update test coverage to omit deprecated re_iding code

.coveragerc

@@ -1,2 +1,13 @@
 [run]
 branch = True
+omit =
+    */site-packages/*
+    */distutils/*
+    */tests/*
+    */test/*
+    */__init__.py
+    */__main__.py
+    */setup.py
+    */re_iding/*
+    */examples/*
+    */nmdc_common/*

pytest.xml

@@ -1 +1 @@
-<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="26" time="8.702" timestamp="2023-12-08T13:12:40.849708" hostname="MBThornton-M92.local"><testcase classname="tests.test_activities" name="test_activies" time="0.040" /><testcase classname="tests.test_config" name="test_config" time="0.048" /><testcase classname="tests.test_config" name="test_config_missing" time="0.001" /><testcase classname="tests.test_imports" name="test_activity_mapper" time="0.081" /><testcase classname="tests.test_imports" name="test_unique_object_mapper" time="0.068" /><testcase classname="tests.test_imports" name="test_multiple_object_mapper" time="0.067" /><testcase classname="tests.test_nmdcapi" name="test_basics" time="0.003" /><testcase classname="tests.test_nmdcapi" name="test_objects" time="0.009" /><testcase classname="tests.test_nmdcapi" name="test_list_funcs" time="0.005" /><testcase classname="tests.test_nmdcapi" name="test_update_op" time="0.003" /><testcase classname="tests.test_nmdcapi" name="test_jobs" time="0.004" /><testcase classname="tests.test_sched" name="test_submit" time="0.041" /><testcase classname="tests.test_sched" name="test_progress" time="0.176" /><testcase classname="tests.test_sched" name="test_multiple_versions" time="0.196" /><testcase classname="tests.test_watch_nmdc" name="test_watcher" time="0.048" /><testcase classname="tests.test_watch_nmdc" name="test_claim_jobs" time="1.074" /><testcase classname="tests.test_watch_nmdc" name="test_reclaim_job" time="0.847" /><testcase classname="tests.test_wfutils" name="test_job" time="0.987" /><testcase classname="tests.test_wfutils" name="test_log" time="0.001" /><testcase classname="tests.test_wfutils" name="test_check_meta" time="0.003" /><testcase classname="tests.test_wfutils" name="test_set_state" time="0.001" /><testcase classname="tests.test_jgi_file_staging.test_file_metadata" name="test_get_access_token" time="0.002" /><testcase classname="tests.test_jgi_file_staging.test_file_metadata" name="test_check_access_token" time="1.009" /><testcase classname="tests.test_jgi_file_staging.test_file_metadata" name="test_check_access_token_invalid" time="1.011" /><testcase classname="tests.test_jgi_file_staging.test_file_metadata" name="test_get_sequence_id" time="2.020" /><testcase classname="tests.test_jgi_file_staging.test_file_metadata" name="test_get_analysis_projects_from_proposal_id" time="0.014" /></testsuite></testsuites>
+<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="95" time="15.756" timestamp="2024-11-26T12:32:34.300291" hostname="MBThornton-M92.local"><testcase classname="tests.test_config" name="test_config" time="0.046" /><testcase classname="tests.test_config" name="test_config_missing" time="0.001" /><testcase classname="tests.test_imports" name="test_gold_mapper_map_sequencing_data" time="0.061" /><testcase classname="tests.test_imports" name="test_gold_mapper_map_data_unique" time="0.061" /><testcase classname="tests.test_imports" name="test_gold_mapper_map_data_multiple" time="0.059" /><testcase classname="tests.test_imports" name="test_gold_mapper_map_workflow_executions" time="5.532" /><testcase classname="tests.test_models" name="test_workflow_process_factory" time="0.005" /><testcase classname="tests.test_models" name="test_workflow_process_factory_incorrect_id" time="1.213" /><testcase classname="tests.test_models" name="test_workflow_process_factory_data_generation_invalid_analyte_category" time="0.001" /><testcase classname="tests.test_models" name="test_workflow_process_factory_metagenome_assembly_with_invalid_execution_resource" time="0.001" /><testcase classname="tests.test_models" name="test_workflow_process_factory_mags_with_mags_list" time="0.001" /><testcase classname="tests.test_models" name="test_process_factory_with_db_record" time="0.001" /><testcase classname="tests.test_models" name="test_workflow_process_node[mags_analysis_record.json-nmdc:MagsAnalysis]" time="0.008" /><testcase classname="tests.test_models" name="test_workflow_process_node[metagenome_annotation_record.json-nmdc:MetagenomeAnnotation]" time="0.007" /><testcase classname="tests.test_models" name="test_workflow_process_node[metagenome_assembly_record.json-nmdc:MetagenomeAssembly]" time="0.007" /><testcase classname="tests.test_models" name="test_workflow_process_node[metatranscriptome_annotation_record.json-nmdc:MetatranscriptomeAnnotation]" time="0.007" /><testcase classname="tests.test_models" name="test_workflow_process_node[metatranscriptome_assembly_record.json-nmdc:MetatranscriptomeAssembly]" time="0.007" /><testcase classname="tests.test_models" name="test_workflow_process_node[metatranscriptome_expression_analysis_record.json-nmdc:MetatranscriptomeExpressionAnalysis]" time="0.007" /><testcase classname="tests.test_models" name="test_workflow_process_node[nucleotide_sequencing_record.json-nmdc:NucleotideSequencing]" time="0.071" /><testcase classname="tests.test_models" name="test_workflow_process_node[read_based_taxonomy_analysis_record.json-nmdc:ReadBasedTaxonomyAnalysis]" time="0.007" /><testcase classname="tests.test_models" name="test_workflow_process_node[read_qc_analysis_record.json-nmdc:ReadQcAnalysis]" time="0.007" /><testcase classname="tests.test_models" name="test_data_object_creation_from_records" time="0.145" /><testcase classname="tests.test_models" name="test_data_object_creation_from_db_records" time="0.165" /><testcase classname="tests.test_models" name="test_data_object_creation_invalid_data_object_type" time="0.001" /><testcase classname="tests.test_models" name="test_data_object_creation_invalid_data_category" time="0.001" /><testcase classname="tests.test_models" name="test_job_output_creation" time="0.001" /><testcase classname="tests.test_models" name="test_job_creation" time="0.001" /><testcase classname="tests.test_nmdcapi" name="test_basics" time="0.013" /><testcase classname="tests.test_nmdcapi" name="test_objects" time="0.012" /><testcase classname="tests.test_nmdcapi" name="test_list_funcs" time="0.006" /><testcase classname="tests.test_nmdcapi" name="test_update_op" time="0.004" /><testcase classname="tests.test_nmdcapi" name="test_jobs" time="0.006" /><testcase classname="tests.test_sched" name="test_scheduler_cycle[workflows.yaml]" time="0.042" /><testcase classname="tests.test_sched" name="test_scheduler_cycle[workflows-mt.yaml]" time="0.047" /><testcase classname="tests.test_sched" name="test_progress[workflows.yaml]" time="0.321" /><testcase classname="tests.test_sched" name="test_progress[workflows-mt.yaml]" time="0.193" /><testcase classname="tests.test_sched" name="test_multiple_versions" time="0.183" /><testcase classname="tests.test_sched" name="test_out_of_range" time="0.083" /><testcase classname="tests.test_sched" name="test_type_resolving" time="0.107" /><testcase classname="tests.test_sched" name="test_scheduler_add_job_rec[workflows.yaml]" time="0.011" /><testcase classname="tests.test_sched" name="test_scheduler_add_job_rec[workflows-mt.yaml]" time="0.009" /><testcase classname="tests.test_sched" name="test_scheduler_find_new_jobs" time="0.073" /><testcase classname="tests.test_watch_nmdc" name="test_file_handler_init_from_state_file" time="0.006" /><testcase classname="tests.test_watch_nmdc" name="test_file_handler_init_from_config_agent_state" time="0.002" /><testcase classname="tests.test_watch_nmdc" name="test_file_handler_init_default_state" time="0.002" /><testcase classname="tests.test_watch_nmdc" name="test_file_handler_read_state" time="0.001" /><testcase classname="tests.test_watch_nmdc" name="test_file_handler_write_state" time="0.005" /><testcase classname="tests.test_watch_nmdc" name="test_file_handler_get_output_path" time="0.001" /><testcase classname="tests.test_watch_nmdc" name="test_file_handler_write_metadata_if_not_exists" time="0.002" /><testcase classname="tests.test_watch_nmdc" name="test_job_manager_init" time="0.001" /><testcase classname="tests.test_watch_nmdc" name="test_job_manager_restore_from_state" time="0.001" /><testcase classname="tests.test_watch_nmdc" name="test_job_manager_job_checkpoint" time="0.001" /><testcase classname="tests.test_watch_nmdc" name="test_job_manager_save_checkpoint" time="0.002" /><testcase classname="tests.test_watch_nmdc" name="test_job_manager_find_job_by_opid" time="0.002" /><testcase classname="tests.test_watch_nmdc" name="test_job_manager_prepare_and_cache_new_job" time="0.001" /><testcase classname="tests.test_watch_nmdc" name="test_job_manager_prepare_and_cache_new_job_force" time="0.002" /><testcase classname="tests.test_watch_nmdc" name="test_job_manager_get_finished_jobs" time="0.002" /><testcase classname="tests.test_watch_nmdc" name="test_job_manager_process_successful_job" time="0.327" /><testcase classname="tests.test_watch_nmdc" name="test_job_manager_get_finished_jobs_1_failure" time="0.003" /><testcase classname="tests.test_watch_nmdc" name="test_job_manager_process_failed_job_1_failure" time="0.004" /><testcase classname="tests.test_watch_nmdc" name="test_job_manager_process_failed_job_2_failures" time="0.003" /><testcase classname="tests.test_watch_nmdc" name="test_claim_jobs" time="2.004" /><testcase classname="tests.test_watch_nmdc" name="test_runtime_manager_get_unclaimed_jobs" time="0.047" /><testcase classname="tests.test_watch_nmdc" name="test_reclaim_job" time="0.001" /><testcase classname="tests.test_watch_nmdc" name="test_watcher_restore_from_checkpoint" time="0.001" /><testcase classname="tests.test_wfutils" name="test_workflow_job" time="0.001" /><testcase classname="tests.test_wfutils" name="test_cromwell_job_runner" time="0.001" /><testcase classname="tests.test_wfutils" name="test_cromwell_job_runner_get_job_status" time="0.003" /><testcase classname="tests.test_wfutils" name="test_cromwell_job_runner_get_job_metadata" time="0.002" /><testcase classname="tests.test_wfutils" name="test_workflow_job_as_workflow_execution_dict" time="0.001" /><testcase classname="tests.test_wfutils" name="test_workflow_state_manager" time="0.001" /><testcase classname="tests.test_wfutils" name="test_workflow_manager_fetch_release_file_success" time="0.002" /><testcase classname="tests.test_wfutils" name="test_workflow_manager_fetch_release_file_failed_download" time="0.001" /><testcase classname="tests.test_wfutils" name="test_workflow_manager_fetch_release_file_failed_write" time="0.002" /><testcase classname="tests.test_wfutils" name="test_cromwell_runner_setup_inputs_and_labels" time="0.001" /><testcase classname="tests.test_wfutils" name="test_cromwell_runner_generate_submission_files" time="0.003" /><testcase classname="tests.test_wfutils" name="test_cromwell_runner_generate_submission_files_exception" time="0.003" /><testcase classname="tests.test_wfutils" name="test_cromwell_job_runner_submit_job_new_job" time="0.002" /><testcase classname="tests.test_wfutils" name="test_workflow_job_data_objects_and_execution_record_mags" time="0.004" /><testcase classname="tests.test_wfutils" name="test_workflow_job_from_database_job_record" time="0.001" /><testcase classname="tests.test_workflow_process" name="test_load_workflow_process_nodes[workflows.yaml]" time="0.025" /><testcase classname="tests.test_workflow_process" name="test_load_workflow_process_nodes[workflows-mt.yaml]" time="0.026" /><testcase classname="tests.test_workflow_process" name="test_load_workflow_process_nodes_with_obsolete_versions" time="0.017" /><testcase classname="tests.test_workflow_process" name="test_resolve_relationships" time="0.019" /><testcase classname="tests.test_workflow_process" name="test_load_workflow_process_nodes_does_not_load_metagenome_sequencing" time="0.014" /><testcase classname="tests.test_workflow_process" name="test_load_workflows[workflows.yaml]" time="0.004" /><testcase classname="tests.test_workflow_process" name="test_load_workflows[workflows-mt.yaml]" time="0.003" /><testcase classname="tests.test_workflow_process" name="test_get_required_data_objects_by_id[workflows.yaml]" time="0.012" /><testcase classname="tests.test_workflow_process" name="test_get_required_data_objects_by_id[workflows-mt.yaml]" time="0.013" /><testcase classname="tests.test_workflow_process" name="test_within_range" time="0.001" /><testcase classname="tests.test_jgi_file_staging.test_file_metadata" name="test_get_access_token" time="0.001" /><testcase classname="tests.test_jgi_file_staging.test_file_metadata" name="test_check_access_token" time="1.009" /><testcase classname="tests.test_jgi_file_staging.test_file_metadata" name="test_check_access_token_invalid" time="1.009" /><testcase classname="tests.test_jgi_file_staging.test_file_metadata" name="test_get_sequence_id" time="2.017" /><testcase classname="tests.test_jgi_file_staging.test_file_metadata" name="test_get_analysis_projects_from_proposal_id" time="0.034" /></testsuite></testsuites>