add n_transcripts_per_cell to benchmark

scverse · Nov 13, 2024 · 81b3bfb · 81b3bfb
1 parent dd8848b
commit 81b3bfb
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Showing 2 changed files with 16 additions and 16 deletions.
diff --git a/benchmarks/README.md b/benchmarks/README.md
@@ -23,15 +23,15 @@ PYTHONWARNINGS="ignore" asv run --python=same --show-stderr -b time_query_boundi
 output:
 
 ```
-[100.00%] ··· ======== ============ ============
-              --              filter_table
-              -------- -------------------------
-               length      True        False
-              ======== ============ ============
-                100      191±2ms      185±2ms
-                1000     399±4ms      382±7ms
-               10000    2.67±0.02s   2.18±0.01s
-              ======== ============ ============
+[50.00%] ··· ======== ============ ============== ============= ===============
+         	--             	filter_table / n_transcripts_per_cell
+         	-------- ---------------------------------------------------------
+          	length   True / 100   True / 10000   False / 100   False / 10000
+         	======== ============ ============== ============= ===============
+           	100  	813±0ms   	1.09±0s    	803±0ms    	980±0ms
+           	1000 	799±0ms   	2.96±0s    	789±0ms    	2.81±0s
+          	10000 	1.32±0s   	24.4±0s    	962±0ms    	21.5±0s
+         	======== ============ ============== ============= ===============
 ```
 
 run everything in new env

diff --git a/benchmarks/spatialdata_benchmark.py b/benchmarks/spatialdata_benchmark.py
@@ -45,19 +45,19 @@ def time_map_blocks(self, _):
 
 class TimeQueries:
 
-    params = ([100, 1000, 10_000], [True, False])
-    param_names = ["length", "filter_table"]
+    params = ([100, 1000, 10_000], [True, False], [100, 10_000])
+    param_names = ["length", "filter_table", "n_transcripts_per_cell"]
 
-    def setup(self, length, filter_table):
+    def setup(self, length, filter_table, n_transcripts_per_cell):
         import shapely
 
-        self.sdata = cluster_blobs(length=length)
+        self.sdata = cluster_blobs(length=length, n_transcripts_per_cell=n_transcripts_per_cell)
         self.polygon = shapely.box(0, 0, length // 2, length // 2)
 
-    def teardown(self, length, filter_table):
+    def teardown(self, length, filter_table, n_transcripts_per_cell):
         del self.sdata
 
-    def time_query_bounding_box(self, length, filter_table):
+    def time_query_bounding_box(self, length, filter_table, n_transcripts_per_cell):
         self.sdata.query.bounding_box(
             axes=["x", "y"],
             min_coordinate=[0, 0],
@@ -66,7 +66,7 @@ def time_query_bounding_box(self, length, filter_table):
             filter_table=filter_table,
         )
 
-    def time_query_polygon_box(self, length, filter_table):
+    def time_query_polygon_box(self, length, filter_table, n_transcripts_per_cell):
         sd.polygon_query(
             self.sdata,
             self.polygon,