diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml new file mode 100644 index 0000000..4eb4f77 --- /dev/null +++ b/.github/workflows/codspeed.yml @@ -0,0 +1,28 @@ +name: CodSpeed + +on: + push: + branches: [main] + pull_request: + workflow_dispatch: + +jobs: + benchmarks: + runs-on: ubuntu-latest + timeout-minutes: 30 + steps: + - uses: actions/checkout@v7 + with: + show-progress: false + + - uses: astral-sh/setup-uv@v5 + + - name: Sync test deps + run: uv sync --extra test + + - name: Run benchmarks + uses: CodSpeedHQ/action@v4 + with: + mode: simulation + token: ${{ secrets.CODSPEED_TOKEN }} + run: uv run pytest tests/benchmarks/ --codspeed diff --git a/pyproject.toml b/pyproject.toml index 78f6a8e..ec6e215 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -46,7 +46,7 @@ Changelog = "https://delaynet.readthedocs.io/en/latest/changelog/" [project.optional-dependencies] lint = ["pre-commit", "ruff"] -test = ["pytest", "pytest-cov", "coverage", "pytest-xdist"] +test = ["pytest", "pytest-cov", "coverage", "pytest-xdist", "pytest-codspeed"] doc = [ "sphinx", "myst-nb", @@ -89,6 +89,15 @@ select = ["NPY201"] minversion = "7.0" addopts = "-ra" testpaths = ["tests"] +filterwarnings = [ + "error", + # eigenvector_centrality warns about symmetric matrix with directed=True + 'default:Parameter .*irected.* was passed buts weight matrix is symmetric.*:UserWarning', + # igraph C extension runtime warnings (disconnected graphs in eigenvector centrality) + 'default::RuntimeWarning', + # numpy longdouble probe warning on uncommon CPUs (e.g. CodSpeed CI runner) + 'default:Signature.*numpy.longdouble.*does not match any known type:UserWarning', +] [tool.coverage.run] branch = true diff --git a/tests/benchmarks/__init__.py b/tests/benchmarks/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/benchmarks/conftest.py b/tests/benchmarks/conftest.py new file mode 100644 index 0000000..646f1b6 --- /dev/null +++ b/tests/benchmarks/conftest.py @@ -0,0 +1,37 @@ +"""Shared fixtures and constants for benchmarks.""" + +import numpy as np +import pytest + +from delaynet.preparation.data_generator import gen_delayed_causal_network + +TIME_POINTS = 200 +LAG_STEPS = 3 +NODE_SIZES = [5, 10] + +CONTINUOUS_METRICS = ["lc", "rc", "gv"] + + +def gen_continuous(n_nodes: int, rng: int = 19425) -> np.ndarray: + _, _, ts = gen_delayed_causal_network( + ts_len=TIME_POINTS, n_nodes=n_nodes, l_dens=0.3, rng=rng + ) + return np.ascontiguousarray(ts.T) + + +@pytest.fixture(scope="module", params=NODE_SIZES, ids=lambda n: f"nodes{n}") +def continuous_data(request) -> np.ndarray: + return gen_continuous(request.param) + + +def pytest_collection_modifyitems(config, items): + if not config.getoption("codspeed", False): + try: + from pytest_codspeed.plugin import has_benchmark_fixture + + msg = pytest.mark.skip(reason="use --codspeed to run benchmarks") + for item in items: + if has_benchmark_fixture(item): + item.add_marker(msg) + except ImportError: + pass diff --git a/tests/benchmarks/test_bench_metrics.py b/tests/benchmarks/test_bench_metrics.py new file mode 100644 index 0000000..10d1a9a --- /dev/null +++ b/tests/benchmarks/test_bench_metrics.py @@ -0,0 +1,69 @@ +"""Isolated single-pair metric benchmarks (no pair-loop overhead).""" + +import numpy as np +import pytest + +from delaynet.connectivities.continuous_ordinal_patterns import random_patterns +from delaynet.connectivities.granger import gt_multi_lag +from delaynet.connectivities.linear_correlation import linear_correlation +from delaynet.connectivities.rank_correlation import rank_correlation +from delaynet.connectivities.mutual_information import mutual_information +from delaynet.connectivities.transfer_entropy import transfer_entropy +from delaynet.preparation.data_generator import gen_delayed_causal_network + +from .conftest import LAG_STEPS + +_ts = np.ascontiguousarray( + gen_delayed_causal_network(ts_len=200, n_nodes=2, l_dens=0.5, rng=0)[2].T +) +TS1, TS2 = _ts[:, 0], _ts[:, 1] + +_disc = np.random.default_rng(0).integers(0, 4, size=(200, 2)) +DTS1, DTS2 = _disc[:, 0], _disc[:, 1] + +N_TESTS = 2 + + +@pytest.mark.benchmark(group="metrics") +@pytest.mark.parametrize( + "metric_func,kwargs", + [ + (linear_correlation, {}), + (rank_correlation, {}), + ], + ids=["lc", "rc"], +) +def test_continuous_metric(benchmark, metric_func, kwargs): + benchmark(metric_func, TS1, TS2, lag_steps=LAG_STEPS, **kwargs) + + +@pytest.mark.benchmark(group="metrics") +def test_granger_f_test(benchmark): + ts = gen_delayed_causal_network(ts_len=50, n_nodes=5, l_dens=0.3, rng=0)[2].T + ts1, ts2 = ts[:, 0], ts[:, 1] + benchmark(gt_multi_lag, ts1, ts2, lag_steps=LAG_STEPS) + + +@pytest.mark.benchmark(group="metrics") +def test_ordinal_patterns(benchmark): + ts = gen_delayed_causal_network(ts_len=50, n_nodes=5, l_dens=0.3, rng=0)[2].T + ts1, ts2 = ts[:, 0], ts[:, 1] + random_patterns(ts1, ts2, p_size=3, num_rnd_patterns=2, lag_steps=1) + benchmark(random_patterns, ts1, ts2, p_size=3, num_rnd_patterns=2, lag_steps=1) + + +@pytest.mark.benchmark(group="metrics") +@pytest.mark.parametrize( + "metric_func", + [mutual_information, transfer_entropy], + ids=["mi", "te"], +) +def test_discrete_metric(benchmark, metric_func): + benchmark( + metric_func, + DTS1, + DTS2, + approach="discrete", + lag_steps=LAG_STEPS, + n_tests=N_TESTS, + ) diff --git a/tests/benchmarks/test_bench_reconstruct_network.py b/tests/benchmarks/test_bench_reconstruct_network.py new file mode 100644 index 0000000..15dbc0b --- /dev/null +++ b/tests/benchmarks/test_bench_reconstruct_network.py @@ -0,0 +1,28 @@ +"""reconstruct_network benchmarks: full pipeline across metrics and sizes.""" + +import pytest + +from delaynet.network_reconstruction import reconstruct_network + +from .conftest import LAG_STEPS, gen_continuous + +_RECON_METRICS = ["lc", "rc", "gc", "gv"] + + +@pytest.mark.benchmark(group="reconstruct-network") +@pytest.mark.parametrize("metric", _RECON_METRICS) +def test_reconstruct(benchmark, continuous_data, metric): + benchmark(reconstruct_network, continuous_data, metric, lag_steps=LAG_STEPS) + + +@pytest.mark.benchmark(group="parallel-scaling") +@pytest.mark.parametrize("workers", [1, 2], ids=["seq", "par2"]) +def test_reconstruct_workers(benchmark, workers): + data = gen_continuous(5) + benchmark( + reconstruct_network, + data, + "lc", + lag_steps=LAG_STEPS, + workers=workers, + ) diff --git a/tests/benchmarks/test_bench_utils.py b/tests/benchmarks/test_bench_utils.py new file mode 100644 index 0000000..4f578ea --- /dev/null +++ b/tests/benchmarks/test_bench_utils.py @@ -0,0 +1,23 @@ +"""find_optimal_lag wrapper overhead, measured with a lightweight metric.""" + +import numpy as np +import pytest + +from delaynet.preparation.data_generator import gen_delayed_causal_network +from delaynet.utils.lag_steps import find_optimal_lag + +from .conftest import LAG_STEPS + +_ts = np.ascontiguousarray( + gen_delayed_causal_network(ts_len=500, n_nodes=2, l_dens=0.5, rng=0)[2].T +) +TS1, TS2 = _ts[:, 0], _ts[:, 1] + + +def _l2_metric(ts1, ts2, lag): + return float(np.sum((ts1[:-lag] - ts2[lag:]) ** 2)) + + +@pytest.mark.benchmark(group="utils") +def test_find_optimal_lag(benchmark): + benchmark(find_optimal_lag, _l2_metric, TS1, TS2, list(range(1, LAG_STEPS + 1))) diff --git a/uv.lock b/uv.lock index 9644ad1..b35b1a4 100644 --- a/uv.lock +++ b/uv.lock @@ -575,6 +575,7 @@ all = [ { name = "networkx" }, { name = "pre-commit" }, { name = "pytest" }, + { name = "pytest-codspeed" }, { name = "pytest-cov" }, { name = "pytest-xdist" }, { name = "ruff" }, @@ -605,6 +606,7 @@ lint = [ test = [ { name = "coverage" }, { name = "pytest" }, + { name = "pytest-codspeed" }, { name = "pytest-cov" }, { name = "pytest-xdist" }, ] @@ -626,6 +628,7 @@ requires-dist = [ { name = "numpy" }, { name = "pre-commit", marker = "extra == 'lint'" }, { name = "pytest", marker = "extra == 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