diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml
index 568be2a..819b86f 100644
--- a/.github/workflows/omv-ci.yml
+++ b/.github/workflows/omv-ci.yml
@@ -13,7 +13,7 @@ jobs:
strategy:
fail-fast: false
matrix:
- python-version: [ "3.9", "3.10" ] # Brian no longer supported on py3.8
+ python-version: [ "3.10", "3.12", "3.13" ] # Brian no longer supported on py3.9!
engine: [ jNeuroML, jNeuroML_NEURON, jNeuroML_PyNN_NEURON, jNeuroML_validate, PyNN_NEURON, PyNN_Nest, PyNN_NeuroML, PyNN_Brian2]
steps:
@@ -26,13 +26,12 @@ jobs:
- name: Install OMV
run: |
- pip install git+https://github.com/OpenSourceBrain/osb-model-validation
+ pip install git+https://github.com/OpenSourceBrain/osb-model-validation
- name: Install additional packages
run: |
- pip install scipy sympy matplotlib cython tables
-
- pip install 'numpy<=1.23.0' # see https://github.com/OpenSourceBrain/osb-model-validation/issues/91
+
+ pip install matplotlib "cython<3.1.0" # let omv handle other deps...
- name: Run OMV tests on engine ${{ matrix.engine }}
diff --git a/NeuroML2/ConnectionsTest.net.nml b/NeuroML2/ConnectionsTest.net.nml
index 2dbb8a2..285088b 100644
--- a/NeuroML2/ConnectionsTest.net.nml
+++ b/NeuroML2/ConnectionsTest.net.nml
@@ -2,8 +2,8 @@
This NeuroML 2 file has been generated from:
PyNN v0.11.0
- libNeuroML v0.6.3
- pyNeuroML v1.3.7
+ libNeuroML v0.6.8
+ pyNeuroML v1.3.19
@@ -17,38 +17,38 @@
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
-
+
diff --git a/NeuroML2/Inputs.net.nml b/NeuroML2/Inputs.net.nml
index d65583f..d3069dd 100644
--- a/NeuroML2/Inputs.net.nml
+++ b/NeuroML2/Inputs.net.nml
@@ -2,8 +2,8 @@
This NeuroML 2 file has been generated from:
PyNN v0.11.0
- libNeuroML v0.6.3
- pyNeuroML v1.3.7
+ libNeuroML v0.6.8
+ pyNeuroML v1.3.19
diff --git a/NeuroML2/LEMS_Sim_Inputs.xml b/NeuroML2/LEMS_Sim_Inputs.xml
index 343bd85..24f72d3 100644
--- a/NeuroML2/LEMS_Sim_Inputs.xml
+++ b/NeuroML2/LEMS_Sim_Inputs.xml
@@ -3,8 +3,8 @@
diff --git a/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml b/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml
index 0c08f73..ca0d527 100644
--- a/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml
+++ b/NeuroML2/LEMS_Sim_PyNN_NeuroML2_Export.xml
@@ -3,8 +3,8 @@
diff --git a/NeuroML2/Positions.net.nml.h5 b/NeuroML2/Positions.net.nml.h5
index 94dde7d..7b958cd 100644
Binary files a/NeuroML2/Positions.net.nml.h5 and b/NeuroML2/Positions.net.nml.h5 differ
diff --git a/NeuroML2/PyNN_NeuroML2_Export.net.nml b/NeuroML2/PyNN_NeuroML2_Export.net.nml
index e3b7a67..c59bb93 100644
--- a/NeuroML2/PyNN_NeuroML2_Export.net.nml
+++ b/NeuroML2/PyNN_NeuroML2_Export.net.nml
@@ -2,8 +2,8 @@
This NeuroML 2 file has been generated from:
PyNN v0.11.0
- libNeuroML v0.6.3
- pyNeuroML v1.3.7
+ libNeuroML v0.6.8
+ pyNeuroML v1.3.19
diff --git a/PyNN/InputsTest.py b/PyNN/InputsTest.py
index 799db30..6d7cc6b 100644
--- a/PyNN/InputsTest.py
+++ b/PyNN/InputsTest.py
@@ -51,7 +51,14 @@
data = pop.get_data('v', gather=False)
analogsignal = data.segments[0].analogsignals[0]
name = analogsignal.name
- source_ids = analogsignal.annotations['source_ids']
+
+ def get_source_ids_as(analogsignal):
+ if 'source_ids' in analogsignal.annotations:
+ return analogsignal.annotations['source_ids']
+ elif 'channel_ids' in analogsignal.annotations: # See https://github.com/NeuralEnsemble/PyNN/pull/762
+ return analogsignal.annotations['channel_ids']
+
+ source_ids = get_source_ids_as(analogsignal)
filename = "%s_%s.dat"%(pop.label,name)
print('Saving data recorded for %s in pop %s, global ids: %s to %s'%(name, pop.label, source_ids, filename))
times_vm_a = []
@@ -94,7 +101,7 @@ def get_source_id(spiketrain):
sim.end()
if '-gui' in sys.argv:
- if simulator_name in ['neuron', 'nest', 'brian']:
+ if simulator_name in ['neuron', 'nest', 'brian2']:
import matplotlib.pyplot as plt
print("Plotting results of simulation in %s"%simulator_name)
diff --git a/PyNN/LEMS_2007One_pynn.py b/PyNN/LEMS_2007One_pynn.py
index d48ba1d..c2507ab 100644
--- a/PyNN/LEMS_2007One_pynn.py
+++ b/PyNN/LEMS_2007One_pynn.py
@@ -9,9 +9,9 @@
This PyNN file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
- org.neuroml.export v1.10.1
- org.neuroml.model v1.10.1
- jLEMS v0.11.1
+ org.neuroml.export v1.11.0
+ org.neuroml.model v1.11.0
+ jLEMS v0.12.0
'''
# Main PyNN script for: net1
diff --git a/PyNN/RS.mod b/PyNN/RS.mod
index 7ac284b..5767bc6 100644
--- a/PyNN/RS.mod
+++ b/PyNN/RS.mod
@@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=RS type=izhikevich2007Cell)
COMMENT
This NEURON file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
- org.neuroml.export v1.10.1
- org.neuroml.model v1.10.1
- jLEMS v0.11.1
+ org.neuroml.export v1.11.0
+ org.neuroml.model v1.11.0
+ jLEMS v0.12.0
ENDCOMMENT
diff --git a/PyNN/RS_Iext.mod b/PyNN/RS_Iext.mod
index 677626d..0aad522 100644
--- a/PyNN/RS_Iext.mod
+++ b/PyNN/RS_Iext.mod
@@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=RS_Iext type=pulseGenerator)
COMMENT
This NEURON file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
- org.neuroml.export v1.10.1
- org.neuroml.model v1.10.1
- jLEMS v0.11.1
+ org.neuroml.export v1.11.0
+ org.neuroml.model v1.11.0
+ jLEMS v0.12.0
ENDCOMMENT
diff --git a/PyNN/RS_Iext_inputdefinition.py b/PyNN/RS_Iext_inputdefinition.py
index 4aedd92..4ccdb17 100644
--- a/PyNN/RS_Iext_inputdefinition.py
+++ b/PyNN/RS_Iext_inputdefinition.py
@@ -9,9 +9,9 @@
---------------------------------------------
This PyNN file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
- org.neuroml.export v1.10.1
- org.neuroml.model v1.10.1
- jLEMS v0.11.1
+ org.neuroml.export v1.11.0
+ org.neuroml.model v1.11.0
+ jLEMS v0.12.0
'''
# Input file for Component: RS_Iext
diff --git a/PyNN/RS_celldefinition.py b/PyNN/RS_celldefinition.py
index 7f6a681..2cdeda3 100644
--- a/PyNN/RS_celldefinition.py
+++ b/PyNN/RS_celldefinition.py
@@ -16,9 +16,9 @@
---------------------------------------------
This PyNN file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
- org.neuroml.export v1.10.1
- org.neuroml.model v1.10.1
- jLEMS v0.11.1
+ org.neuroml.export v1.11.0
+ org.neuroml.model v1.11.0
+ jLEMS v0.12.0
'''
# Cell file for Component: RS