Tweak benchmarks (#631)

* remove unnecessary files

* add benchmarks

* add rounds

* add benchmarks

.gitignore

@@ -150,4 +150,4 @@ test.*
 
 # benchmarking files
 .benchmarks
-benchmarks/output.json
+output.json

benchmarks/algorithms.py

@@ -0,0 +1,20 @@
+import xgi
+
+rounds = 10
+fname = "benchmarks/email-eu.json"
+
+
+def test_connected(benchmark):
+    def setup():
+        H = xgi.read_hif(fname)
+        return (H,), {}
+
+    benchmark.pedantic(xgi.is_connected, setup=setup, rounds=rounds)
+
+
+def test_clustering_coefficient(benchmark):
+    def setup():
+        H = xgi.read_hif(fname)
+        return (H,), {}
+
+    benchmark.pedantic(xgi.clustering_coefficient, setup=setup, rounds=rounds)

benchmarks/core.py

@@ -1,40 +1,36 @@
-import random
-
-import numpy as np
-import pandas as pd
-import pytest
-
 import xgi
 
-rounds = 100
+rounds = 10
+fname = "benchmarks/email-eu.json"
+
 
 def test_construct_from_edgelist(benchmark):
     def setup():
-        H = xgi.read_hif("benchmarks/email-enron.json")
+        H = xgi.read_hif(fname)
         return (H.edges.members(),), {}
 
     benchmark.pedantic(xgi.Hypergraph, setup=setup, rounds=rounds)
 
 
 def test_construct_from_edgedict(benchmark):
     def setup():
-        H = xgi.read_hif("benchmarks/email-enron.json")
+        H = xgi.read_hif(fname)
         return (H.edges.members(dtype=dict),), {}
 
     benchmark.pedantic(xgi.Hypergraph, setup=setup, rounds=rounds)
 
 
 def test_construct_from_df(benchmark):
     def setup():
-        H = xgi.read_hif("benchmarks/email-enron.json")
+        H = xgi.read_hif(fname)
         return (xgi.to_bipartite_pandas_dataframe(H),), {}
 
     benchmark.pedantic(xgi.Hypergraph, setup=setup, rounds=rounds)
 
 
 def test_node_memberships(benchmark):
     def setup():
-        H = xgi.read_hif("benchmarks/email-enron.json")
+        H = xgi.read_hif(fname)
         return (H,), {}
 
     def node_memberships(H):
@@ -45,7 +41,7 @@ def node_memberships(H):
 
 def test_edge_members(benchmark):
     def setup():
-        H = xgi.read_hif("benchmarks/email-enron.json")
+        H = xgi.read_hif(fname)
         return (H,), {}
 
     def edge_members(H):
@@ -56,7 +52,7 @@ def edge_members(H):
 
 def test_node_attributes(benchmark):
     def setup():
-        H = xgi.read_hif("benchmarks/email-enron.json")
+        H = xgi.read_hif(fname)
         return (H,), {}
 
     def node_attributes(H):
@@ -67,7 +63,7 @@ def node_attributes(H):
 
 def test_edge_attributes(benchmark):
     def setup():
-        H = xgi.read_hif("benchmarks/email-enron.json")
+        H = xgi.read_hif(fname)
         return (H,), {}
 
     def edge_attributes(H):
@@ -78,7 +74,7 @@ def edge_attributes(H):
 
 def test_degree(benchmark):
     def setup():
-        H = xgi.read_hif("benchmarks/email-enron.json")
+        H = xgi.read_hif(fname)
         return (H,), {}
 
     def degree(H):
@@ -89,7 +85,7 @@ def degree(H):
 
 def test_nodestats_degree(benchmark):
     def setup():
-        H = xgi.read_hif("benchmarks/email-enron.json")
+        H = xgi.read_hif(fname)
         return (H,), {}
 
     def degree(H):
@@ -100,7 +96,7 @@ def degree(H):
 
 def test_nodestats_degree(benchmark):
     def setup():
-        H = xgi.read_hif("benchmarks/email-enron.json")
+        H = xgi.read_hif(fname)
         return (H,), {}
 
     def degree(H):
@@ -111,7 +107,7 @@ def degree(H):
 
 def test_edge_size(benchmark):
     def setup():
-        H = xgi.read_hif("benchmarks/email-enron.json")
+        H = xgi.read_hif(fname)
         return (H,), {}
 
     def degree(H):
@@ -122,7 +118,7 @@ def degree(H):
 
 def test_isolates(benchmark):
     def setup():
-        H = xgi.read_hif("benchmarks/email-enron.json")
+        H = xgi.read_hif(fname)
         return (H,), {}
 
     def isolates(H):
@@ -133,7 +129,7 @@ def isolates(H):
 
 def test_singletons(benchmark):
     def setup():
-        H = xgi.read_hif("benchmarks/email-enron.json")
+        H = xgi.read_hif(fname)
         return (H,), {}
 
     def singletons(H):
@@ -144,7 +140,7 @@ def singletons(H):
 
 def test_copy(benchmark):
     def setup():
-        H = xgi.read_hif("benchmarks/email-enron.json")
+        H = xgi.read_hif(fname)
         return (H,), {}
 
     def copy(H):
@@ -155,7 +151,7 @@ def copy(H):
 
 def test_dual(benchmark):
     def setup():
-        H = xgi.read_hif("benchmarks/email-enron.json")
+        H = xgi.read_hif(fname)
         return (H,), {}
 
     def dual(H):