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