Start fixing some of the tests

PopPUNK/network.py

@@ -279,7 +279,7 @@ def translate_network_indices(G_ref_df, reference_indices):
     G_ref = generate_cugraph(G_ref_df, len(reference_indices) - 1, renumber = True)
     return(G_ref)
 
-def extractReferences(G, dbOrder, outPrefix, merged_queries, outSuffix = '', type_isolate = None,
+def extractReferences(G, dbOrder, outPrefix, merged_queries = list(), outSuffix = '', type_isolate = None,
                         existingRefs = None, threads = 1, use_gpu = False, fast_mode = False):
     """Extract references for each cluster based on cliques
 

test/run_test.py

@@ -75,9 +75,10 @@
 subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query some_queries.txt --db example_db --model-dir example_refine --output example_query --run-qc --max-pi-dist 0.04 --max-zero-dist 1 --betweenness --overwrite", shell=True, check=True)
 subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query more_queries.txt --db example_db --model-dir example_refine --output example_query --run-qc --max-zero-dist 0.3 --overwrite", shell=True, check=True)
 subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query more_queries.txt --db example_db --model-dir example_refine --output example_query --run-qc --max-zero-dist 1 --max-merge 3 --overwrite", shell=True, check=True)
-subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query some_queries.txt --db example_db --model-dir example_dbscan --output example_query_update --update-db --graph-weights --overwrite", shell=True, check=True) # uses graph weights
-subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query even_more_queries.txt --db example_query_update --model-dir example_dbscan --previous-clustering example_query_update --output example_query_update_2 --update-db --graph-weights --overwrite", shell=True, check=True) # uses graph weights
-subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query single_query.txt --db example_db --model-dir example_refine --output example_single_query --update-db --overwrite", shell=True, check=True)
+subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query some_queries.txt --db example_db --model-dir example_dbscan --output example_query_update --update-db full --graph-weights --overwrite", shell=True, check=True) # uses graph weights
+subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query some_queries.txt --db example_db --model-dir example_dbscan --output example_query_update_fast --update-db fast --graph-weights --overwrite", shell=True, check=True) # uses graph weights
+subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query even_more_queries.txt --db example_query_update --model-dir example_dbscan --previous-clustering example_query_update --output example_query_update_2 --update-db full --graph-weights --overwrite", shell=True, check=True) # uses graph weights
+subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query single_query.txt --db example_db --model-dir example_refine --output example_single_query --update-db full --overwrite", shell=True, check=True)
 subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query inref_query.txt --db example_db --model-dir example_refine --output example_single_query --write-references", shell=True, check=True) # matched name, but should be renamed in the output
 subprocess.run(python_cmd + " ../poppunk_assign-runner.py --query some_queries.txt --db example_db --model-dir example_refine --model-dir example_lineages --output example_lineage_query --overwrite", shell=True, check=True)
 

test/test-update.py

@@ -76,8 +76,8 @@ def old_get_seq_tuples(rows,cols):
     subprocess.run(python_cmd + " ../poppunk-runner.py --create-db --r-files rfile1.txt --output batch1 --overwrite", shell=True, check=True)
     subprocess.run(python_cmd + " ../poppunk-runner.py --fit-model lineage --ref-db batch1 --ranks 1,2 --overwrite" + lineage_option_string, shell=True, check=True)
     print("../poppunk-runner.py --fit-model lineage --ref-db batch1 --ranks 1,2 --overwrite\n\n")
-    subprocess.run(python_cmd + " ../poppunk_assign-runner.py --db batch1 --query rfile2.txt --output batch2 --update-db --overwrite --max-a-dist 1", shell=True, check=True)
-    print(" ../poppunk_assign-runner.py --db batch1 --query rfile2.txt --output batch2 --update-db --overwrite --max-a-dist 1\n\n")
+    subprocess.run(python_cmd + " ../poppunk_assign-runner.py --db batch1 --query rfile2.txt --output batch2 --update-db full --overwrite --max-a-dist 1", shell=True, check=True)
+    print(" ../poppunk_assign-runner.py --db batch1 --query rfile2.txt --output batch2 --update-db full --overwrite --max-a-dist 1\n\n")
 
     # Load updated distance order
     with open("batch2/batch2.dists.pkl", 'rb') as pickle_file:
@@ -103,8 +103,8 @@ def old_get_seq_tuples(rows,cols):
     subprocess.run(python_cmd + " ../poppunk-runner.py --create-db --r-files rfile123.txt --output batch123 --overwrite", shell=True, check=True)
     subprocess.run(python_cmd + " ../poppunk-runner.py --fit-model lineage --ref-db batch123 --ranks 1,2 --overwrite" + lineage_option_string, shell=True, check=True)
     print("../poppunk-runner.py --fit-model lineage --ref-db batch123 --ranks 1,2 --overwrite\n\n")
-    subprocess.run(python_cmd + " ../poppunk_assign-runner.py --db batch2 --query rfile3.txt --output batch3 --update-db --overwrite", shell=True, check=True)
-    print(python_cmd + " ../poppunk_assign-runner.py --db batch2 --query rfile3.txt --output batch3 --update-db --overwrite\n\n")
+    subprocess.run(python_cmd + " ../poppunk_assign-runner.py --db batch2 --query rfile3.txt --output batch3 --update-db full --overwrite", shell=True, check=True)
+    print(python_cmd + " ../poppunk_assign-runner.py --db batch2 --query rfile3.txt --output batch3 --update-db full --overwrite\n\n")
 
     # Load updated distances order
     with open("batch3/batch3.dists.pkl", 'rb') as pickle_file: