diff --git a/.github/workflows/basic.yml b/.github/workflows/basic.yml
index 2e903bfc94f577a6ce78f8486973749aedbd8f4b..e563ce38be1f6aabdb1c7da03ea468a3f1e5291c 100644
--- a/.github/workflows/basic.yml
+++ b/.github/workflows/basic.yml
@@ -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
diff --git a/.github/workflows/sanitize.yml b/.github/workflows/sanitize.yml
index 805090d92d13d7acafa657aa8d522900daf701c0..3d6ee63de21e6cb67c2109789be9fe413b3d5d1c 100644
--- a/.github/workflows/sanitize.yml
+++ b/.github/workflows/sanitize.yml
@@ -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
diff --git a/python/test/unit/runner.py b/python/test/unit/runner.py
index d27357cf42ec430eb6d12956c809b51ec05475e2..3b12c40260b5445872e5a8eae15a070de86d3e5c 100644
--- a/python/test/unit/runner.py
+++ b/python/test/unit/runner.py
@@ -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
diff --git a/python/test/unit/test_decor.py b/python/test/unit/test_decor.py
index 81fe7e497d530f8138fa70ef23e3ea64a1ef9947..2ec68d753e1845df0005710cfa30f19af8e7283a 100644
--- a/python/test/unit/test_decor.py
+++ b/python/test/unit/test_decor.py
@@ -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)
diff --git a/python/test/unit/test_simulator.py b/python/test/unit/test_simulator.py
deleted file mode 100644
index bee420b3f82bfb926b520be9d4d34d2b585b5827..0000000000000000000000000000000000000000
--- a/python/test/unit/test_simulator.py
+++ /dev/null
@@ -1,252 +0,0 @@
-# -*- 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()
diff --git a/python/test/unit_distributed/runner.py b/python/test/unit_distributed/runner.py
index cb8ddf5d83474329fde6d3e33319ddd92682b798..48c6c3a588a085ea5939052eec6432f864f5d159 100644
--- a/python/test/unit_distributed/runner.py
+++ b/python/test/unit_distributed/runner.py
@@ -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