Removed unreusable reusable code for better readability #3510

Helveg · 2025-06-25T08:36:45Z

This code was written by me with a lot of initial enthusiasm for pytest during a hackathon experimenting with best patterns for pytest, and it completely missed its mark for providing an easy reusable simulation fixture. I've removed it in favor of straightforward, less complex, much more readable test code.

heplesser · 2025-06-25T14:51:41Z

testsuite/pytests/sli2py_neurons/test_iaf_ps_dc_accuracy.py

+    to function print_details.
+    """
+    nest.ResetKernel()
+    nest.SetKernelStatus({"tics_per_ms": 2**14, "resolution": resolution})


nest.set

Suggested change

nest.SetKernelStatus({"tics_per_ms": 2**14, "resolution": resolution})

nest.set(tics_per_ms=2**14, resolution=resolution)

heplesser · 2025-06-25T14:52:17Z

testsuite/pytests/sli2py_neurons/test_iaf_ps_dc_accuracy.py

+    neuron = nest.Create(model, params=params)
+    nest.Simulate(duration)
+
+    V_m = nest.GetStatus(neuron, "V_m")[0]


Suggested change

V_m = nest.GetStatus(neuron, "V_m")[0]

heplesser · 2025-06-25T14:53:11Z

testsuite/pytests/sli2py_neurons/test_iaf_ps_dc_accuracy.py

+    V_m = nest.GetStatus(neuron, "V_m")[0]
+    expected_V_m = params["I_e"] * params["tau_m"] / params["C_m"] * (1.0 - math.exp(-duration / params["tau_m"]))
+
+    assert math.fabs(V_m - expected_V_m) < tolerance


Suggested change

assert math.fabs(V_m - expected_V_m) < tolerance

assert neuron.V_m == pytest.approx(expected_V_m)

heplesser · 2025-06-25T14:54:30Z

testsuite/pytests/sli2py_neurons/test_iaf_ps_dc_accuracy.py

+
+    nest.Simulate(duration)
+
+    spike_times = nest.GetStatus(spike_recorder, "events")[0]["times"]


Suggested change

spike_times = nest.GetStatus(spike_recorder, "events")[0]["times"]

spike_times = spike_recorder.get("events", "times")

heplesser · 2025-06-25T15:02:51Z

testsuite/pytests/sli2py_neurons/test_iaf_psc_alpha_1to2.py

+    events = nest.GetStatus(vm, "events")[0]
+    times = np.array(events["times"]).reshape(-1, 1)
+    V_m = np.array(events["V_m"]).reshape(-1, 1)
+    results = np.hstack((times, V_m))
+
+    actual, expected = testutil.get_comparable_timesamples(
+        results,
+        np.array(
+            [
+                [0.1, -70],
+                [0.2, -70],
+                [0.3, -70],
+                [0.4, -70],
+                [0.5, -70],
+                [2.8, -70],
+                [2.9, -70],
+                [3.0, -70],
+                [3.1, -70],
+                [3.2, -70],
+                [3.3, -70],
+                [3.4, -70],
+                [3.5, -70],
+                [4.8, -70],
+                [4.9, -70],
+                [5.0, -70],
+                [5.1, -69.9974],
+                [5.2, -69.9899],
+                [5.3, -69.9781],
+                [5.4, -69.9624],
+                [5.5, -69.9434],
+                [5.6, -69.9213],
+                [5.7, -69.8967],
+                [5.8, -69.8699],
+                [5.9, -69.8411],
+                [6.0, -69.8108],
+            ]
+        ),
+    )
+    assert actual == expected


Suggested change

events = nest.GetStatus(vm, "events")[0]

times = np.array(events["times"]).reshape(-1, 1)

V_m = np.array(events["V_m"]).reshape(-1, 1)

results = np.hstack((times, V_m))

actual, expected = testutil.get_comparable_timesamples(

results,

np.array(

[

[0.1, -70],

[0.2, -70],

[0.3, -70],

[0.4, -70],

[0.5, -70],

[2.8, -70],

[2.9, -70],

[3.0, -70],

[3.1, -70],

[3.2, -70],

[3.3, -70],

[3.4, -70],

[3.5, -70],

[4.8, -70],

[4.9, -70],

[5.0, -70],

[5.1, -69.9974],

[5.2, -69.9899],

[5.3, -69.9781],

[5.4, -69.9624],

[5.5, -69.9434],

[5.6, -69.9213],

[5.7, -69.8967],

[5.8, -69.8699],

[5.9, -69.8411],

[6.0, -69.8108],

]

),

)

assert actual == expected

res = vm.get("events", ["times", "V_m"])

vm_expected = testutil.get_samples_at_nearest_times(res["times"],

np.array(

[

[0.1, -70],

[0.2, -70],

[0.3, -70],

[0.4, -70],

[0.5, -70],

[2.8, -70],

[2.9, -70],

[3.0, -70],

[3.1, -70],

[3.2, -70],

[3.3, -70],

[3.4, -70],

[3.5, -70],

[4.8, -70],

[4.9, -70],

[5.0, -70],

[5.1, -69.9974],

[5.2, -69.9899],

[5.3, -69.9781],

[5.4, -69.9624],

[5.5, -69.9434],

[5.6, -69.9213],

[5.7, -69.8967],

[5.8, -69.8699],

[5.9, -69.8411],

[6.0, -69.8108],

]

),

)

assert actual == pytest.approx(expected)

Helveg · 2025-07-07T11:43:22Z

@heplesser It seems like the tests do rely on get_comparable_timesamples to subselect both the measured and expected samples. One way we could completely remove this util function altogether is by running the old tests and by exfiltrating the exact solutions into separate arrays that we can then simply assert measured == pytest.approx(expected)? We'd probably be duplicating the solutions a couple of times but perhaps that is preferred? I think using this util function leaves a lot of room for errors in the times of samples being masked because they're filtered out in both the measured and expected array.

terhorstd · 2025-08-11T10:01:41Z

Hi @Helveg are there any updates on this?

Helveg · 2025-08-11T10:43:21Z

I'd need some input. I think the best way forward is to run the old version of the tests and see which data points end up being used, and assume those are the correct and intended reference points, hardcore them, and remove the flawed utility function.

The danger is ofcourse that this propagates incorrect tests, but I don't have the time/experience to assess what the correct outcomemof each test should be.

github-actions · 2025-11-09T08:36:48Z

Pull request automatically marked stale!

Helveg · 2025-11-10T08:40:56Z

I'll get around to finding out what the corret input is some weekend day soon hopefully. But if anyone can just check what the current values on main are and whether they're the correct and expected output, this could be merged.

heplesser · 2025-11-29T23:01:53Z

@Helveg I am looking at it, will get back to you within a day or two.

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Helveg · 2025-11-30T11:03:49Z

I merged your PR :) does this align these tests with the original SLI code/results again?

heplesser · 2025-11-30T16:34:33Z

@Helveg Something strange has happened here so that Github shows 458 files changed and two conflicts. When I compare my corresponding branch (https://github.com/heplesser/nest-simulator/tree/helveg_3510) to master, it shows me only 11 files (the expected ones). Would you mind if I closed your PR and opened a new one from my branch (including all your commits)? The test now do what the original tests did.

Helveg · 2025-11-30T16:52:10Z

yes, go ahead

heplesser · 2025-11-30T17:00:26Z

Replaced by #3661 due to git mix-up that led to 458 files changed in this PR.

Simplify test implementation and remove complex reusable code for better readability (replacement for #3510)

removed unreusable reusable code for better readability

64f7b55

Helveg requested a review from heplesser June 25, 2025 08:36

Helveg added 3 commits June 25, 2025 10:40

fix copyright headers

c2b7414

black formatting

9ed820a

isort

e11a6b9

heplesser reviewed Jun 25, 2025

View reviewed changes

use modern nest notations

57e0d29

heplesser added S: Normal Handle this with default priority T: Maintenance Work to keep up the quality of the code and documentation. I: No breaking change Previously written code will work as before, no one should note anything changing (aside the fix) labels Jun 30, 2025

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github-project-automation bot moved this to To do in Build system and CI Jul 25, 2025

github-actions bot added the stale Automatic marker for inactivity, please have another look here label Nov 9, 2025

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heplesser mentioned this pull request Nov 30, 2025

Simplify test implementation and remove complex reusable code for better readability (replacement for #3510) #3661

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heplesser closed this Nov 30, 2025

github-project-automation bot moved this from To do to Done in Build system and CI Nov 30, 2025

terhorstd added a commit that referenced this pull request Dec 2, 2025

Merge pull request #3661 from heplesser/helveg_3510

7ab0c23

Simplify test implementation and remove complex reusable code for better readability (replacement for #3510)

	nest.SetKernelStatus({"tics_per_ms": 2**14, "resolution": resolution})
	nest.set(tics_per_ms=2**14, resolution=resolution)

	assert math.fabs(V_m - expected_V_m) < tolerance
	assert neuron.V_m == pytest.approx(expected_V_m)


		nest.Simulate(duration)

		spike_times = nest.GetStatus(spike_recorder, "events")[0]["times"]

	spike_times = nest.GetStatus(spike_recorder, "events")[0]["times"]
	spike_times = spike_recorder.get("events", "times")

Removed unreusable reusable code for better readability #3510

Removed unreusable reusable code for better readability #3510

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Helveg commented Jun 25, 2025

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Helveg commented Jul 7, 2025 •

edited

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