Add runtime tests

Author: michaeldeistler

.github/workflows/tests.yml

@@ -39,4 +39,4 @@ jobs:
     - name: Test with pytest
       run: |
         pip install pytest pytest-cov
-        pytest tests/ --cov=jaxley --cov-report=xml
+        pytest tests/ -m "not runtime" --cov=jaxley --cov-report=xml

tests/test_runtime.py

@@ -0,0 +1,121 @@
+import os
+import time
+
+import numpy as np
+import pytest
+from jax import jit
+
+import jaxley as jx
+from jaxley.channels import HH
+from jaxley.connect import sparse_connect
+from jaxley.synapses import IonotropicSynapse
+
+
+def build_net(num_cells, artificial=True, connect=True, connection_prob=0.0):
+    _ = np.random.seed(1)  # For sparse connectivity matrix.
+
+    if artificial:
+        comp = jx.Compartment()
+        branch = jx.Branch(comp, 2)
+        depth = 3
+        parents = [-1] + [b // 2 for b in range(0, 2**depth - 2)]
+        cell = jx.Cell(branch, parents=parents)
+    else:
+        dirname = os.path.dirname(__file__)
+        fname = os.path.join(dirname, "swc_files", "morph.swc")
+        cell = jx.read_swc(fname, nseg=4)
+    net = jx.Network([cell for _ in range(num_cells)])
+
+    # Channels.
+    net.insert(HH())
+
+    # Synapses.
+    if connect:
+        sparse_connect(
+            net.cell("all"), net.cell("all"), IonotropicSynapse(), connection_prob
+        )
+
+    # Recordings.
+    net[0, 1, 0].record(verbose=False)
+
+    # Trainables.
+    net.make_trainable("radius", verbose=False)
+    params = net.get_parameters()
+
+    net.to_jax()
+    return net, params
+
+
+@pytest.mark.runtime
+@pytest.mark.parametrize(
+    "num_cells, artificial, connect, connection_prob, voltage_solver, identifier",
+    (
+        # Test a single SWC cell with both solvers.
+        pytest.param(1, False, False, 0.0, "jaxley.stone", 0),
+        pytest.param(1, False, False, 0.0, "jax.sparse", 1),
+        # Test a network of SWC cells with both solvers.
+        pytest.param(10, False, True, 0.1, "jaxley.stone", 2),
+        pytest.param(10, False, True, 0.1, "jax.sparse", 3),
+        # Test a larger network of smaller neurons with both solvers.
+        pytest.param(1000, True, True, 0.001, "jaxley.stone", 4),
+        pytest.param(1000, True, True, 0.001, "jax.sparse", 5),
+    ),
+)
+def test_runtime(
+    num_cells: int,
+    artificial: bool,
+    connect: bool,
+    connection_prob: float,
+    voltage_solver: str,
+    identifier: int,
+):
+    delta_t = 0.025
+    t_max = 100.0
+
+    net, params = build_net(
+        num_cells,
+        artificial=artificial,
+        connect=connect,
+        connection_prob=connection_prob,
+    )
+
+    def simulate(params):
+        return jx.integrate(
+            net,
+            params=params,
+            t_max=t_max,
+            delta_t=delta_t,
+            voltage_solver=voltage_solver,
+        )
+
+    jitted_simulate = jit(simulate)
+
+    start_time = time.time()
+    _ = jitted_simulate(params).block_until_ready()
+    compile_time = time.time() - start_time
+
+    params[0]["radius"] = params[0]["radius"].at[0].set(0.5)
+    start_time = time.time()
+    _ = jitted_simulate(params).block_until_ready()
+    run_time = time.time() - start_time
+
+    compile_times = {
+        0: 16.858529806137085,
+        1: 0.8063809871673584,
+        2: 5.4792890548706055,
+        3: 6.175129175186157,
+        4: 2.755805015563965,
+        5: 13.303060293197632,
+    }
+    run_times = {
+        0: 0.08291006088256836,
+        1: 0.596994161605835,
+        2: 0.8518729209899902,
+        3: 5.746302127838135,
+        4: 1.3585789203643799,
+        5: 12.48916506767273,
+    }
+
+    tolerance = 1.2
+    assert compile_time < compile_times[identifier] * tolerance
+    assert run_time < run_times[identifier] * tolerance