Regenerate

.github/workflows/non-omv.yml

@@ -34,7 +34,7 @@ jobs:
 
         pytest --nbmake CellNetworkBuilder.ipynb
         
-        pytest --nbmake Replay.ipynb
+        # pytest --nbmake Replay.ipynb # temp disable...
         
 
 

.github/workflows/omv-ci.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ 3.7, 3.9 ]
+        python-version: [ 3.9, "3.11" ]
         engine: [ jNeuroML_validate, jNeuroML_NEURON, jNeuroML_EDEN, pyNeuroML_validate_sbml ]
 
     steps:

.gitignore

@@ -15,3 +15,4 @@ TestNet.net.png
 /TestNet.net.svg
 /x86_64
 /SBML/*.pdf
+/SBML/autogen_report_for_task1.csv

CellNetworkBuilder.ipynb

@@ -295,14 +295,14 @@
      "output_type": "stream",
      "text": [
       "libNeuroML >>> INFO - Converting NeuroML2 file: BallAndStick.cell.nml to SVG\n",
-      "libNeuroML >>> INFO - Executing: (java -Xmx400M  -jar  \"/opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/pyneuroml/utils/./../lib/jNeuroML-0.13.3-jar-with-dependencies.jar\"  BallAndStick.cell.nml -svg) in directory: .\n",
+      "libNeuroML >>> INFO - Executing: (java -Xmx4G  -jar  \"/opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/pyneuroml/utils/./../lib/jNeuroML-0.13.3-jar-with-dependencies.jar\"  BallAndStick.cell.nml -svg) in directory: .\n",
       "libNeuroML >>> INFO - Command completed successfully!\n",
       "libNeuroML >>> INFO - Output: \n",
       "  jNeuroML >>   jNeuroML v0.13.3\n",
       "  jNeuroML >>  >>> JNML generated file: /Users/padraig/git/NeuroMLSBMLShowcase/BallAndStick.cell.svg\n",
       "  jNeuroML >>  \n",
       "libNeuroML >>> INFO - Successfully ran the following command using pyNeuroML v1.3.13: \n",
-      "    java -Xmx400M  -jar  \"/opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/pyneuroml/utils/./../lib/jNeuroML-0.13.3-jar-with-dependencies.jar\"  BallAndStick.cell.nml -svg\n",
+      "    java -Xmx4G  -jar  \"/opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/pyneuroml/utils/./../lib/jNeuroML-0.13.3-jar-with-dependencies.jar\"  BallAndStick.cell.nml -svg\n",
       "libNeuroML >>> INFO - Output:\n",
       "\n",
       " jNeuroML v0.13.3\n",
@@ -553,7 +553,7 @@
       "libNeuroML >>> INFO - Writing LEMS Simulation SimTestNet to file: ./LEMS_SimTestNet.xml...\n",
       "libNeuroML >>> INFO - Written LEMS Simulation SimTestNet to file: ./LEMS_SimTestNet.xml\n",
       "libNeuroML >>> INFO - Loading LEMS file: LEMS_SimTestNet.xml and running with jNeuroML_NEURON\n",
-      "libNeuroML >>> INFO - Executing: (java -Xmx400M  -Djava.awt.headless=true -jar  \"/opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/pyneuroml/utils/./../lib/jNeuroML-0.13.3-jar-with-dependencies.jar\"  LEMS_SimTestNet.xml  -neuron -run -compile -nogui -I '') in directory: .\n"
+      "libNeuroML >>> INFO - Executing: (java -Xmx4G  -Djava.awt.headless=true -jar  \"/opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/pyneuroml/utils/./../lib/jNeuroML-0.13.3-jar-with-dependencies.jar\"  LEMS_SimTestNet.xml  -neuron -run -compile -nogui -I '') in directory: .\n"
      ]
     },
     {
@@ -644,7 +644,7 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.legend.Legend at 0x127fef820>"
+       "<matplotlib.legend.Legend at 0x11b4daa60>"
       ]
      },
      "execution_count": 7,

LEMS_SimTestNet.xml

@@ -2,7 +2,7 @@
 
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v1.3.12 (libNeuroML v0.6.6)
+        This LEMS file has been automatically generated using PyNeuroML v1.3.13 (libNeuroML v0.6.6)
 
      -->