Merge pull request #114 from SpiNNakerManchester/intro_lab

Merge in Intro lab

.github/workflows/python_actions.yml

@@ -53,12 +53,12 @@ jobs:
       uses: ./support/actions/install-matplotlib
 
     - name: Lint with flake8
-      run: flake8 examples
+      run: flake8 examples balanced_random learning sudoku synfire
 
     - name: Lint with pylint
       uses: ./support/actions/pylint
       with:
-        package: examples
+        package: examples balanced_random learning sudoku synfire
         exitcheck: 39
 
   validate:
@@ -72,9 +72,11 @@ jobs:
         repository: SpiNNakerManchester/SupportScripts
         path: support
     - name: Run rat copyright enforcement
+      if: matrix.python-version == 3.12
       uses: ./support/actions/check-copyrights
       with:
         config_file: rat_asl20.xml
 
     - name: Validate CITATION.cff
+      if: matrix.python-version == 3.12
       uses: dieghernan/cff-validator@main

.gitignore

@@ -7,4 +7,5 @@ __pycache__
 .pytest_cache
 *application_generated_data_files/
 *reports/
+.cache/
 .mypy_cache/

.ratexcludes

@@ -8,4 +8,11 @@
 **/SpiNNFrontEndCommon/**
 **/sPyNNaker/**
 **/sPyNNaker8/**
+**/.pylintrc
+**/*.dll
+**/*.exe
+**/*.png
+**/*linux
+**/*osx
+**/*.exe
 **/.pylintrc

CITATION.cff

@@ -105,4 +105,4 @@ contact:
   name: SpiNNaker Software Team
   post-code: M13 9PL
 license: Apache-2.0
-repository: https://github.com/SpiNNakerManchester/PyNN8Examples
+repository: https://github.com/SpiNNakerManchester/PyNNExamples

balanced_random/__init__.py

@@ -0,0 +1,13 @@
+# Copyright (c) 2017 The University of Manchester
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

balanced_random/balanced_random.py

@@ -0,0 +1,111 @@
+# Copyright (c) 2017 The University of Manchester
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import matplotlib.pyplot as pylab
+import numpy
+from pyNN.random import RandomDistribution
+from pyNN.utility.plotting import Figure, Panel
+import pyNN.spiNNaker as p
+
+p.setup(timestep=0.1)
+p.set_number_of_neurons_per_core(p.IF_curr_exp, 64)
+p.set_number_of_neurons_per_core(p.SpikeSourcePoisson, 64)
+n_neurons = 500
+n_exc = int(round(n_neurons * 0.8))
+n_inh = int(round(n_neurons * 0.2))
+weight_exc = 0.1
+weight_inh = -5.0 * weight_exc
+weight_input = 0.001
+
+pop_input = p.Population(100, p.SpikeSourcePoisson(rate=0.0),
+                         additional_parameters={
+                             "max_rate": 50.0,
+                             "seed": 0},
+                         label="Input")
+
+pop_exc = p.Population(n_exc, p.IF_curr_exp, label="Excitatory", seed=1)
+pop_inh = p.Population(n_inh, p.IF_curr_exp, label="Inhibitory", seed=2)
+stim_exc = p.Population(
+    n_exc, p.SpikeSourcePoisson(rate=1000.0), label="Stim_Exc",
+    additional_parameters={"seed": 3})
+stim_inh = p.Population(
+    n_inh, p.SpikeSourcePoisson(rate=1000.0), label="Stim_Inh",
+    additional_parameters={"seed": 4})
+
+delays_exc = RandomDistribution(
+    "normal_clipped", mu=1.5, sigma=0.75, low=1.0, high=1.6)
+weights_exc = RandomDistribution(
+    "normal_clipped", mu=weight_exc, sigma=0.1, low=0, high=numpy.inf)
+conn_exc = p.FixedProbabilityConnector(0.1)
+synapse_exc = p.StaticSynapse(weight=weights_exc, delay=delays_exc)
+delays_inh = RandomDistribution(
+    "normal_clipped", mu=0.75, sigma=0.375, low=1.0, high=1.6)
+weights_inh = RandomDistribution(
+    "normal_clipped", mu=weight_inh, sigma=0.1, low=-numpy.inf, high=0)
+conn_inh = p.FixedProbabilityConnector(0.1)
+synapse_inh = p.StaticSynapse(weight=weights_inh, delay=delays_inh)
+p.Projection(
+    pop_exc, pop_exc, conn_exc, synapse_exc, receptor_type="excitatory")
+p.Projection(
+    pop_exc, pop_inh, conn_exc, synapse_exc, receptor_type="excitatory")
+p.Projection(
+    pop_inh, pop_inh, conn_inh, synapse_inh, receptor_type="inhibitory")
+p.Projection(
+    pop_inh, pop_exc, conn_inh, synapse_inh, receptor_type="inhibitory")
+
+conn_stim = p.OneToOneConnector()
+synapse_stim = p.StaticSynapse(weight=weight_exc, delay=1.0)
+p.Projection(
+    stim_exc, pop_exc, conn_stim, synapse_stim, receptor_type="excitatory")
+p.Projection(
+    stim_inh, pop_inh, conn_stim, synapse_stim, receptor_type="excitatory")
+
+delays_input = RandomDistribution(
+    "normal_clipped", mu=1.5, sigma=0.75, low=1.0, high=1.6)
+weights_input = RandomDistribution(
+    "normal_clipped", mu=weight_input, sigma=0.01, low=0, high=numpy.inf)
+p.Projection(pop_input, pop_exc, p.AllToAllConnector(), p.StaticSynapse(
+    weight=weights_input, delay=delays_input))
+
+pop_exc.initialize(
+    v=RandomDistribution("uniform", low=-65.0, high=-55.0))
+pop_inh.initialize(
+    v=RandomDistribution("uniform", low=-65.0, high=-55.0))
+
+pop_exc.record("spikes")
+
+p.run(1000)
+
+pop_input.set(rate=50.0)
+p.run(1000)
+
+pop_input.set(rate=10.0)
+p.run(1000)
+
+pop_input.set(rate=20.0)
+p.run(1000)
+
+data = pop_exc.get_data("spikes")
+end_time = p.get_current_time()
+
+p.end()
+
+Figure(
+    # raster plot of the presynaptic neuron spike times
+    Panel(data.segments[0].spiketrains,
+          yticks=True, markersize=2.0, xlim=(0, end_time)),
+    title="Balanced Random Network",
+    annotations="Simulated with {}".format(p.name())
+)
+pylab.show()

balanced_random/split/balanced_random_split.py

@@ -0,0 +1,118 @@
+import pylab
+import numpy
+from pyNN.random import RandomDistribution
+from pyNN.utility.plotting import Figure, Panel
+import pyNN.spiNNaker as p
+from spynnaker.pyNN.extra_algorithms.splitter_components import (
+    SplitterPoissonDelegate, SplitterAbstractPopulationVertexNeuronsSynapses)
+
+p.setup(timestep=0.1, time_scale_factor=1)
+p.set_number_of_neurons_per_core(p.IF_curr_exp, 64)
+p.set_number_of_neurons_per_core(p.SpikeSourcePoisson, 64)
+n_neurons = 500
+n_exc = int(round(n_neurons * 0.8))
+n_inh = int(round(n_neurons * 0.2))
+weight_exc = 0.1
+weight_inh = -5.0 * weight_exc
+weight_input = 0.001
+
+pop_input_splitter = SplitterPoissonDelegate()
+pop_input = p.Population(100, p.SpikeSourcePoisson(rate=0.0),
+                         additional_parameters={
+                             "max_rate": 50.0,
+                             "seed": 0,
+                             "splitter": pop_input_splitter},
+                         label="Input")
+
+pop_exc_splitter = \
+    SplitterAbstractPopulationVertexNeuronsSynapses(1, 128, False)
+pop_exc = p.Population(n_exc, p.IF_curr_exp, label="Excitatory",
+                       additional_parameters={"splitter": pop_exc_splitter,
+                                              "seed": 1})
+pop_inh_splitter = \
+    SplitterAbstractPopulationVertexNeuronsSynapses(1, 128, False)
+pop_inh = p.Population(n_inh, p.IF_curr_exp, label="Inhibitory",
+                       additional_parameters={"splitter": pop_inh_splitter,
+                                              "seed": 2})
+stim_exc_splitter = SplitterPoissonDelegate()
+stim_exc = p.Population(
+    n_exc, p.SpikeSourcePoisson(rate=1000.0), label="Stim_Exc",
+    additional_parameters={"seed": 3, "splitter": stim_exc_splitter})
+stim_inh_splitter = SplitterPoissonDelegate()
+stim_inh = p.Population(
+    n_inh, p.SpikeSourcePoisson(rate=1000.0), label="Stim_Inh",
+    additional_parameters={"seed": 4, "splitter": stim_inh_splitter})
+
+delays_exc = RandomDistribution(
+    "normal_clipped", mu=1.5, sigma=0.75, low=1.0, high=1.6)
+weights_exc = RandomDistribution(
+    "normal_clipped", mu=weight_exc, sigma=0.1, low=0, high=numpy.inf)
+conn_exc = p.FixedProbabilityConnector(0.1)
+synapse_exc = p.StaticSynapse(weight=weights_exc, delay=delays_exc)
+delays_inh = RandomDistribution(
+    "normal_clipped", mu=0.75, sigma=0.375, low=1.0, high=1.6)
+weights_inh = RandomDistribution(
+    "normal_clipped", mu=weight_inh, sigma=0.1, low=-numpy.inf, high=0)
+conn_inh = p.FixedProbabilityConnector(0.1)
+synapse_inh = p.StaticSynapse(weight=weights_inh, delay=delays_inh)
+p.Projection(
+    pop_exc, pop_exc, conn_exc, synapse_exc, receptor_type="excitatory",
+    label="exc_exc")
+p.Projection(
+    pop_exc, pop_inh, conn_exc, synapse_exc, receptor_type="excitatory",
+    label="exc_inh")
+p.Projection(
+    pop_inh, pop_inh, conn_inh, synapse_inh, receptor_type="inhibitory",
+    label="inh_inh")
+p.Projection(
+    pop_inh, pop_exc, conn_inh, synapse_inh, receptor_type="inhibitory",
+    label="inh_exc")
+
+conn_stim = p.OneToOneConnector()
+synapse_stim = p.StaticSynapse(weight=weight_exc, delay=1.0)
+p.Projection(
+    stim_exc, pop_exc, conn_stim, synapse_stim, receptor_type="excitatory",
+    label="stim_exc_exc")
+p.Projection(
+    stim_inh, pop_inh, conn_stim, synapse_stim, receptor_type="excitatory",
+    label="stim_inh_inh")
+
+delays_input = RandomDistribution(
+    "normal_clipped", mu=1.5, sigma=0.75, low=1.0, high=1.6)
+weights_input = RandomDistribution(
+    "normal_clipped", mu=weight_input, sigma=0.01, low=0, high=numpy.inf)
+p.Projection(pop_input, pop_exc, p.AllToAllConnector(), p.StaticSynapse(
+    weight=weights_input, delay=delays_input),
+    label="input_exc")
+
+pop_exc.initialize(
+    v=RandomDistribution("uniform", low=-65.0, high=-55.0))
+pop_inh.initialize(
+    v=RandomDistribution("uniform", low=-65.0, high=-55.0))
+
+pop_exc.record("spikes")
+
+p.run(1000)
+
+pop_input.set(rate=50.0)
+p.run(1000)
+
+pop_input.set(rate=10.0)
+p.run(1000)
+
+pop_input.set(rate=20.0)
+p.run(1000)
+
+data = pop_exc.get_data("spikes")
+end_time = p.get_current_time()
+
+p.end()
+
+Figure(
+    # raster plot of the presynaptic neuron spike times
+    Panel(data.segments[0].spiketrains,
+          yticks=True, markersize=2.0, xlim=(0, end_time)),
+    title="Balanced Random Network",
+    annotations="Simulated with {}".format(p.name())
+)
+pylab.show()

balanced_random/split/spynnaker.cfg

@@ -0,0 +1,2 @@
+[Mode]
+violate_1ms_wall_clock_restriction = True

integration_tests/script_builder.py

@@ -33,7 +33,9 @@ def build_scripts(self):
         too_long = {}
         too_long["stdp_triplet.py"] = "10 minutes"
 
-        self.create_test_scripts(["examples"], too_long, exceptions)
+        self.create_test_scripts(
+            ["examples","balanced_random", "learning", "synfire"],
+            too_long, exceptions)
 
 
 if __name__ == '__main__':