Merge pull request #13 from openworm/development

Development changes

.github/workflows/non-omv.yml

@@ -10,7 +10,7 @@ on:
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       matrix:

.github/workflows/omv-ci.yml

@@ -12,7 +12,7 @@ on:
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       matrix:

NeuroML2/GenerateNeuroML.py

@@ -359,7 +359,7 @@ def generate_nmllite(
     sim, net = create_new_model(
         reference,
         duration,
-        dt=0.025,  # ms
+        dt=0.005,  # ms
         temperature=34,  # degC
         default_region="Worm",
         parameters=parameters,
@@ -1246,9 +1246,18 @@ def create_cells(channels_to_include, duration=700, stim_delay=310, stim_duratio
     # For testing, as some channel gates take quite some time to reach steady state, e.g. s on kqt3
     additional_transient_phase = 2000
 
+    duration = 400 + additional_transient_phase
+    stim_delay = 310 + additional_transient_phase
+
+    import sys
+
+    if "-short" in sys.argv:
+        duration = 70
+        stim_delay = 10
+
     create_cells(
         channels_to_include,
-        duration=400 + additional_transient_phase,
-        stim_delay=310 + additional_transient_phase,
+        duration=duration,
+        stim_delay=stim_delay,
         stim_duration=50,
     )

NeuroML2/IClamp_RMD.net.nml

@@ -10,7 +10,7 @@
     <pulseGenerator id="iclamp_0" delay="2310ms" duration="50ms" amplitude="10pA"/>
     <network id="IClamp_RMD" type="networkWithTemperature" temperature="34.0degC">
         <notes>A network model: IClamp_RMD</notes>
-        <property tag="recommended_dt_ms" value="0.025"/>
+        <property tag="recommended_dt_ms" value="0.005"/>
         <property tag="recommended_duration_ms" value="2400.0"/>
         <population id="pop_RMD" component="RMD" size="1" type="populationList">
             <property tag="color" value="0 0.8 0"/>

NeuroML2/LEMS_Sim_IClamp_RMD.xml

@@ -18,7 +18,7 @@
     <Include file="IClamp_RMD.net.nml"/>
     <Include file="RMD.cell.nml"/>
 
-    <Simulation id="Sim_IClamp_RMD" length="2400.0ms" step="0.025ms" target="IClamp_RMD" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
+    <Simulation id="Sim_IClamp_RMD" length="2400.0ms" step="0.005ms" target="IClamp_RMD" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
         <Display id="pop_RMD_0_biophys/membraneProperties/bk2_chans/RMD_bk2/h/q" title="Plots of pop_RMD_0_biophys/membraneProperties/bk2_chans/RMD_bk2/h/q" timeScale="1ms" xmin="-240.0" xmax="2640.0" ymin="-1" ymax="1">
             <Line id="pop_RMD_0_RMD_biophys_membraneProperties_bk2_chans_RMD_bk2_h_q" quantity="pop_RMD/0/RMD/biophys/membraneProperties/bk2_chans/RMD_bk2/h/q" scale="1" color="#d54f33" timeScale="1ms"/>
         </Display>

NeuroML2/Sim_IClamp_AWCon.json

@@ -3,7 +3,7 @@
         "version": "NeuroMLlite v0.6.0",
         "network": "IClamp_AWCon.json",
         "duration": 2400.0,
-        "dt": 0.025,
+        "dt": 0.005,
         "seed": 12345,
         "record_traces": {
             "all": "*"

NeuroML2/Sim_IClamp_RMD.json

@@ -3,7 +3,7 @@
         "version": "NeuroMLlite v0.6.0",
         "network": "IClamp_RMD.json",
         "duration": 2400.0,
-        "dt": 0.025,
+        "dt": 0.005,
         "seed": 12345,
         "record_traces": {
             "all": "*"

NeuroML2/TestXPP.py

@@ -6,6 +6,13 @@
 cell = "RMD"
 
 parsed_data = parse_script("../%s.ode" % cell.replace("on", ""))
+
+import sys
+
+short_simulation = "-short" in sys.argv
+if short_simulation:
+    parsed_data = parse_script("../XPP_tests/%s_edited.ode" % cell.replace("on", ""))
+
 pprint(parsed_data)
 
 all_g = [
@@ -113,9 +120,15 @@
 
 parsed_data["settings"]["total"] = 400 + additional_transient_phase
 parsed_data["settings"]["trans"] = 0
-parsed_data["settings"]["dt"] = 0.01
+parsed_data["settings"]["dt"] = 0.005
 parsed_data["parameters"]["ton"] = 310 + additional_transient_phase
 parsed_data["parameters"]["toff"] = 360 + additional_transient_phase
+
+if short_simulation:
+    parsed_data["settings"]["total"] = 70
+    parsed_data["parameters"]["ton"] = 10
+    parsed_data["parameters"]["toff"] = 60
+
 new_ode = to_xpp(parsed_data, new_ode_file)
 
 mp_fig = "Membrane potentials"

NeuroML2/regenerateAndTestShort.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+set -ex
+
+# Format the code
+black *.py
+
+# This script loads in the XPP using the parser in pyNeuroML, and converts the channels to NeuroML
+# It will also run a test simulation of the cells and save the results
+# NOTE: make sure to update to a recent version of pyNeuroML!
+python GenerateNeuroML.py -jnml -short
+
+
+# This will load the original XPP using pyNeuroML, run it, save the results and plot them against the 
+# results generated by the NeuroML in GenerateNeuroML.py
+python TestXPP.py -short
+
+