Merge remote-tracking branch 'origin/master' into eprop_adaptive_update

.github/workflows/python_actions.yml

@@ -4,7 +4,7 @@
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
 #
-#     http://www.apache.org/licenses/LICENSE-2.0
+#     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,
@@ -40,7 +40,7 @@ jobs:
     - name: Install pip, etc
       uses: ./support/actions/python-tools
     - name: Install Spinnaker Dependencies
-      uses: ./support/actions/checkout-spinn-deps
+      uses: ./support/actions/install-spinn-deps
       with:
         repositories: >
           SpiNNUtils SpiNNMachine SpiNNMan PACMAN DataSpecification spalloc
@@ -72,7 +72,9 @@ jobs:
         repository: SpiNNakerManchester/SupportScripts
         path: support
     - name: Run rat copyright enforcement
-      if: matrix.python-version == 3.8
       uses: ./support/actions/check-copyrights
       with:
         config_file: rat_asl20.xml
+
+    - name: Validate CITATION.cff
+      uses: dieghernan/cff-validator@main

.pylintrc

@@ -4,7 +4,7 @@
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
 #
-#     http://www.apache.org/licenses/LICENSE-2.0
+#     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,

CITATION.cff

@@ -0,0 +1,108 @@
+# 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.
+
+cff-version: 1.2.0
+message: If you use this software, please cite it as below.
+preferred-citation:
+  type: article
+  doi: 10.3389/fnins.2018.00816
+  issn: 1662-453X
+  url: https://www.frontiersin.org/articles/10.3389/fnins.2018.00816
+  title: "sPyNNaker: A Software Package for Running PyNN Simulations on SpiNNaker"
+  journal: Frontiers in Neuroscience
+  volume: 12
+  year: 2018
+  month: 11
+  abstract: This work presents sPyNNaker 4.0.0, the latest version of the software package for simulating PyNN-defined spiking neural networks (SNNs) on the SpiNNaker neuromorphic platform. Operations underpinning realtime SNN execution are presented, including an event-based operating system facilitating efficient time-driven neuron state updates and pipelined event-driven spike processing. Preprocessing, realtime execution, and neuron/synapse model implementations are discussed, all in the context of a simple example SNN. Simulation results are demonstrated, together with performance profiling providing insights into how software interacts with the underlying hardware to achieve realtime execution. System performance is shown to be within a factor of 2 of the original design target of 10,000 synaptic events per millisecond, however SNN topology is shown to influence performance considerably. A cost model is therefore developed characterizing the effect of network connectivity and SNN partitioning. This model enables users to estimate SNN simulation performance, allows the SpiNNaker team to make predictions on the impact of performance improvements, and helps demonstrate the continued potential of the SpiNNaker neuromorphic hardware.
+  authors:
+  - given-names: Oliver
+    family-names: Rhodes
+    affiliation: University Of Manchester
+    orcid: https://orcid.org/0000-0003-1728-2828
+    website: https://research.manchester.ac.uk/en/persons/oliver.rhodes
+  - given-names: Petrut
+    family-names: Bogdan
+    affiliation: University Of Manchester
+    orcid: https://orcid.org/0000-0001-5535-7865
+  - given-names: Christian Y.
+    family-names: Brenninkmeijer
+    affiliation: University Of Manchester
+    email: christian.brenninkmeijer@manchester.ac.uk
+    orcid: https://orcid.org/0000-0002-2937-7819
+    website: https://www.researchgate.net/profile/Christian_Brenninkmeijer
+  - given-names: Simon
+    family-names: Davidson
+    affiliation: University Of Manchester
+    orcid: https://orcid.org/0000-0001-5385-442X
+    website: https://research.manchester.ac.uk/en/persons/simon.davidson
+  - given-names: Donal
+    family-names: Fellows
+    affiliation: University Of Manchester
+    orcid: https://orcid.org/0000-0002-9091-5938
+    website: https://www.researchgate.net/profile/Donal-Fellows
+  - given-names: Andrew
+    family-names: Gait
+    affiliation: University Of Manchester
+    orcid: https://orcid.org/0000-0001-9349-1096
+    website: https://personalpages.manchester.ac.uk/staff/andrew.gait/
+  - given-names: David R.
+    family-names: Lester
+    affiliation: University Of Manchester
+    orcid: https://orcid.org/0000-0002-7267-291X
+  - given-names: Mantas
+    family-names: Mikaitis
+    affiliation: University Of Manchester
+    orcid: https://orcid.org/0000-0001-8706-1436
+    website: https://research.manchester.ac.uk/en/persons/mantas.mikaitis
+  - given-names: Luis A.
+    family-names: Plana
+    affiliation: University Of Manchester
+    orcid: https://orcid.org/0000-0002-6113-3929
+    website: https://research.manchester.ac.uk/en/persons/luis.plana
+  - given-names: Andrew G. D.
+    family-names: Rowley
+    affiliation: University Of Manchester
+    email: Andrew.Rowley@manchester.ac.uk
+    orcid: https://orcid.org/0000-0002-2646-8520
+    website: https://www.researchgate.net/profile/Andrew_Rowley2
+  - given-names: Alan B.
+    family-names: Stokes
+    affiliation: University Of Manchester
+    orcid: https://orcid.org/0000-0002-6110-1484
+  - given-names: Steve B.
+    family-names: Furber
+    affiliation: University Of Manchester
+    orcid: https://orcid.org/0000-0002-6524-3367
+    website: https://research.manchester.ac.uk/en/persons/steve.furber
+
+title: This repository holds miscellaneous examples of using sPyNNaker for PyNN
+authors:
+    - name: SpiNNaker Software Team
+      alias: For a list of contributors see https://github.com/SpiNNakerManchester/PyNN8Examples/graphs/contributors or for a combined list see https://spinnakermanchester.github.io/latest/LicenseAgreement.html#contributors
+      address: University of Manchester, Oxford Road
+      city: Manchester
+      country: GB
+      email: spinnakerusers@googlegroups.com
+      post-code: M13 9PL
+      website: https://apt.cs.manchester.ac.uk/projects/SpiNNaker/
+url: https://spinnakermanchester.github.io/
+contact:
+- address: University of Manchester, Oxford Road
+  city: Manchester
+  country: GB
+  email: spinnakerusers@googlegroups.com
+  name: SpiNNaker Software Team
+  post-code: M13 9PL
+license: Apache-2.0
+repository: https://github.com/SpiNNakerManchester/PyNN8Examples

LICENSE

@@ -1,7 +1,7 @@
 
                                  Apache License
                            Version 2.0, January 2004
-                        http://www.apache.org/licenses/
+                        https://www.apache.org/licenses/
 
    TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
 
@@ -193,7 +193,7 @@
    you may not use this file except in compliance with the License.
    You may obtain a copy of the License at
 
-       http://www.apache.org/licenses/LICENSE-2.0
+       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,

LICENSE.md → LICENSE_POLICY.md

@@ -1,23 +1,23 @@
 # License Agreement
 
-Up to date information for the whole [SpiNNakerManchester Projects](https://github.com/SpiNNakerManchester) can be found [here](http://spinnakermanchester.github.io/common_pages/4.0.0/LicenseAgreement.html)
+Up to date information for the whole [SpiNNakerManchester Projects](https://github.com/SpiNNakerManchester) can be found [here](https://spinnakermanchester.github.io/latest/LicenseAgreement.html)
 
-As shown there the software is currently being released under the GPL version 3 license listed [here](http://www.gnu.org/copyleft/gpl.html)
+As shown there the software is currently being released under the Apache License 2.0 listed [here](https://www.apache.org/licenses/LICENSE-2.0)
 
 
 # Paper Authorship
 
-See: [here](http://spinnakermanchester.github.io/common_pages/4.0.0/LicenseAgreement.html#paper-authorship)
+See: [here](https://spinnakermanchester.github.io/latest/LicenseAgreement.html#paper-authorship)
 
 # Modifications
 
-See: [here](http://spinnakermanchester.github.io/common_pages/4.0.0/LicenseAgreement.html#modifications)
+See: [here](https://spinnakermanchester.github.io/latest/LicenseAgreement.html#modifications)
 
 # Contributors
 
 For up to date information on Contributors see the graphs/contributors pages on each project.
 
 For example [https://github.com/SpiNNakerManchester/PyNN8Examples/graphs/contributors](https://github.com/SpiNNakerManchester/PyNN8Examples/graphs/contributors)
 
-[Combined list](http://spinnakermanchester.github.io/common_pages/4.0.0/LicenseAgreement.html#contributors)
+[Combined list](https://spinnakermanchester.github.io/latest/LicenseAgreement.html#contributors)
 

examples/__init__.py

@@ -4,7 +4,7 @@
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
 #
-#     http://www.apache.org/licenses/LICENSE-2.0
+#     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,

examples/current_injection_example.py

@@ -4,7 +4,7 @@
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
 #
-#     http://www.apache.org/licenses/LICENSE-2.0
+#     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,
@@ -24,7 +24,8 @@
 
 Any other current waveforms could be implemented using StepCurrentSource.
 
-Script from http://neuralensemble.org/docs/PyNN/examples/current_injection.html
+Script from
+https://neuralensemble.org/docs/PyNN/examples/current_injection.html
 
 """
 

examples/external_devices_examples/__init__.py

@@ -4,7 +4,7 @@
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
 #
-#     http://www.apache.org/licenses/LICENSE-2.0
+#     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,

examples/external_devices_examples/live_examples/__init__.py

@@ -4,7 +4,7 @@
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
 #
-#     http://www.apache.org/licenses/LICENSE-2.0
+#     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,

examples/external_devices_examples/live_examples/balanced_random_live_rate.py

@@ -4,7 +4,7 @@
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
 #
-#     http://www.apache.org/licenses/LICENSE-2.0
+#     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,

examples/external_devices_examples/live_examples/spike_io.py

@@ -4,7 +4,7 @@
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
 #
-#     http://www.apache.org/licenses/LICENSE-2.0
+#     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,

examples/external_devices_examples/live_examples/spike_io_interactive_demo_with_c_vis.py

@@ -4,7 +4,7 @@
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
 #
-#     http://www.apache.org/licenses/LICENSE-2.0
+#     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,

examples/external_devices_examples/live_examples/synfire_if_curr_exp_live.py

@@ -4,7 +4,7 @@
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
 #
-#     http://www.apache.org/licenses/LICENSE-2.0
+#     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,

examples/external_devices_examples/motor_example.py

@@ -4,7 +4,7 @@
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
 #
-#     http://www.apache.org/licenses/LICENSE-2.0
+#     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,

examples/external_devices_examples/pushbot_ethernet_example.py

@@ -4,22 +4,21 @@
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
 #
-#     http://www.apache.org/licenses/LICENSE-2.0
+#     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.
 
-from spynnaker.pyNN.protocols import MUNICH_MODES
 import pyNN.spiNNaker as p
 
 p.setup(1.0)
 
 # Set up the PushBot devices
 pushbot_protocol = p.external_devices.MunichIoSpiNNakerLinkProtocol(
-    mode=MUNICH_MODES.PUSH_BOT, uart_id=0)
+    mode=p.external_devices.protocols.MUNICH_MODES.PUSH_BOT, uart_id=0)
 motor_0 = p.external_devices.PushBotEthernetMotorDevice(
     p.external_devices.PushBotMotor.MOTOR_0_PERMANENT, pushbot_protocol)
 motor_1 = p.external_devices.PushBotEthernetMotorDevice(
@@ -52,7 +51,8 @@
     len(devices), p.external_devices.PushBotLifEthernet(
         protocol=pushbot_protocol,
         devices=devices,
-        pushbot_ip_address="10.162.177.57",
+        pushbot_ip_address="10.10.10.1",
+        pushbot_port=3000,
         # "pushbot_ip_address": "127.0.0.1",
         tau_syn_E=500.0),
     label="PushBot"
@@ -76,14 +76,14 @@
     p.external_devices.PushBotEthernetRetinaDevice(
         protocol=pushbot_protocol,
         resolution=retina_resolution,
-        pushbot_ip_address="10.162.177.57"
+        pushbot_ip_address="10.10.10.1",
+        pushbot_port=3000,
+        retina_injector_label="Retina"
     ))
 
-viewer = p.external_devices.PushBotRetinaViewer(
-    retina_resolution.value, port=17895)
+retina_viewer = p.external_devices.PushBotRetinaViewer(
+    retina_resolution, pushbot_retina.label, p)
 p.external_devices.activate_live_output_for(
-    pushbot_retina, port=viewer.local_port, notify=False)
+    pushbot_retina, database_notify_port_num=retina_viewer.port)
 
-viewer.start()
-p.run(len(devices) * 1000)
-p.end()
+retina_viewer.run(len(devices) * 1000)