Merge branch 'networkx:main' into wf_tests

.gitignore

@@ -127,3 +127,7 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# asv 
+results/
+html/

README.md

@@ -1,20 +1,18 @@
 ## nx-parallel
 
-nx-parallel is a NetworkX backend plugin that uses joblib and multiprocessing for parallelization. This project aims to provide parallelized implementations of various NetworkX functions to improve performance.
+nx-parallel is a NetworkX backend that uses joblib for parallelization. This project aims to provide parallelized implementations of various NetworkX functions to improve performance.
 
 ## Features
 
 nx-parallel provides parallelized implementations for the following NetworkX functions:
 
-```
-├── centrality
-│   ├── betweenness_centrality
-│   ├── closeness_vitality
-├── tournament
-│   ├── is_reachable
-├── efficiency_measures
-│   ├── local_efficiency
-```
+- [betweeness_centrality](https://github.com/networkx/nx-parallel/blob/main/nx_parallel/algorithms/centrality/betweenness.py#L17)
+- [local_efficiency](https://github.com/networkx/nx-parallel/blob/main/nx_parallel/algorithms/efficiency_measures.py#L12)
+- [number_of_isolates](https://github.com/networkx/nx-parallel/blob/main/nx_parallel/algorithms/isolate.py#L9)
+- [all_pairs_bellman_ford_path](https://github.com/networkx/nx-parallel/blob/main/nx_parallel/algorithms/shortest_paths/weighted.py#L9)
+- [is_reachable](https://github.com/networkx/nx-parallel/blob/main/nx_parallel/algorithms/tournament.py#L11)
+- [tournament_is_strongly_connected](https://github.com/networkx/nx-parallel/blob/main/nx_parallel/algorithms/tournament.py#L103)
+- [closeness_vitality](https://github.com/networkx/nx-parallel/blob/main/nx_parallel/algorithms/vitality.py#L9)
 
 ![alt text](timing/heatmap_all_functions.png)
 

benchmarks/README.md

@@ -0,0 +1,22 @@
+## Preview benchmarks locally
+
+1. clone this repo
+2. `cd benchmarks`
+3. If you are working on a different branch then update the `branches` in the `asv.conf.json` file.
+4. `asv run` will run the benchmarks on the last commit 
+    - or use `asv continuous base_commit_hash test_commit_hash` to run the benchmark to compare two commits
+    - or `asv run -b <benchmark_file_name> -k <benchmark_name>` to run a particular benchmark.
+    - if you are running benchmarks for the first time, you will be asked to enter your machine information after this command.
+5. `asv publish` will create a `html` folder with the results
+6. `asv preview` will host the results locally at http://127.0.0.1:8080/
+
+<hr>
+
+## Structure of benchmarks
+
+* Each `bench_` file corresponds to a folder/file in the [networkx/algorithms](https://github.com/networkx/networkx/tree/main/networkx/algorithms) directory in NetworkX
+* Each class inside a `bench_` file corresponds to every file in a folder(one class if it’s a file) in networkx/algorithms
+* The class name corresponds to the file name and the `x` in `bench_x` corresponds to the folder name(class name and `x` are the same if it’s a file in networkx/algorithms)
+* Each `time_` function corresponds to each function in the file.
+* For other folders in [networkx/networkx](https://github.com/networkx/networkx/tree/main/networkx) like `generators`, `classes`, `linalg`, `utils` etc. we can have different `bench_` files for each of them having different classes corresponding to different files in each of these folders.
+* For example: `bench_centrality.py` corresponds to `networkx/algorithms/centrality` folder in NetworkX and the `Betweenness` class inside it corresponds to the `betweenness.py` file in `networkx/algorithms/centrality` folder in NetworkX. And the `time_betweenness_centrality` function corresponds to the `betweenness_centrality` function.

benchmarks/asv.conf.json

@@ -0,0 +1,20 @@
+{
+    "version": 1,
+    "project": "nx-parallel",
+    "project_url": "https://github.com/networkx/nx-parallel",
+    "repo": "..",
+    "branches": ["main"],
+    "build_command": [
+        "python -m pip install build",
+        "python -m build --wheel -o {build_cache_dir} {build_dir}"
+    ],
+    "dvcs": "git",
+    "environment_type": "virtualenv",
+    "show_commit_url": "https://github.com/networkx/nx-parallel/commit/",
+    "matrix": {"networkx": ["3.2"], "nx-parallel": []},
+    "benchmark_dir": "benchmarks",
+    "env_dir": "env",
+    "results_dir": "results",
+    "html_dir": "html",
+    "build_cache_size": 8
+}

benchmarks/benchmarks/__init__.py

@@ -0,0 +1 @@
+

benchmarks/benchmarks/bench_centrality.py

@@ -0,0 +1,11 @@
+from .common import *
+import networkx as nx
+
+
+class Betweenness(Benchmark):
+    params = [(backends), (num_nodes), (edge_prob)]
+    param_names = ["backend", "num_nodes", "edge_prob"]
+
+    def time_betweenness_centrality(self, backend, num_nodes, edge_prob):
+        G = get_cached_gnp_random_graph(num_nodes, edge_prob)
+        _ = nx.betweenness_centrality(G, backend=backend)

benchmarks/benchmarks/bench_efficiency_measures.py

@@ -0,0 +1,11 @@
+from .common import *
+import networkx as nx
+
+
+class EfficiencyMeasures(Benchmark):
+    params = [(backends), (num_nodes), (edge_prob)]
+    param_names = ["backend", "num_nodes", "edge_prob"]
+
+    def time_local_efficiency(self, backend, num_nodes, edge_prob):
+        G = get_cached_gnp_random_graph(num_nodes, edge_prob)
+        _ = nx.local_efficiency(G, backend=backend)

benchmarks/benchmarks/bench_isolate.py

@@ -0,0 +1,11 @@
+from .common import *
+import networkx as nx
+
+
+class Isolate(Benchmark):
+    params = [(backends), (num_nodes), (edge_prob)]
+    param_names = ["backend", "num_nodes", "edge_prob"]
+
+    def time_number_of_isolates(self, backend, num_nodes, edge_prob):
+        G = get_cached_gnp_random_graph(num_nodes, edge_prob)
+        _ = nx.number_of_isolates(G, backend=backend)

benchmarks/benchmarks/bench_shortest_paths.py

@@ -0,0 +1,11 @@
+from .common import *
+import networkx as nx
+
+
+class Weighted(Benchmark):
+    params = [(backends), (num_nodes), (edge_prob)]
+    param_names = ["backend", "num_nodes", "edge_prob"]
+
+    def time_all_pairs_bellman_ford_path(self, backend, num_nodes, edge_prob):
+        G = get_cached_gnp_random_graph(num_nodes, edge_prob, is_weighted=True)
+        _ = dict(nx.all_pairs_bellman_ford_path(G, backend=backend))

benchmarks/benchmarks/bench_tournament.py

@@ -0,0 +1,11 @@
+from .common import *
+import networkx as nx
+
+
+class Tournament(Benchmark):
+    params = [(backends), (num_nodes)]
+    param_names = ["backend", "num_nodes"]
+
+    def time_is_reachable(self, backend, num_nodes):
+        G = nx.tournament.random_tournament(num_nodes, seed=42)
+        _ = nx.tournament.is_reachable(G, 1, num_nodes, backend=backend)

benchmarks/benchmarks/bench_vitality.py

@@ -0,0 +1,11 @@
+from .common import *
+import networkx as nx
+
+
+class Vitality(Benchmark):
+    params = [(backends), (num_nodes), (edge_prob)]
+    param_names = ["backend", "num_nodes", "edge_prob"]
+
+    def time_closeness_vitality(self, backend, num_nodes, edge_prob):
+        G = get_cached_gnp_random_graph(num_nodes, edge_prob)
+        _ = nx.closeness_vitality(G, backend=backend)

benchmarks/benchmarks/common.py

@@ -0,0 +1,33 @@
+from functools import lru_cache
+from pathlib import Path
+import random
+
+import networkx as nx
+
+__all__ = [
+    "backends",
+    "num_nodes",
+    "edge_prob",
+    "get_cached_gnp_random_graph",
+    "Benchmark",
+]
+
+CACHE_ROOT = Path(__file__).resolve().parent.parent / "env" / "nxp_benchdata"
+
+backends = ["parallel", None]
+num_nodes = [50, 100, 200, 400, 800]
+edge_prob = [0.8, 0.6, 0.4, 0.2]
+
+
+@lru_cache(typed=True)
+def get_cached_gnp_random_graph(num_nodes, edge_prob, is_weighted=False):
+    G = nx.fast_gnp_random_graph(num_nodes, edge_prob, seed=42, directed=False)
+    if is_weighted:
+        random.seed(42)
+        for (u, v) in G.edges():
+            G.edges[u, v]["weight"] = random.random()
+    return G
+
+
+class Benchmark:
+    pass

pyproject.toml

@@ -30,7 +30,7 @@ developer = [
     'pytest',
 ]
 
-[project.entry-points."networkx.plugins"]
+[project.entry-points."networkx.backends"]
 parallel = "nx_parallel.interface:Dispatcher"
 
 [tool.setuptools]