Added benchmark action with pytest-benchmark (#630)

* updates

* Update benchmark.yml

* Update benchmark.yml

* Update benchmark.yml

* Update bench.py

.github/workflows/benchmark.yml

@@ -0,0 +1,40 @@
+name: Benchmark XGI
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+permissions:
+  contents: write
+  deployments: write
+
+jobs:
+  benchmark:
+    name: Run pytest-benchmark benchmarks
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.13
+      - name: Run benchmarks
+        run: |
+          cd benchmarks
+          pip install --upgrade pip
+          pip install .[benchmark]
+          pytest bench.py --benchmark-json output.json
+
+      - name: Store benchmark results
+        uses: benchmark-action/github-action-benchmark@v1
+        with:
+          name: Python Benchmark with pytest-benchmark
+          tool: 'pytest'
+          output-file-path: benchmarks/output.json
+          # Use personal access token instead of GITHUB_TOKEN due to https://github.saobby.my.eu.orgmunity/t/github-action-not-triggering-gh-pages-upon-push/16096
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          auto-push: true
+          # Show alert with commit comment on detecting possible performance regression
+          alert-threshold: '200%'
+          comment-on-alert: false
+          fail-on-alert: true

benchmarks/bench.py

@@ -0,0 +1,163 @@
+import random
+
+import numpy as np
+import pandas as pd
+import pytest
+
+import xgi
+
+
+def test_construct_from_edgelist(benchmark):
+    def setup():
+        H = xgi.read_hif("email-enron.json")
+        return (H.edges.members(),), {}
+
+    benchmark.pedantic(xgi.Hypergraph, setup=setup, rounds=10)
+
+
+def test_construct_from_edgedict(benchmark):
+    def setup():
+        H = xgi.read_hif("email-enron.json")
+        return (H.edges.members(dtype=dict),), {}
+
+    benchmark.pedantic(xgi.Hypergraph, setup=setup, rounds=10)
+
+
+def test_construct_from_df(benchmark):
+    def setup():
+        H = xgi.read_hif("email-enron.json")
+        return (xgi.to_bipartite_pandas_dataframe(H),), {}
+
+    benchmark.pedantic(xgi.Hypergraph, setup=setup, rounds=10)
+
+
+def test_node_memberships(benchmark):
+    def setup():
+        H = xgi.read_hif("email-enron.json")
+        return (H,), {}
+
+    def node_memberships(H):
+        [H.nodes.memberships(n) for n in H.nodes]
+
+    benchmark.pedantic(node_memberships, setup=setup, rounds=10)
+
+
+def test_edge_members(benchmark):
+    def setup():
+        H = xgi.read_hif("email-enron.json")
+        return (H,), {}
+
+    def edge_members(H):
+        [H.edges.members(eid) for eid in H.edges]
+
+    benchmark.pedantic(edge_members, setup=setup, rounds=10)
+
+
+def test_node_attributes(benchmark):
+    def setup():
+        H = xgi.read_hif("email-enron.json")
+        return (H,), {}
+
+    def node_attributes(H):
+        [H.nodes[nid] for nid in H.nodes]
+
+    benchmark.pedantic(node_attributes, setup=setup, rounds=10)
+
+
+def test_edge_attributes(benchmark):
+    def setup():
+        H = xgi.read_hif("email-enron.json")
+        return (H,), {}
+
+    def edge_attributes(H):
+        [H.edges[eid] for eid in H.edges]
+
+    benchmark.pedantic(edge_attributes, setup=setup, rounds=10)
+
+
+def test_degree(benchmark):
+    def setup():
+        H = xgi.read_hif("email-enron.json")
+        return (H,), {}
+
+    def degree(H):
+        H.degree()
+
+    benchmark.pedantic(degree, setup=setup, rounds=10)
+
+
+def test_nodestats_degree(benchmark):
+    def setup():
+        H = xgi.read_hif("email-enron.json")
+        return (H,), {}
+
+    def degree(H):
+        H.nodestats.degree.asnumpy()
+
+    benchmark.pedantic(degree, setup=setup, rounds=10)
+
+
+def test_nodestats_degree(benchmark):
+    def setup():
+        H = xgi.read_hif("email-enron.json")
+        return (H,), {}
+
+    def degree(H):
+        H.nodes.degree.asnumpy()
+
+    benchmark.pedantic(degree, setup=setup, rounds=10)
+
+
+def test_edge_size(benchmark):
+    def setup():
+        H = xgi.read_hif("email-enron.json")
+        return (H,), {}
+
+    def degree(H):
+        H.edges.size.asnumpy()
+
+    benchmark.pedantic(degree, setup=setup, rounds=10)
+
+
+def test_isolates(benchmark):
+    def setup():
+        H = xgi.read_hif("email-enron.json")
+        return (H,), {}
+
+    def isolates(H):
+        H.nodes.isolates()
+
+    benchmark.pedantic(isolates, setup=setup, rounds=10)
+
+
+def test_singletons(benchmark):
+    def setup():
+        H = xgi.read_hif("email-enron.json")
+        return (H,), {}
+
+    def singletons(H):
+        H.edges.singletons()
+
+    benchmark.pedantic(singletons, setup=setup, rounds=10)
+
+
+def test_copy(benchmark):
+    def setup():
+        H = xgi.read_hif("email-enron.json")
+        return (H,), {}
+
+    def copy(H):
+        H.copy()
+
+    benchmark.pedantic(copy, setup=setup, rounds=10)
+
+
+def test_dual(benchmark):
+    def setup():
+        H = xgi.read_hif("email-enron.json")
+        return (H,), {}
+
+    def dual(H):
+        H.dual()
+
+    benchmark.pedantic(dual, setup=setup, rounds=10)