSED [ 55%]
tests/test_opentargets.py::TestOpenTargets::test_opentargets_interactions_simple_filter PASSED [ 56%]
tests/test_opentargets.py::TestOpenTargets::test_opentargets_tractability PASSED [ 56%]
tests/test_opentargets.py::TestOpenTargets::test_error_opentargets_bad_resource PASSED [ 56%]
tests/test_opentargets.py::TestOpenTargets::test_opentargets_pharmacogenetics PASSED [ 56%]
tests/test_opentargets.py::TestOpenTargets::test_opentargets_diseases PASSED [ 57%]
tests/test_opentargets.py::TestOpenTargetsExpressionMocked::test_expression_json PASSED [ 57%]
tests/test_opentargets.py::TestOpenTargetsExpressionMocked::test_expression_limit PASSED [ 57%]
tests/test_opentargets.py::TestOpenTargetsExpressionMocked::test_expression_parses_baseline_rows PASSED [ 57%]
tests/test_opentargets.py::TestOpenTargetsExpressionMocked::test_expression_empty_is_graceful PASSED [ 58%]
tests/test_muscle.py::TestMuscleAA::test_muscle_aa PASSED                [ 58%]
tests/test_muscle.py::TestMusclePrints::test_muscle_print_nt PASSED      [ 58%]
tests/test_muscle.py::TestMuscleAASuper::test_muscle_aa_super5 PASSED    [ 58%]
tests/test_muscle.py::TestMuscleSeqsInput::test_muscle_seqs_as_input PASSED [ 59%]
tests/test_muscle.py::TestMuscleSuper::test_muscle_nt_super5 PASSED      [ 59%]
tests/test_muscle.py::TestMuscle::test_muscle_nt_txt PASSED              [ 59%]
tests/test_muscle.py::TestMuscle::test_muscle_nt PASSED                  [ 59%]
tests/test_seq.py::TestSeq::test_seq_transcript_gene_WB PASSED           [ 59%]
tests/test_seq.py::TestSeq::test_seq_missing_uniprot_gene_name PASSED    [ 60%]
tests/test_seq.py::TestSeq::test_seq_gene_iso PASSED                     [ 60%]
tests/test_seq.py::TestSeq::test_seq_transcript_gene PASSED              [ 60%]
tests/test_seq.py::TestSeq::test_seq_transcript_transcript_iso PASSED    [ 60%]
tests/test_seq.py::TestSeq::test_seq_transcript_transcript_WB PASSED     [ 61%]
tests/test_seq.py::TestSeq::test_seq_gene PASSED                         [ 61%]
tests/test_seq.py::TestSeq::test_seq_gene_transcript_iso PASSED          [ 61%]
tests/test_seq.py::TestSeq::test_seq_transcript_gene_iso PASSED          [ 61%]
tests/test_seq.py::TestSeq::test_seq_transcript PASSED                   [ 62%]
tests/test_blat.py::TestBlat::test_blat_nt_DNA PASSED                    [ 62%]
tests/test_blat.py::TestBlat::test_blat_nt_transDNA PASSED               [ 62%]
tests/test_blat.py::TestBlat::test_blat_aa_protein PASSED                [ 62%]
tests/test_blat.py::TestBlat::test_blat_aa PASSED                        [ 63%]
tests/test_blat.py::TestBlat::test_blat_bad_fasta PASSED                 [ 63%]
tests/test_blat.py::TestBlat::test_blat_bad_txt PASSED                   [ 63%]
tests/test_blat.py::TestBlat::test_blat_nt_RNA PASSED                    [ 63%]
tests/test_blat.py::TestBlat::test_blat_nt_protein PASSED                [ 63%]
tests/test_blat.py::TestBlat::test_blat_nt PASSED                        [ 64%]
tests/test_blat.py::TestBlat::test_blat_bad_assembly PASSED              [ 64%]
tests/test_blat.py::TestBlat::test_blat_bad_fileformat PASSED            [ 64%]
tests/test_blat.py::TestBlat::test_blat_aa_RNA PASSED                    [ 64%]
tests/test_blat.py::TestBlat::test_blat_shortseq PASSED                  [ 65%]
tests/test_blat.py::TestBlat::test_blat_nt_fasta PASSED                  [ 65%]
tests/test_blat.py::TestBlat::test_blat_nt_txt PASSED                    [ 65%]
tests/test_blat.py::TestBlat::test_blat_nt_json PASSED                   [ 65%]
tests/test_blat.py::TestBlat::test_blat_bad_seqtype PASSED               [ 66%]
tests/test_gpt.py::TestGpt::test_gpt PASSED                              [ 66%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_worm PASSED             [ 66%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_transcription PASSED    [ 66%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_yeast PASSED            [ 67%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_bad_background_list PASSED [ 67%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_plot PASSED             [ 67%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_diseases_drugs PASSED   [ 67%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_celltypes PASSED        [ 68%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_ontology PASSED         [ 68%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_bad_species PASSED      [ 68%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_json PASSED             [ 68%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_background_ensembl PASSED [ 68%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_fly PASSED              [ 69%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_mouse_is_human PASSED   [ 69%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_bad_gene PASSED         [ 69%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_bad_database_shortcut PASSED [ 69%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_kinase_interactions PASSED [ 70%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_bad_background PASSED   [ 70%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_pathway PASSED          [ 70%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_fish PASSED             [ 70%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_ensembl_ids PASSED      [ 71%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_background PASSED       [ 71%]
tests/test_enrichr.py::TestEnrichr::test_enrichr_none PASSED             [ 71%]
tests/test_pdb.py::TestPDB::test_pdb_mmcif PASSED                        [ 71%]
tests/test_pdb.py::TestPDB::test_pdb_assembly PASSED                     [ 72%]
tests/test_pdb.py::TestPDB::test_pdb_pdb PASSED                          [ 72%]
tests/test_pdb.py::TestPDB::test_pdb_legacy_fallback_to_mmcif PASSED     [ 72%]
tests/test_alphafold.py::TestAlphafoldJackhmmerSavedir::test_default_dir PASSED [ 72%]
tests/test_alphafold.py::TestAlphafoldJackhmmerSavedir::test_cli_exposes_jackhmmer_savedir_flag PASSED [ 72%]
tests/test_alphafold.py::TestAlphafoldJackhmmerSavedir::test_clean_up_default_dir_when_none PASSED [ 73%]
tests/test_alphafold.py::TestAlphafoldJackhmmerSavedir::test_custom_dir PASSED [ 73%]
tests/test_alphafold.py::TestAlphafoldJackhmmerSavedir::test_clean_up_missing_dir_is_safe PASSED [ 73%]
tests/test_alphafold.py::TestAlphafoldJackhmmerSavedir::test_clean_up_removes_custom_dir PASSED [ 73%]
tests/test_utils.py::TestUtils::test_ref_species_options PASSED          [ 74%]
tests/test_utils.py::TestUtils::test_rest_query PASSED                   [ 74%]
tests/test_utils.py::TestUtils::test_get_uniprot_seqs PASSED             [ 74%]
tests/test_utils.py::TestUtils::test_ref_iv_species_options PASSED       [ 74%]
tests/test_utils.py::TestUtils::test_n_colors PASSED                     [ 75%]
tests/test_utils.py::TestUtils::test_search_iv_species_options PASSED    [ 75%]
tests/test_utils.py::TestUtils::test_search_species_options PASSED       [ 75%]
tests/test_utils.py::TestUtils::test_ref_species_options_bad_type PASSED [ 75%]
tests/test_utils.py::TestUtils::test_get_uniprot_info_gene PASSED        [ 76%]
tests/test_utils.py::TestUtils::test_read_fasta PASSED                   [ 76%]
tests/test_utils.py::TestUtils::test_find_latest_ens_rel PASSED          [ 76%]
tests/test_utils.py::TestUtils::test_rest_query_bad_type PASSED          [ 76%]
tests/test_utils.py::TestUtils::test_get_uniprot_info_transcript PASSED  [ 77%]
tests/test_utils.py::TestUtils::test_aa_colors PASSED                    [ 77%]
tests/test_utils.py::TestUtils::test_search_species_options_bad_type PASSED [ 77%]
tests/test_diamond.py::TestDiamond::test_diamond_seqs_single PASSED      [ 77%]
tests/test_diamond.py::TestDiamond::test_diamond_ref_file PASSED         [ 77%]
tests/test_diamond.py::TestDiamond::test_diamond_seqs_multiple PASSED    [ 78%]
tests/test_diamond.py::TestDiamond::test_diamond_JSON_out PASSED         [ 78%]
tests/test_diamond.py::TestDiamond::test_diamond_both_files PASSED       [ 78%]
tests/test_diamond.py::TestDiamond::test_diamond_query_file PASSED       [ 78%]
tests/test_cbio.py::TestCbioSearch::test_cbio_search PASSED              [ 79%]
tests/test_cbio.py::TestCbio::test_error_cbio_download PASSED            [ 79%]
tests/test_cbio.py::TestCbio::test_cbio_download PASSED                  [ 79%]
tests/test_cbio.py::TestCbio::test_cbio_download_partially_existing_files PASSED [ 79%]
tests/test_search.py::TestSearch::test_search_gene_two_sw_or PASSED      [ 80%]
tests/test_search.py::TestSearch::test_search_transcript_two_sw_or PASSED [ 80%]
tests/test_search.py::TestSearch::test_search_gene_bad_species PASSED    [ 80%]
tests/test_search.py::TestSearch::test_search_gene_one_sw_json PASSED    [ 80%]
tests/test_search.py::TestSearch::test_search_octopus PASSED             [ 81%]
tests/test_search.py::TestSearch::test_search_transcript_bad_andor PASSED [ 81%]
tests/test_search.py::TestSearch::test_search_plant PASSED               [ 81%]
tests/test_search.py::TestSearch::test_search_db PASSED                  [ 81%]
tests/test_search.py::TestSearch::test_search_plant_db PASSED            [ 81%]
tests/test_search.py::TestSearch::test_search_gene_two_sw_and PASSED     [ 82%]
tests/test_search.py::TestSearch::test_search_transcript_one_sw PASSED   [ 82%]
tests/test_search.py::TestSearch::test_search_gene_one_sw PASSED         [ 82%]
tests/test_search.py::TestSearch::test_search_transcript_bad_species PASSED [ 82%]
tests/test_search.py::TestSearch::test_search_transcript_two_sw_and PASSED [ 83%]
tests/test_search.py::TestSearch::test_search_gene_two_sw_limit PASSED   [ 83%]
tests/test_search.py::TestSearch::test_search_gene_one_sw_limit PASSED   [ 83%]
tests/test_search.py::TestSearch::test_search_release PASSED             [ 83%]
tests/test_search.py::TestSearch::test_search_gene_bad_andor PASSED      [ 84%]
tests/test_mutate.py::test_mismatch_error PASSED                         [ 84%]
tests/test_mutate.py::test_csv_of_mutations PASSED                       [ 84%]
tests/test_mutate.py::TestMutate::test_multi_delins_with_true_right_repeats PASSED [ 84%]
tests/test_mutate.py::TestMutate::test_multi_deletion PASSED             [ 85%]
tests/test_mutate.py::TestMutate::test_intron_mutation_minus PASSED      [ 85%]
tests/test_mutate.py::TestMutate::test_multi_insertion_with_left_repeats PASSED [ 85%]
tests/test_mutate.py::TestMutate::test_multi_deletion_with_right_repeats PASSED [ 85%]
tests/test_mutate.py::TestMutate::test_single_insertion PASSED           [ 86%]
tests/test_mutate.py::TestMutate::test_single_substitution_near_left_end PASSED [ 86%]
tests/test_mutate.py::TestMutate::test_multi_dup PASSED                  [ 86%]
tests/test_mutate.py::TestMutate::test_multi_delins_with_true_left_repeats PASSED [ 86%]
tests/test_mutate.py::TestMutate::test_single_deletion_with_right_repeats PASSED [ 86%]
tests/test_mutate.py::TestMutate::test_single_deletion PASSED            [ 87%]
tests/test_mutate.py::TestMutate::test_multi_insertion PASSED            [ 87%]
tests/test_mutate.py::TestMutate::test_multi_delins_with_psuedo_left_repeats PASSED [ 87%]
tests/test_mutate.py::TestMutate::test_multi_delins PASSED               [ 87%]
tests/test_mutate.py::TestMutate::test_list_of_mutations PASSED          [ 88%]
tests/test_mutate.py::TestMutate::test_single_dup PASSED                 [ 88%]
tests/test_mutate.py::TestMutate::test_single_substitution PASSED        [ 88%]
tests/test_mutate.py::TestMutate::test_inversion_with_overlaps PASSED    [ 88%]
tests/test_mutate.py::TestMutate::test_posttranslational_mutation PASSED [ 89%]
tests/test_mutate.py::TestMutate::test_ambiguous_mutation PASSED         [ 89%]
tests/test_mutate.py::TestMutate::test_single_substitution_near_right_end PASSED [ 89%]
tests/test_mutate.py::TestMutate::test_uncertain_mutation PASSED         [ 89%]
tests/test_mutate.py::TestMutate::test_large_k PASSED                    [ 90%]
tests/test_mutate.py::TestMutate::test_index_error PASSED                [ 90%]
tests/test_mutate.py::TestMutate::test_single_delins PASSED              [ 90%]
tests/test_mutate.py::TestMutate::test_single_deletion_with_left_repeats PASSED [ 90%]
tests/test_mutate.py::TestMutate::test_intron_mutation_plus PASSED       [ 90%]
tests/test_8cube.py::TestGeneExpression::test_gene_expression_basic PASSED [ 91%]
tests/test_8cube.py::TestPsiBlock::test_psi_block_basic PASSED           [ 91%]
tests/test_8cube.py::TestSpecificity::test_specificity_basic PASSED      [ 91%]
tests/test_compile.py::TestCompilerWindows::test_compiler_windows PASSED [ 91%]
tests/test_bgee.py::TestBgee::test_bgee_expression PASSED                [ 92%]
tests/test_bgee.py::TestBgee::test_bgee_expression_multiple PASSED       [ 92%]
tests/test_bgee.py::TestBgee::test_error_bgee_orthologs_no_exist PASSED  [ 92%]
tests/test_bgee.py::TestBgee::test_error_bgee_unknown_type PASSED        [ 92%]
tests/test_bgee.py::TestBgee::test_error_bgee_expression_no_exist PASSED [ 93%]
tests/test_bgee.py::TestBgee::test_bgee_orthologs PASSED                 [ 93%]
tests/test_archs4.py::TestArchs4MissingColor::test_tissue_missing_color_does_not_crash PASSED [ 93%]
tests/test_archs4.py::TestArchs4::test_archs4_tissue PASSED              [ 93%]
tests/test_archs4.py::TestArchs4::test_archs4_bad_which PASSED           [ 94%]
tests/test_archs4.py::TestArchs4::test_archs4_tissue_ensembl PASSED      [ 94%]
tests/test_archs4.py::TestArchs4::test_archs4_mouse_json_ensembl PASSED  [ 94%]
tests/test_archs4.py::TestArchs4::test_archs4_tissue_mouse PASSED        [ 94%]
tests/test_archs4.py::TestArchs4::test_archs4_tissue_json PASSED         [ 95%]
tests/test_archs4.py::TestArchs4::test_archs4_defaults PASSED            [ 95%]
tests/test_archs4.py::TestArchs4::test_archs4_bad_species PASSED         [ 95%]
tests/test_archs4.py::TestArchs4::test_archs4_bad_gene_tissue PASSED     [ 95%]
tests/test_archs4.py::TestArchs4::test_archs4_bad_gene PASSED            [ 95%]
tests/test_archs4.py::TestArchs4::test_archs4_bad_ensembl PASSED         [ 96%]
tests/test_cellxgene.py::TestCellxgene::test_cellxgene_metadata_macaca_mulatta SKIPPED [ 96%]
tests/test_cellxgene.py::TestCellxgene::test_cellxgene_metadata SKIPPED  [ 96%]
tests/test_cellxgene.py::TestCellxgene::test_cellxgene_adata SKIPPED     [ 96%]
tests/test_cellxgene.py::TestCellxgeneValidation::test_supported_species_includes_new_primates PASSED [ 97%]
tests/test_cellxgene.py::TestCellxgeneValidation::test_typo_species_raises_valueerror PASSED [ 97%]
tests/test_cellxgene.py::TestCellxgeneValidation::test_invalid_species_raises_valueerror PASSED [ 97%]
tests/test_info.py::TestInfo::test_info_mix PASSED                       [ 97%]
tests/test_info.py::TestInfo::test_info_ncbifalse_uniprotfalse PASSED    [ 98%]
tests/test_info.py::TestInfo::test_info_transcript PASSED                [ 98%]
tests/test_info.py::TestInfo::test_info_ncbifalse_uniprottrue PASSED     [ 98%]
tests/test_info.py::TestInfo::test_info_gene PASSED                      [ 98%]
tests/test_info.py::TestInfo::test_info_exon PASSED                      [ 99%]
tests/test_info.py::TestInfo::test_info_WB_transcript PASSED             [ 99%]
tests/test_info.py::TestInfo::test_info_ncbitrue_uniprotfalse PASSED     [ 99%]
tests/test_info.py::TestInfo::test_info_gene_list_non_model PASSED       [ 99%]
tests/test_cosmic.py::TestCosmicWorkflow::test_cosmic_defaults PASSED    [100%]

=============================== warnings summary ===============================
tests/test_ref.py: 11 warnings
tests/test_utils.py: 1 warning
  /home/runner/work/gget/gget/gget/utils.py:998: DeprecationWarning: Call to deprecated method findAll. (Replaced by find_all) -- Deprecated since version 4.0.0.
    for subsoup in soup.body.findAll("a"):

tests/test_ref.py: 39 warnings
  /home/runner/work/gget/gget/gget/gget_ref.py:49: DeprecationWarning: Call to deprecated method findAll. (Replaced by find_all) -- Deprecated since version 4.0.0.
    links = [stuff.text.strip() for stuff in soup.findAll("td")]

tests/test_ref.py::TestRef::test_ref_ftp
tests/test_ref.py::TestRef::test_ref
  /home/runner/work/gget/gget/gget/gget_ref.py:325: DeprecationWarning: Call to deprecated method findAll. (Replaced by find_all) -- Deprecated since version 4.0.0.
    links = [stuff.text.strip() for stuff in soup.findAll("td")]

tests/test_ref.py: 24 warnings
tests/test_utils.py: 4 warnings
  /home/runner/work/gget/gget/gget/utils.py:975: DeprecationWarning: Call to deprecated method findAll. (Replaced by find_all) -- Deprecated since version 4.0.0.
    for subsoup in soup.body.findAll("a"):

tests/test_ref.py: 7 warnings
tests/test_search.py: 19 warnings
  /home/runner/work/gget/gget/gget/utils.py:922: DeprecationWarning: Call to deprecated method findAll. (Replaced by find_all) -- Deprecated since version 4.0.0.
    for subsoup in soup.body.findAll("a"):

tests/test_utils.py::TestUtils::test_search_iv_species_options
tests/test_utils.py::TestUtils::test_search_iv_species_options
tests/test_utils.py::TestUtils::test_search_iv_species_options
tests/test_utils.py::TestUtils::test_search_iv_species_options
tests/test_search.py::TestSearch::test_search_transcript_two_sw_or
tests/test_search.py::TestSearch::test_search_transcript_two_sw_or
tests/test_search.py::TestSearch::test_search_transcript_two_sw_or
tests/test_search.py::TestSearch::test_search_transcript_two_sw_or
  /home/runner/work/gget/gget/gget/utils.py:883: DeprecationWarning: Call to deprecated method findAll. (Replaced by find_all) -- Deprecated since version 4.0.0.
    for subsoup in soup.body.findAll("a"):

tests/test_utils.py::TestUtils::test_search_species_options
tests/test_search.py::TestSearch::test_search_transcript_two_sw_or
tests/test_search.py::TestSearch::test_search_gene_bad_species
tests/test_search.py::TestSearch::test_search_release
  /home/runner/work/gget/gget/gget/utils.py:899: DeprecationWarning: Call to deprecated method findAll. (Replaced by find_all) -- Deprecated since version 4.0.0.
    for subsoup in soup.body.findAll("a"):

tests/test_cbio.py::TestCbioSearch::test_cbio_search
tests/test_cbio.py::TestCbioSearch::test_cbio_search
  /home/runner/.local/share/hatch/env/virtual/gget/dY-b3nRT/hatch-test.py3.14/lib/python3.14/site-packages/swagger_spec_validator/validator12.py:18: DeprecationWarning: jsonschema.RefResolver is deprecated as of v4.18.0, in favor of the https://github.com/python-jsonschema/referencing library, which provides more compliant referencing behavior as well as more flexible APIs for customization. A future release will remove RefResolver. Please file a feature request (on referencing) if you are missing an API for the kind of customization you need.
    from jsonschema import RefResolver

tests/test_cbio.py::TestCbioSearch::test_cbio_search
  /home/runner/.local/share/hatch/env/virtual/gget/dY-b3nRT/hatch-test.py3.14/lib/python3.14/site-packages/swagger_spec_validator/ref_validators.py:14: DeprecationWarning: jsonschema.RefResolver is deprecated as of v4.18.0, in favor of the https://github.com/python-jsonschema/referencing library, which provides more compliant referencing behavior as well as more flexible APIs for customization. A future release will remove RefResolver. Please file a feature request (on referencing) if you are missing an API for the kind of customization you need.
    from jsonschema.validators import RefResolver

tests/test_cbio.py::TestCbioSearch::test_cbio_search
  /home/runner/.local/share/hatch/env/virtual/gget/dY-b3nRT/hatch-test.py3.14/lib/python3.14/site-packages/swagger_spec_validator/validator20.py:18: DeprecationWarning: jsonschema.RefResolver is deprecated as of v4.18.0, in favor of the https://github.com/python-jsonschema/referencing library, which provides more compliant referencing behavior as well as more flexible APIs for customization. A future release will remove RefResolver. Please file a feature request (on referencing) if you are missing an API for the kind of customization you need.
    from jsonschema.validators import RefResolver

tests/test_cbio.py::TestCbioSearch::test_cbio_search
tests/test_cbio.py::TestCbioSearch::test_cbio_search
  /home/runner/.local/share/hatch/env/virtual/gget/dY-b3nRT/hatch-test.py3.14/lib/python3.14/site-packages/bravado_core/swagger20_validator.py:6: DeprecationWarning: jsonschema.RefResolver is deprecated as of v4.18.0, in favor of the https://github.com/python-jsonschema/referencing library, which provides more compliant referencing behavior as well as more flexible APIs for customization. A future release will remove RefResolver. Please file a feature request (on referencing) if you are missing an API for the kind of customization you need.
    from jsonschema import RefResolver

tests/test_cbio.py::TestCbioSearch::test_cbio_search
  /home/runner/.local/share/hatch/env/virtual/gget/dY-b3nRT/hatch-test.py3.14/lib/python3.14/site-packages/bravado_core/spec.py:14: DeprecationWarning: jsonschema.RefResolver is deprecated as of v4.18.0, in favor of the https://github.com/python-jsonschema/referencing library, which provides more compliant referencing behavior as well as more flexible APIs for customization. A future release will remove RefResolver. Please file a feature request (on referencing) if you are missing an API for the kind of customization you need.
    from jsonschema.validators import RefResolver

tests/test_cbio.py: 16 warnings
  /home/runner/.local/share/hatch/env/virtual/gget/dY-b3nRT/hatch-test.py3.14/lib/python3.14/site-packages/bravado_core/model.py:888: DeprecationWarning: jsonschema.RefResolver.in_scope is deprecated and will be removed in a future release.
    with spec.resolver.in_scope(additional_uri):

tests/test_search.py: 10 warnings
  /home/runner/work/gget/gget/gget/gget_search.py:267: UserWarning: pandas only supports SQLAlchemy connectable (engine/connection) or database string URI or sqlite3 DBAPI2 connection. Other DBAPI2 objects are not tested. Please consider using SQLAlchemy.
    df_temp = pd.read_sql(query, con=db_connection)

tests/test_search.py::TestSearch::test_search_transcript_two_sw_or
tests/test_search.py::TestSearch::test_search_transcript_one_sw
tests/test_search.py::TestSearch::test_search_transcript_two_sw_and
tests/test_search.py::TestSearch::test_search_gene_two_sw_limit
  /home/runner/work/gget/gget/gget/gget_search.py:302: UserWarning: pandas only supports SQLAlchemy connectable (engine/connection) or database string URI or sqlite3 DBAPI2 connection. Other DBAPI2 objects are not tested. Please consider using SQLAlchemy.
    df_temp = pd.read_sql(query, con=db_connection)

tests/test_mutate.py: 29 warnings
  /home/runner/work/gget/gget/gget/gget_mutate.py:667: UserWarning: This pattern is interpreted as a regular expression, and has match groups. To actually get the groups, use str.extract.
    mask = mutations[mut_column].str.contains(combined_pattern)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
============================= slowest 10 durations =============================
179.86s call     tests/test_virus.py::TestVirus::test_virus_integer_virus_id
134.97s call     tests/test_virus.py::TestVirus::test_virus_with_source_database_filter
129.82s call     tests/test_virus.py::TestVirus::test_virus_with_max_ambiguous_chars_filter
129.34s call     tests/test_virus.py::TestVirus::test_virus_with_lab_passaged_filter
92.53s call     tests/test_blast.py::TestBlast::test_blast_nt
67.87s call     tests/test_virus.py::TestVirus::test_virus_with_has_proteins_filter
31.46s call     tests/test_virus.py::TestVirus::test_virus_with_annotated_filter
26.90s call     tests/test_virus.py::TestVirus::test_virus_with_protein_count_filters
22.52s call     tests/test_virus.py::TestVirus::test_virus_host_filter_verification
22.03s call     tests/test_virus.py::TestVirus::test_virus_with_host_filter
=========================== short test summary info ============================
SKIPPED [1] tests/test_cellxgene.py:65: cellxgene-census is not installed
SKIPPED [1] tests/test_cellxgene.py:55: cellxgene-census is not installed
SKIPPED [1] tests/test_cellxgene.py:45: cellxgene-census is not installed
========== 419 passed, 3 skipped, 185 warnings in 1249.22s (0:20:49) ===========
