Merge branch 'dev' of https://github.com/VirtualFlyBrain/VFBquery into dev

Author: Robbie1977

performance.md

@@ -1,9 +1,9 @@
 # VFBquery Performance Test Results
 
-**Test Date:** 2025-11-09 10:54:37 UTC
-**Git Commit:** 14fe1f3e49e3ecb3b9aaac85e988567072d3e406
+**Test Date:** 2025-11-09 11:13:45 UTC
+**Git Commit:** dfdf33429d125399e09b65821f2951ccab6a3cd2
 **Branch:** dev
-**Workflow Run:** [19207206293](https://github.com/VirtualFlyBrain/VFBquery/actions/runs/19207206293)
+**Workflow Run:** [19207570634](https://github.com/VirtualFlyBrain/VFBquery/actions/runs/19207570634)
 
 ## Test Overview
 
@@ -95,13 +95,13 @@ Test anatomical hierarchy queries ... ok
 test_05_tract_lineage_queries (src.test.test_query_performance.QueryPerformanceTest)
 Test tract/nerve and lineage clone queries ... ok
 test_05b_image_queries (src.test.test_query_performance.QueryPerformanceTest)
-Test image and developmental lineage queries ... FAIL
+Test image and developmental lineage queries ... ok
 test_06_instance_queries (src.test.test_query_performance.QueryPerformanceTest)
 Test instance retrieval queries ... ok
 test_07_connectivity_queries (src.test.test_query_performance.QueryPerformanceTest)
 Test neuron connectivity queries ... ok
 test_08_similarity_queries (src.test.test_query_performance.QueryPerformanceTest)
-Test NBLAST similarity queries ... FAIL
+Test NBLAST similarity queries ... ok
 test_09_neuron_input_queries (src.test.test_query_performance.QueryPerformanceTest)
 Test neuron input/synapse queries ... ok
 test_10_expression_queries (src.test.test_query_performance.QueryPerformanceTest)
@@ -115,28 +115,10 @@ Test dataset and template queries ... ok
 test_14_publication_transgene_queries (src.test.test_query_performance.QueryPerformanceTest)
 Test publication and transgene queries ... ok
 
-======================================================================
-FAIL: test_05b_image_queries (src.test.test_query_performance.QueryPerformanceTest)
-Test image and developmental lineage queries
-----------------------------------------------------------------------
-Traceback (most recent call last):
-  File "/home/runner/work/VFBquery/VFBquery/src/test/test_query_performance.py", line 310, in test_05b_image_queries
-    self.assertLess(duration, self.THRESHOLD_SLOW, "epFrag exceeded threshold")
-AssertionError: 591.6025040149689 not less than 10.0 : epFrag exceeded threshold
-
-======================================================================
-FAIL: test_08_similarity_queries (src.test.test_query_performance.QueryPerformanceTest)
-Test NBLAST similarity queries
 ----------------------------------------------------------------------
-Traceback (most recent call last):
-  File "/home/runner/work/VFBquery/VFBquery/src/test/test_query_performance.py", line 373, in test_08_similarity_queries
-    self.assertLess(duration, self.THRESHOLD_SLOW, "SimilarMorphologyTo exceeded threshold")
-AssertionError: 13.371644020080566 not less than 10.0 : SimilarMorphologyTo exceeded threshold
+Ran 15 tests in 326.969s
 
-----------------------------------------------------------------------
-Ran 15 tests in 1244.766s
-
-FAILED (failures=2)
+OK
 VFBquery caching enabled: TTL=2160h (90 days), Memory=2048MB
 VFBquery functions patched with caching support
 VFBquery: Caching enabled by default (3-month TTL, 2GB memory)
@@ -151,120 +133,119 @@ TERM INFO QUERIES
 DEBUG: Cache lookup for FBbt_00003748: MISS
 ✅ Neo4j connection established
 ✅ Neo4j connection established
-get_term_info (mushroom body): 608.6476s ✅
+get_term_info (mushroom body): 276.1710s ✅
 DEBUG: Cache lookup for VFB_00101567: MISS
-Error executing query function get_all_datasets: get_all_datasets() got multiple values for argument 'return_dataframe'
-get_term_info (individual): 2.3331s ✅
+get_term_info (individual): 4.1479s ✅
 
 ================================================================================
 NEURON PART OVERLAP QUERIES
 ================================================================================
-NeuronsPartHere: 1.0753s ✅
+NeuronsPartHere: 1.7737s ✅
 
 ================================================================================
 SYNAPTIC TERMINAL QUERIES
 ================================================================================
-NeuronsSynaptic: 0.9649s ✅
-NeuronsPresynapticHere: 0.9651s ✅
-NeuronsPostsynapticHere: 0.8903s ✅
-NeuronNeuronConnectivity: 1.0729s ✅
+NeuronsSynaptic: 1.2937s ✅
+NeuronsPresynapticHere: 0.9768s ✅
+NeuronsPostsynapticHere: 1.1193s ✅
+NeuronNeuronConnectivity: 0.9697s ✅
 
 ================================================================================
 ANATOMICAL HIERARCHY QUERIES
 ================================================================================
-ComponentsOf: 0.8690s ✅
-PartsOf: 0.8611s ✅
-SubclassesOf: 0.7052s ✅
+ComponentsOf: 0.9852s ✅
+PartsOf: 1.0964s ✅
+SubclassesOf: 1.3073s ✅
 
 ================================================================================
 TRACT/NERVE AND LINEAGE QUERIES
 ================================================================================
-NeuronClassesFasciculatingHere: 0.6805s ✅
-TractsNervesInnervatingHere: 0.6984s ✅
-LineageClonesIn: 0.6856s ✅
+NeuronClassesFasciculatingHere: 0.9830s ✅
+TractsNervesInnervatingHere: 1.1085s ✅
+LineageClonesIn: 0.9755s ✅
 
 ================================================================================
 IMAGE AND DEVELOPMENTAL QUERIES
 ================================================================================
-ImagesNeurons: 1.1065s ✅
-ImagesThatDevelopFrom: 0.8066s ✅
-epFrag: 591.6025s ✅
+ImagesNeurons: 1.4226s ✅
+ImagesThatDevelopFrom: 0.9944s ✅
+epFrag: 0.9932s ✅
 
 ================================================================================
 INSTANCE QUERIES
 ================================================================================
-ListAllAvailableImages: 0.8754s ✅
+ListAllAvailableImages: 0.9536s ✅
 
 ================================================================================
 CONNECTIVITY QUERIES
 ================================================================================
-NeuronNeuronConnectivityQuery: 0.8835s ✅
-NeuronRegionConnectivityQuery: 0.7876s ✅
+NeuronNeuronConnectivityQuery: 0.9908s ✅
+NeuronRegionConnectivityQuery: 0.9711s ✅
 
 ================================================================================
 SIMILARITY QUERIES (Neo4j NBLAST)
 ================================================================================
-SimilarMorphologyTo: 13.3716s ✅
+SimilarMorphologyTo: 9.3175s ✅
 
 ================================================================================
 NEURON INPUT QUERIES (Neo4j)
 ================================================================================
-NeuronInputsTo: 3.4685s ✅
+NeuronInputsTo: 3.7596s ✅
 
 ================================================================================
 EXPRESSION PATTERN QUERIES (Neo4j)
 ================================================================================
-ExpressionOverlapsHere: 0.8755s ✅
+ExpressionOverlapsHere: 0.8590s ✅
   └─ Found 3922 total expression patterns, returned 10
 
 ================================================================================
 TRANSCRIPTOMICS QUERIES (Neo4j scRNAseq)
 ================================================================================
-anatScRNAseqQuery: 0.8030s ✅
+anatScRNAseqQuery: 0.9584s ✅
   └─ Found 0 total clusters
-clusterExpression: 0.5871s ✅
+clusterExpression: 1.0496s ✅
   └─ Found 0 genes expressed
-expressionCluster: 0.5859s ✅
+expressionCluster: 0.7598s ✅
   └─ Found 0 clusters expressing gene
-scRNAdatasetData: 0.6444s ✅
+scRNAdatasetData: 0.7922s ✅
   └─ Found 0 clusters in dataset
 
 ================================================================================
 NBLAST SIMILARITY QUERIES
 ================================================================================
-SimilarMorphologyTo: 0.9659s ✅
+SimilarMorphologyTo: 1.0310s ✅
   └─ Found 227 NBLAST matches, returned 10
-SimilarMorphologyToPartOf: 0.5565s ✅
+SimilarMorphologyToPartOf: 0.9013s ✅
   └─ Found 0 NBLASTexp matches
-SimilarMorphologyToPartOfexp: 0.5361s ✅
+SimilarMorphologyToPartOfexp: 0.8998s ✅
   └─ Found 0 reverse NBLASTexp matches
-SimilarMorphologyToNB: 0.6602s ✅
+SimilarMorphologyToNB: 0.8881s ✅
   └─ Found 15 NeuronBridge matches, returned 10
-SimilarMorphologyToNBexp: 0.6289s ✅
+SimilarMorphologyToNBexp: 0.7458s ✅
   └─ Found 15 NeuronBridge expression matches, returned 10
 ✅ All NBLAST similarity queries completed
 
 ================================================================================
 DATASET/TEMPLATE QUERIES
 ================================================================================
-PaintedDomains: 0.5739s ✅
+PaintedDomains: 0.7761s ✅
   └─ Found 0 painted domains
-DatasetImages: 0.6545s ✅
+DatasetImages: 0.7672s ✅
   └─ Found 0 images in dataset
-AllAlignedImages: 0.5679s ✅
+AllAlignedImages: 0.7536s ✅
   └─ Found 0 aligned images
-AlignedDatasets: 0.8436s ✅
+AlignedDatasets: 0.9391s ✅
   └─ Found 0 aligned datasets
-AllDatasets: 0.7601s ✅
+AllDatasets: 0.9832s ✅
   └─ Found 115 total datasets, returned 20
 ✅ All dataset/template queries completed
 
 ================================================================================
 PUBLICATION/TRANSGENE QUERIES
 ================================================================================
-TermsForPub: 0.5162s ✅
+TermsForPub: 0.7270s ✅
   └─ Found 0 terms for publication
-TransgeneExpressionHere: 0.6500s ✅
+TransgeneExpressionHere: 0.8227s ✅
   └─ Found 2339 transgene expressions, returned 10
 ✅ All publication/transgene queries completed
 
@@ -277,7 +258,7 @@ test_term_info_performance (src.test.term_info_queries_test.TermInfoQueriesTest)
 Performance test for specific term info queries. ... ok
 
 ----------------------------------------------------------------------
-Ran 1 test in 1.589s
+Ran 1 test in 2.241s
 
 OK
 VFBquery caching enabled: TTL=2160h (90 days), Memory=2048MB
@@ -292,9 +273,9 @@ VFBquery: Caching enabled by default (3-month TTL, 2GB memory)
 ==================================================
 Performance Test Results:
 ==================================================
-FBbt_00003748 query took: 0.8036 seconds
-VFB_00101567 query took: 0.7848 seconds
-Total time for both queries: 1.5884 seconds
+FBbt_00003748 query took: 1.1269 seconds
+VFB_00101567 query took: 1.1135 seconds
+Total time for both queries: 2.2404 seconds
 Performance Level: 🟡 Good (1.5-3 seconds)
 ==================================================
 Performance test completed successfully!
@@ -313,4 +294,4 @@ Track performance trends across commits:
 - [GitHub Actions History](https://github.com/VirtualFlyBrain/VFBquery/actions/workflows/performance-test.yml)
 
 ---
-*Last updated: 2025-11-09 10:54:37 UTC*
+*Last updated: 2025-11-09 11:13:45 UTC*