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Unverified Commit 5661a74b authored by Nora Abi Akar's avatar Nora Abi Akar Committed by GitHub
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Python unit test clean-up (#1595) 

* Remove test_simulator.py.
* Add missing python unit test file and fix errors.
* Run python unit tests in verbose mode to display which were skipped.
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.github/workflows/basic.yml
+ 3
− 3
View file @ 5661a74b
......@@ -186,11 +186,11 @@ jobs:
- name: Run python tests
run: |
cd build
python ../python/test/unit/runner.py
python ../python/test/unit/runner.py -v2
cd -
- if: ${{ matrix.config.mpi == 'ON' }}
name: Run python+MPI tests
run: mpirun -n 4 -oversubscribe python python/test/unit_distributed/runner.py
run: mpirun -n 4 -oversubscribe python python/test/unit_distributed/runner.py -v2
- name: Run Python examples
run: |
python python/example/network_ring.py
......@@ -201,4 +201,4 @@ jobs:
python python/example/single_cell_swc.py python/example/single_cell_detailed.swc
python python/example/single_cell_detailed.py python/example/single_cell_detailed.swc
python python/example/single_cell_detailed_recipe.py python/example/single_cell_detailed.swc
python python/example/single_cell_cable.py
\ No newline at end of file
python python/example/single_cell_cable.py
.github/workflows/sanitize.yml
+ 3
− 3
View file @ 5661a74b
......@@ -113,10 +113,10 @@ jobs:
mpirun -n 4 -oversubscribe build/bin/ring
mpirun -n 4 -oversubscribe build/bin/single-cell
- name: Run python tests
run: python python/test/unit/runner.py
run: python python/test/unit/runner.py -v2
- if: ${{ matrix.mpi == 'ON' }}
name: Run python+MPI tests
run: mpirun -n 4 -oversubscribe python python/test/unit_distributed/runner.py
run: mpirun -n 4 -oversubscribe python python/test/unit_distributed/runner.py -v2
- name: Run Python examples
run: |
python python/example/network_ring.py
......@@ -127,4 +127,4 @@ jobs:
python python/example/single_cell_swc.py python/example/single_cell_detailed.swc
python python/example/single_cell_detailed.py python/example/single_cell_detailed.swc
python python/example/single_cell_detailed_recipe.py python/example/single_cell_detailed.swc
python python/example/single_cell_cable.py
\ No newline at end of file
python python/example/single_cell_cable.py
python/test/unit/runner.py
+ 13
− 10
View file @ 5661a74b
......@@ -10,39 +10,42 @@ sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '../.
try:
import options
import test_cable_probes
import test_catalogues
import test_contexts
import test_decor
import test_domain_decomposition
import test_event_generators
import test_identifiers
import test_tests
import test_schedules
import test_cable_probes
import test_morphology
import test_catalogues
import test_schedules
import test_spikes
import test_tests
# add more if needed
except ModuleNotFoundError:
from test import options
from test.unit import test_contexts
from test.unit import test_cable_probes
from test.unit import test_catalogues
from test.unit import test_contexts
from test.unit import test_decor
from test.unit import test_domain_decompositions
from test.unit import test_event_generators
from test.unit import test_identifiers
from test.unit import test_schedules
from test.unit import test_cable_probes
from test.unit import test_morphology
from test.unit import test_schedules
from test.unit import test_spikes
# add more if needed
test_modules = [\
test_contexts,\
test_cable_probes,\
test_catalogues,\
test_contexts,\
test_decor,\
test_domain_decompositions,\
test_event_generators,\
test_identifiers,\
test_schedules,\
test_cable_probes,\
test_morphology,\
test_schedules,\
test_spikes,\
] # add more if needed
......
python/test/unit/test_decor.py
+ 3
− 3
View file @ 5661a74b
......@@ -24,7 +24,7 @@ class DecorClasses(unittest.TestCase):
self.assertEqual(0, clamp.frequency)
self.assertEqual([(0, 10)], clamp.envelope)
clamp = A.iclamp(10, 20);
clamp = A.iclamp(10, frequency=20);
self.assertEqual(20, clamp.frequency)
self.assertEqual([(0, 10)], clamp.envelope)
......@@ -33,7 +33,7 @@ class DecorClasses(unittest.TestCase):
self.assertEqual(0, clamp.frequency)
self.assertEqual([(100, 3), (120, 3), (120, 0)], clamp.envelope)
clamp = A.iclamp(100, 20, 3, 7);
clamp = A.iclamp(100, 20, 3, frequency=7);
self.assertEqual(7, clamp.frequency)
self.assertEqual([(100, 3), (120, 3), (120, 0)], clamp.envelope)
......@@ -43,7 +43,7 @@ class DecorClasses(unittest.TestCase):
self.assertEqual(0, clamp.frequency)
self.assertEqual(envelope, clamp.envelope)
clamp = A.iclamp(envelope, 7);
clamp = A.iclamp(envelope, frequency=7);
self.assertEqual(7, clamp.frequency)
self.assertEqual(envelope, clamp.envelope)
......
python/test/unit/test_simulator.py deleted 100644 → 0
+ 0
− 252
View file @ 51e35898
# -*- coding: utf-8 -*-
#
# test_simulator.py
import unittest
import numpy as np
import arbor as A
# to be able to run .py file from child directory
import sys, os
sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '../../')))
try:
import options
except ModuleNotFoundError:
from test import options
"""
all tests for the simulator wrapper
"""
# Test recipe cc2 comprises two cable cells and some probes.
class cc2_recipe(A.recipe):
def __init__(self):
A.recipe.__init__(self)
st = A.segment_tree()
i = st.append(A.mnpos, (0, 0, 0, 10), (1, 0, 0, 10), 1)
st.append(i, (1, 3, 0, 5), 1)
st.append(i, (1, -4, 0, 3), 1)
self.the_morphology = A.morphology(st)
self.the_cat = A.default_catalogue()
self.the_props = A.neuron_cable_properties()
self.the_props.register(self.the_cat)
def num_cells(self):
return 2
def cell_kind(self, gid):
return A.cell_kind.cable
def connections_on(self, gid):
return []
def event_generators(self, gid):
return []
def global_properties(self, kind):
return self.the_props
def probes(self, gid):
# Cell 0 has three voltage probes:
# 0, 0: end of branch 1
# 0, 1: end of branch 2
# 0, 2: all terminal points
# Values sampled from (0, 0) and (0, 1) should correspond
# to the values sampled from (0, 2).
# Cell 1 has whole cell probes:
# 0, 0: all membrane voltages
# 0, 1: all expsyn state variable 'g'
if gid==0:
return [A.cable_probe_membrane_voltage('(location 1 1)'),
A.cable_probe_membrane_voltage('(location 2 1)'),
A.cable_probe_membrane_voltage('(terminal)')]
elif gid==1:
return [A.cable_probe_membrane_voltage_cell(),
A.cable_probe_point_state_cell('expsyn', 'g')]
else:
return []
def cell_description(self, gid):
c = A.cable_cell(self.the_morphology, A.label_dict())
c.set_properties(Vm=0.0, cm=0.01, rL=30, tempK=300)
c.paint('(all)', "pas")
c.place('(location 0 0)', A.iclamp(current=10 if gid==0 else 20))
c.place('(sum (on-branches 0.3) (location 0 0.6))', "expsyn")
return c
# Test recipe lif2 comprises two independent LIF cells driven by a regular, rapid
# sequence of incoming spikes. The cells have differing refactory periods.
class lif2_recipe(A.recipe):
def __init__(self):
A.recipe.__init__(self)
def num_cells(self):
return 2
def cell_kind(self, gid):
return A.cell_kind.lif
def connections_on(self, gid):
return []
def event_generators(self, gid):
sched_dt = 0.25
weight = 400
return [A.event_generator((gid,0), weight, A.regular_schedule(sched_dt)) for gid in range(0, self.num_cells())]
def probes(self, gid):
return []
def cell_description(self, gid):
c = A.lif_cell()
if gid==0:
c.t_ref = 2
if gid==1:
c.t_ref = 4
return c
class Simulator(unittest.TestCase):
def init_sim(self, recipe):
context = A.context()
dd = A.partition_load_balance(recipe, context)
return A.simulation(recipe, dd, context)
def test_simple_run(self):
sim = self.init_sim(cc2_recipe())
sim.run(1.0, 0.01)
def test_probe_meta(self):
sim = self.init_sim(cc2_recipe())
self.assertEqual([A.location(1, 1)], sim.probe_metadata((0, 0)))
self.assertEqual([A.location(2, 1)], sim.probe_metadata((0, 1)))
self.assertEqual([A.location(1, 1), A.location(2, 1)], sorted(sim.probe_metadata((0, 2)), key=lambda x:(x.branch, x.pos)))
# Default CV policy is one per branch, which also gives a tivial CV over the branch point.
# Expect metadata cables to be one for each full branch, plus three length-zero cables corresponding to the branch point.
self.assertEqual([A.cable(0, 0, 1), A.cable(0, 1, 1), A.cable(1, 0, 0), A.cable(1, 0, 1), A.cable(2, 0, 0), A.cable(2, 0, 1)],
sorted(sim.probe_metadata((1,0))[0], key=lambda x:(x.branch, x.prox, x.dist)))
# Four expsyn synapses; the two on branch zero should be coalesced, giving a multiplicity of 2.
# Expect entries to be in target index order.
m11 = sim.probe_metadata((1,1))[0]
self.assertEqual(4, len(m11))
self.assertEqual([0, 1, 2, 3], [x.target for x in m11])
self.assertEqual([2, 2, 1, 1], [x.multiplicity for x in m11])
self.assertEqual([A.location(0, 0.3), A.location(0, 0.6), A.location(1, 0.3), A.location(2, 0.3)], [x.location for x in m11])
def test_probe_scalar_recorders(self):
sim = self.init_sim(cc2_recipe())
ts = [0, 0.1, 0.3, 0.7]
h = sim.sample((0, 0), A.explicit_schedule(ts))
dt = 0.01
sim.run(10., dt)
s, meta = sim.samples(h)[0]
self.assertEqual(A.location(1, 1), meta)
for i, t in enumerate(s[:,0]):
self.assertLess(abs(t-ts[i]), dt)
sim.remove_sampler(h)
sim.reset()
h = sim.sample(A.cell_member(0, 0), A.explicit_schedule(ts), A.sampling_policy.exact)
sim.run(10., dt)
s, meta = sim.samples(h)[0]
for i, t in enumerate(s[:,0]):
self.assertEqual(t, ts[i])
def test_probe_multi_scalar_recorders(self):
sim = self.init_sim(cc2_recipe())
ts = [0, 0.1, 0.3, 0.7]
h0 = sim.sample((0, 0), A.explicit_schedule(ts))
h1 = sim.sample((0, 1), A.explicit_schedule(ts))
h2 = sim.sample((0, 2), A.explicit_schedule(ts))
dt = 0.01
sim.run(10., dt)
r0 = sim.samples(h0)
self.assertEqual(1, len(r0))
s0, meta0 = r0[0]
r1 = sim.samples(h1)
self.assertEqual(1, len(r1))
s1, meta1 = r1[0]
r2 = sim.samples(h2)
self.assertEqual(2, len(r2))
s20, meta20 = r2[0]
s21, meta21 = r2[1]
# Probe id (0, 2) has probes over the two locations that correspond to probes (0, 0) and (0, 1).
# (order is not guaranteed to line up though)
if meta20==meta0:
self.assertEqual(meta1, meta21)
self.assertTrue((s0[:,1]==s20[:,1]).all())
self.assertTrue((s1[:,1]==s21[:,1]).all())
else:
self.assertEqual(meta1, meta20)
self.assertTrue((s1[:,1]==s20[:,1]).all())
self.assertEqual(meta0, meta21)
self.assertTrue((s0[:,1]==s21[:,1]).all())
def test_probe_vector_recorders(self):
sim = self.init_sim(cc2_recipe())
ts = [0, 0.1, 0.3, 0.7]
h0 = sim.sample((1, 0), A.explicit_schedule(ts), A.sampling_policy.exact)
h1 = sim.sample((1, 1), A.explicit_schedule(ts), A.sampling_policy.exact)
sim.run(10., 0.01)
# probe (1, 0) is the whole cell voltage; expect time + 6 sample values per row in returned data (see test_probe_meta above).
s0, meta0 = sim.samples(h0)[0]
self.assertEqual(6, len(meta0))
self.assertEqual((len(ts), 7), s0.shape)
for i, t in enumerate(s0[:,0]):
self.assertEqual(t, ts[i])
# probe (1, 1) is the 'g' state for all expsyn synapses.
# With the default descretization, expect two synapses with multiplicity 2 and two with multiplicity 1.
s1, meta1 = sim.samples(h1)[0]
self.assertEqual(4, len(meta1))
self.assertEqual((len(ts), 5), s1.shape)
for i, t in enumerate(s1[:,0]):
self.assertEqual(t, ts[i])
meta1_mult = {(m.location.branch, m.location.pos): m.multiplicity for m in meta1}
self.assertEqual(2, meta1_mult[(0, 0.3)])
self.assertEqual(2, meta1_mult[(0, 0.6)])
self.assertEqual(1, meta1_mult[(1, 0.3)])
self.assertEqual(1, meta1_mult[(2, 0.3)])
def test_spikes(self):
sim = self.init_sim(lif2_recipe())
sim.record(A.spike_recording.all)
sim.run(21, 0.01)
spikes = sim.spikes().tolist()
s0 = sorted([t for s, t in spikes if s==(0, 0)])
s1 = sorted([t for s, t in spikes if s==(1, 0)])
self.assertEqual([0, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20], s0)
self.assertEqual([0, 4, 8, 12, 16, 20], s1)
def suite():
# specify class and test functions in tuple (here: all tests starting with 'test' from class Contexts
suite = unittest.makeSuite(Simulator, ('test'))
return suite
def run():
v = options.parse_arguments().verbosity
runner = unittest.TextTestRunner(verbosity = v)
runner.run(suite())
if __name__ == "__main__":
run()
python/test/unit_distributed/runner.py
+ 1
− 0
View file @ 5661a74b
......@@ -21,6 +21,7 @@ try:
import test_contexts_arbmpi
import test_contexts_mpi4py
import test_domain_decompositions
import test_simulator
# add more if needed
except ModuleNotFoundError:
from test import options
......
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