Merge pull request #14 from OpenSourceBrain/development

 Regenerated

Author: pgleeson

.github/workflows/non-omv.yml

@@ -13,14 +13,14 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ 3.9, "3.12" ]
+        python-version: [ "3.12", "3.13" ]
         runs-on: [ ubuntu-latest, macos-latest ]
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
     - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version:  ${{ matrix.python-version }}
 
@@ -40,6 +40,7 @@ jobs:
         omv install neuron
         omv install netpyne
         omv install pyNeuroML
+        omv install pynn
 
         pip list
 

.github/workflows/omv-ci.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ 3.9, "3.10", "3.12" ]
+        python-version: [ "3.10", "3.12" ]
         engine: [ NetPyNE, jNeuroML, jNeuroML_NEURON, jNeuroML_NetPyNE, jNeuroML_EDEN, jNeuroML_validate ]
 
     steps:
@@ -28,7 +28,7 @@ jobs:
 
     - name: Ensure setuptools is up-to-date
       run: |
-        pip install --upgrade setuptools
+        pip install setuptools==80 # needed for EDEN on py3.12
 
     - name: Install OMV
       run: |

.gitignore

@@ -196,3 +196,15 @@ arm64
 /NetPyNE/TwoCells/*dat
 /NeuroML2/TwoCells/*_netpyne.py
 /NeuroML2/TwoCells/LEMS_TwoCell_netpyne_data.json
+/NeuroML2/gaps/Example_GapJunctions.json
+/NeuroML2/gaps/*.dat
+/NeuroML2/gaps/report.SimExampleGJ.txt
+/NeuroML2/gaps/SimExampleGJ.json
+/NeuroML2/TwoCells/LEMS_TwoCell_netpyne_data.json-e
+/NeuroML2/gaps/*_netpyne.py
+/NeuroML2/gaps/*_nrn.py
+/NeuroML2/gaps/*.mod
+/NeuroML2/gaps/*.hoc
+/NeuroML2/aarch64
+/NeuroML2/gaps/aarch64
+aarch64

NetPyNE/TwoCells/LEMS_TwoCell_netpyne_data.json

@@ -677,7 +677,7 @@
         }
     },
     "netpyne_changeset": "",
-    "netpyne_version": "1.0.7",
+    "netpyne_version": "1.1.0",
     "simConfig": {
         "addSynMechs": true,
         "allowConnsWithWeight0": true,
@@ -860,6 +860,7 @@
         "saveFileStep": 0.01,
         "saveFolder": "",
         "saveHDF5": false,
+        "saveIMembrane": false,
         "saveJson": true,
         "saveLFPCells": false,
         "saveLFPPops": false,

NetPyNE/TwoCells/loadNML.py

@@ -1,7 +1,12 @@
 from LEMS_TwoCell_netpyne import NetPyNESimulation
 
+print('------ stage 1')
 n = NetPyNESimulation()
+print('------ stage 2')
+
+# Run nrnivmodl first...
 n.generate_json_only()
+print('------ stage 3')
 
 print("Validating: %s"%n.simConfig.validateNetParams)