add some basic benchmarks

Author: arashbm

.gitignore

@@ -49,3 +49,4 @@ wheelhouse
 
 .cache
 compile_commands.json
+.asv

asv.conf.json

@@ -0,0 +1,184 @@
+{
+    // The version of the config file format.  Do not change, unless
+    // you know what you are doing.
+    "version": 1,
+
+    // The name of the project being benchmarked
+    "project": "reticula",
+
+    // The project's homepage
+    "project_url": "https://reticula.network/",
+
+    // The URL or local path of the source code repository for the
+    // project being benchmarked
+    "repo": ".",
+
+    // The Python project's subdirectory in your repo.  If missing or
+    // the empty string, the project is assumed to be located at the root
+    // of the repository.
+    // "repo_subdir": "",
+
+    // Customizable commands for building the project.
+    // See asv.conf.json documentation.
+    // To build the package using pyproject.toml (PEP518), uncomment the following lines
+    "build_command": [
+        "python -m pip wheel -v -w {build_cache_dir} {build_dir}"
+    ],
+
+    // Customizable commands for installing and uninstalling the project.
+    // See asv.conf.json documentation.
+    // "install_command": ["in-dir={env_dir} python -mpip install {wheel_file}"],
+    // "uninstall_command": ["return-code=any python -mpip uninstall -y {project}"],
+
+    "branches": ["main"], // for git
+
+    // The DVCS being used.  If not set, it will be automatically
+    // determined from "repo" by looking at the protocol in the URL
+    // (if remote), or by looking for special directories, such as
+    // ".git" (if local).
+    // "dvcs": "git",
+
+    // The tool to use to create environments.  May be "conda",
+    // "virtualenv", "mamba" (above 3.8)
+    // or other value depending on the plugins in use.
+    // If missing or the empty string, the tool will be automatically
+    // determined by looking for tools on the PATH environment
+    // variable.
+    "environment_type": "virtualenv",
+
+    // timeout in seconds for installing any dependencies in environment
+    // defaults to 10 min
+    //"install_timeout": 600,
+
+    // the base URL to show a commit for the project.
+    "show_commit_url": "http://github.com/reticula-network/reticula-python/commit/",
+
+    // The Pythons you'd like to test against.  If not provided, defaults
+    // to the current version of Python used to run `asv`.
+    // "pythons": ["3.8", "3.12"],
+
+    // The list of conda channel names to be searched for benchmark
+    // dependency packages in the specified order
+    // "conda_channels": ["conda-forge", "defaults"],
+
+    // A conda environment file that is used for environment creation.
+    // "conda_environment_file": "environment.yml",
+
+    // The matrix of dependencies to test.  Each key of the "req"
+    // requirements dictionary is the name of a package (in PyPI) and
+    // the values are version numbers.  An empty list or empty string
+    // indicates to just test against the default (latest)
+    // version. null indicates that the package is to not be
+    // installed. If the package to be tested is only available from
+    // PyPi, and the 'environment_type' is conda, then you can preface
+    // the package name by 'pip+', and the package will be installed
+    // via pip (with all the conda available packages installed first,
+    // followed by the pip installed packages).
+    //
+    // The ``@env`` and ``@env_nobuild`` keys contain the matrix of
+    // environment variables to pass to build and benchmark commands.
+    // An environment will be created for every combination of the
+    // cartesian product of the "@env" variables in this matrix.
+    // Variables in "@env_nobuild" will be passed to every environment
+    // during the benchmark phase, but will not trigger creation of
+    // new environments.  A value of ``null`` means that the variable
+    // will not be set for the current combination.
+    //
+    // "matrix": {
+    //     "req": {
+    //         "numpy": ["1.6", "1.7"],
+    //         "six": ["", null],  // test with and without six installed
+    //         "pip+emcee": [""]   // emcee is only available for install with pip.
+    //     },
+    //     "env": {"ENV_VAR_1": ["val1", "val2"]},
+    //     "env_nobuild": {"ENV_VAR_2": ["val3", null]},
+    // },
+
+    // Combinations of libraries/python versions can be excluded/included
+    // from the set to test. Each entry is a dictionary containing additional
+    // key-value pairs to include/exclude.
+    //
+    // An exclude entry excludes entries where all values match. The
+    // values are regexps that should match the whole string.
+    //
+    // An include entry adds an environment. Only the packages listed
+    // are installed. The 'python' key is required. The exclude rules
+    // do not apply to includes.
+    //
+    // In addition to package names, the following keys are available:
+    //
+    // - python
+    //     Python version, as in the *pythons* variable above.
+    // - environment_type
+    //     Environment type, as above.
+    // - sys_platform
+    //     Platform, as in sys.platform. Possible values for the common
+    //     cases: 'linux2', 'win32', 'cygwin', 'darwin'.
+    // - req
+    //     Required packages
+    // - env
+    //     Environment variables
+    // - env_nobuild
+    //     Non-build environment variables
+    //
+    // "exclude": [
+    //     {"python": "3.2", "sys_platform": "win32"}, // skip py3.2 on windows
+    //     {"environment_type": "conda", "req": {"six": null}}, // don't run without six on conda
+    //     {"env": {"ENV_VAR_1": "val2"}}, // skip val2 for ENV_VAR_1
+    // ],
+    //
+    // "include": [
+    //     // additional env for python3.12
+    //     {"python": "3.12", "req": {"numpy": "1.26"}, "env_nobuild": {"FOO": "123"}},
+    //     // additional env if run on windows+conda
+    //     {"platform": "win32", "environment_type": "conda", "python": "3.12", "req": {"libpython": ""}},
+    // ],
+
+    // The directory (relative to the current directory) that benchmarks are
+    // stored in.  If not provided, defaults to "benchmarks"
+    // "benchmark_dir": "benchmarks",
+
+    // The directory (relative to the current directory) to cache the Python
+    // environments in.  If not provided, defaults to "env"
+    "env_dir": ".asv/env",
+
+    // The directory (relative to the current directory) that raw benchmark
+    // results are stored in.  If not provided, defaults to "results".
+    "results_dir": ".asv/results",
+
+    // The directory (relative to the current directory) that the html tree
+    // should be written to.  If not provided, defaults to "html".
+    "html_dir": ".asv/html",
+
+    // The number of characters to retain in the commit hashes.
+    // "hash_length": 8,
+
+    // `asv` will cache results of the recent builds in each
+    // environment, making them faster to install next time.  This is
+    // the number of builds to keep, per environment.
+    // "build_cache_size": 2,
+
+    // The commits after which the regression search in `asv publish`
+    // should start looking for regressions. Dictionary whose keys are
+    // regexps matching to benchmark names, and values corresponding to
+    // the commit (exclusive) after which to start looking for
+    // regressions.  The default is to start from the first commit
+    // with results. If the commit is `null`, regression detection is
+    // skipped for the matching benchmark.
+    //
+    // "regressions_first_commits": {
+    //    "some_benchmark": "352cdf",  // Consider regressions only after this commit
+    //    "another_benchmark": null,   // Skip regression detection altogether
+    // },
+
+    // The thresholds for relative change in results, after which `asv
+    // publish` starts reporting regressions. Dictionary of the same
+    // form as in ``regressions_first_commits``, with values
+    // indicating the thresholds.  If multiple entries match, the
+    // maximum is taken. If no entry matches, the default is 5%.
+    //
+    // "regressions_thresholds": {
+    //    "some_benchmark": 0.01,     // Threshold of 1%
+    //    "another_benchmark": 0.5,   // Threshold of 50%
+    // },
+}

benchmarks/__init__.py

@@ -0,0 +1,9 @@
+class ModuleImport:
+    """
+    Benchmark total import time.
+    """
+
+    def timeraw_import_reticula(self):
+        return """
+        import reticula
+        """

benchmarks/ba_sequence.json

@@ -0,0 +1,123 @@
+import reticula as ret
+
+import random
+import json
+import pathlib
+
+
+class Construction:
+    """
+    Benchmarking the construction and basic operation of static graphs.
+    """
+
+    def setup(self):
+        self.n = 2**16
+        k = 32
+        self.g = ret.regular_ring_lattice[ret.int64](size=self.n, degree=k)
+        self.verts = list(self.g.vertices())
+
+        self.edges = list(self.g.edges())
+        self.tuples = []
+        for e in self.edges:
+            verts = e.incident_verts()
+            self.tuples.append((verts[0], verts[-1]))
+
+        rand = random.Random(42)
+
+        self.shuffled_edges = rand.sample(self.edges, k=len(self.edges))
+        self.shuffled_tuples = []
+        for e in self.shuffled_edges:
+            verts = e.incident_verts()
+            if rand.random() > 0.5:
+                self.shuffled_tuples.append((verts[0], verts[-1]))
+            else:
+                self.shuffled_tuples.append((verts[-1], verts[0]))
+
+    def time_copy_construction(self):
+        ret.undirected_network[ret.int64](self.g)
+
+    def time_tuple_construction(self):
+        ret.undirected_network[ret.int64](
+            verts=self.verts, edges=self.tuples)
+
+    def time_shuffled_tuple_construction(self):
+        ret.undirected_network[ret.int64](
+            verts=self.verts, edges=self.shuffled_tuples)
+
+    def time_edge_obj_construction(self):
+        ret.undirected_network[ret.int64](
+            verts=self.verts, edges=self.edges)
+
+    def time_shuffled_edge_obj_construction(self):
+        ret.undirected_network[ret.int64](
+            verts=self.verts, edges=self.shuffled_edges)
+
+
+class Graphicallity:
+    def setup(self):
+        base_path = pathlib.Path(__file__).parent
+        with open(base_path / "ba_sequence.json") as f:
+            self.ba_sequence = json.load(f)
+
+    def time_is_graphic(self):
+        ret.is_graphic(self.ba_sequence)
+
+
+class Algorithms:
+    def setup(self):
+        self.n = 2**16
+        k = 32
+        self.g = ret.regular_ring_lattice[ret.int64](size=self.n, degree=k)
+        self.g_isolated = ret.undirected_network[ret.int64](
+            edges=[], verts=range(self.n))
+
+    def time_degree(self):
+        ret.degree(self.g, 12)
+
+    def time_degree_sequence(self):
+        ret.degree_sequence(self.g)
+
+    def time_density(self):
+        ret.density(self.g)
+
+    def time_assortativity(self):
+        ret.degree_assortativity(self.g)
+
+    def time_attribute_assortativity_lambda(self):
+        ret.attribute_assortativity(self.g, lambda x: x)
+
+    def time_connected_component(self):
+        ret.connected_component(self.g, 12)
+
+    def time_connected_component_isolated(self):
+        ret.connected_component(self.g_isolated, 12)
+
+    def time_connected_components(self):
+        ret.connected_components(self.g)
+
+    def time_connected_components_isolated(self):
+        ret.connected_components(self.g_isolated)
+
+    def time_is_connected(self):
+        ret.is_connected(self.g)
+
+    def time_is_connected_isolated(self):
+        ret.is_connected(self.g_isolated)
+
+    def time_largest_connected_component(self):
+        ret.largest_connected_component(self.g)
+
+    def time_largest_connected_component_isolated(self):
+        ret.largest_connected_component(self.g_isolated)
+
+    def time_is_reachable(self):
+        ret.is_reachable(self.g, 0, self.n//2)
+
+    def time_is_reachable_isolated(self):
+        ret.is_reachable(self.g_isolated, 0, self.n//2)
+
+    def time_shortest_path_lengths_from(self):
+        ret.shortest_path_lengths_from(self.g, 0)
+
+    def time_shortest_path_lengths_to(self):
+        ret.shortest_path_lengths_to(self.g, 0)