Merge pull request #343 from NeuroML/experimental

Minor fixes and tests for XPP export; to v1.2.10

Author: sanjayankur31

.github/workflows/python-publish.yml

@@ -18,9 +18,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies

.gitignore

@@ -171,3 +171,5 @@ arm64
 .vscode
 /tests/pyneuroml_20*
 /pyneuroml/xppaut/report.txt
+/examples/test_data/xppaut/fhn_2.ode
+/examples/test_data/xppaut/fhn_brain.py

examples/test_data/xppaut/fhn.ode

@@ -0,0 +1,10 @@
+# Forced Fitzhugh-Nagumo fhn.ode 
+dv/dt = f(v)-w+s(t)+I_0
+dw/dt = eps*(v-gamma*w)
+f(v)=v*(1-v)*(v-a)
+s(t)=al*sin(omega*t)
+param a=.25,eps=.05,gamma=1,I_0=.25
+param al=0,omega=2
+@ total=100,dt=.2,xhi=100
+@ nplot=2,xp2=t,yp2=w
+done

examples/test_data/xppaut/nca.ode

@@ -0,0 +1,81 @@
+# Excitatory cortical neurons, normal [Ca].
+#
+number Cm=1.0
+number pms=3,pns=4
+number VNa=55.0,t_tauh=-40.5,t_taun=-27.0
+number thetaa=-50.0,sigmaa=20.0,thetab=-80.0,sigmab=-6.0,tauBs=15.0
+number thetam=-30.0,sigmam=9.5,sigmah=-7.0,sigman=10.0,sigmaz=5.0
+number VCa=120
+number thetar=-20.0,sigmar=10.0,thetac=-30,sigmac=7
+number pwrc=1,pwrq=4
+# 
+p gNa=35.0,gKdr=6.0,gL=0.05,Iapp=1.0
+p gA=1.4,gNaP=0.2,gZ=1.0
+p thetaz=-39.0,tauZs=75.0
+p phi=10.0, thetah=-45.0
+p thetan=-35.0,thetap=-41.0,sigmap=3.0
+p VK=-90.0,VL=-70.0
+p gCa=0.08,gKCa=10.0,gKAHP=5
+p tauRs=1.0,aq=2,ac=6,tauq=450,tauCa=13,uuCa=0.13,tauKc=2
+#
+GAMMAF(VV,theta,sigma)=1.0/(1.0+exp(-(VV-theta)/sigma))
+ZFUNC(AA,CA,zz)=1/(1+(AA^zz/CA^zz))
+#
+VVs'=(-gL*(VVs-VL)-INa-INaP-IKdr-IA-Iz-ICa-IKC-IAHP+Iappx)/Cm
+hhs'=phi*(GAMMAF(VVs,thetah,sigmah)-hhs)/(1.0+7.5*GAMMAF(VVs,t_tauh,-6.0))
+nns'=phi*(GAMMAF(VVs,thetan,sigman)-nns)/(1.0+5.0*GAMMAF(VVs,t_taun,-15.0))
+bbs'=(GAMMAF(VVs,thetab,sigmab)-bbs)/tauBs
+zzs'=(GAMMAF(VVs,thetaz,sigmaz)-zzs)/tauZs
+rrs'=(GAMMAF(VVs,thetar,sigmar)-rrs)/tauRs
+ccs'=(GAMMAF(VVs,thetac,sigmac)-ccs)/tauKc
+qqs'=(ZFUNC(aq,Ca,pwrq)-qqs)/tauq
+Ca'=-uuCa*ICa-Ca/tauCa
+#
+Iappx=Iapp
+Minfs=GAMMAF(VVs,thetam,sigmam)
+Pinfs=GAMMAF(VVs,thetap,sigmap)
+Ainfs=GAMMAF(VVs,thetaa,sigmaa)
+mKCa=ZFUNC(ac,Ca,pwrc)
+#
+INa=gNa*(Minfs^pms)*hhs*(VVs-VNa)
+INaP=gNaP*Pinfs*(VVs-VNa)
+IKdr=gKdr*(nns^pns)*(VVs-VK)
+IA=gA*Ainfs^3*bbs*(VVs-VK)
+Iz=gZ*zzs*(VVs-VK)
+ICa=gCa*rrs^2*(VVs-VCa)
+IKC=gKCa*mKCa*ccs*(VVs-VK)
+IAHP=gKAHP*qqs*(VVs-VK) 
+#
+VVs(0)=-71.962
+hhs(0)=0.979199
+nns(0)=0.0242166
+bbs(0)=0.207565
+zzs(0)=0.0013689
+Ca[0]=0.000787
+rrs(0)=0.005507
+ccs(0)=0.002486
+qqs(0)=0.0
+#
+@ MAXSTOR=800000
+@ BACK=Black
+@ XP=T
+@ YP=VVs
+@ AXES=2
+@ TOTAL=500.0
+@ DT=0.05
+@ NJMP=1
+@ T0=0.0
+@ TRANS=0.0
+@ NMESH=40
+@ METH=rungekutta
+@ DTMIN=0.001
+@ DTMAX=1.0
+@ TOLER=0.00001
+@ BOUND=10000.0
+@ DELAY=0
+@ XLO=0.0, XHI=500.0, YLO=-90.0, YHI=30.0
+@ NTST=50,NMAX=2000,NPR=50
+@ DS=0.02,DSMIN=0.001,DSMAX=0.5
+@ PARMIN=-10,PARMAX=50,NORMMIN=0.0,NORMMAX=10000.0
+@ AUTOVAR=VVs1,AUTOXMIN=-10.0,AUTOXMAX=50.0,AUTOYMIN=-90.0,AUTOYMAX=50.0
+done

examples/test_data/xppaut/wc.ode

@@ -0,0 +1,14 @@
+# wilson-cowan
+f(u)=1/(1+exp(-1*(u)))
+par aee=10,aie=8,aei=12,aii=3,ze=.2,zi=4
+par tau=1
+i_e(t)=ie0+ie1*sin(w*t)
+i_i(t)=ii0+ii1*sin(w*t)
+par ie0=0,ie1=0,w=.25
+par ii0=0,ii1=0
+init u=.1,v=.05
+u'=-u+f(aee*u-aie*v-ze+i_e(t))
+v'=(-v+f(aei*u-aii*v-zi+i_i(t)))/tau
+@ total=40
+@ xp=u,yp=v,xlo=-.1,xhi=1,ylo=-.1,yhi=1
+done

pyneuroml/utils/__init__.py

@@ -23,7 +23,6 @@
 from datetime import datetime
 from pathlib import Path
 
-import libsedml
 import neuroml
 import numpy
 import pyneuroml.utils.misc
@@ -556,6 +555,7 @@ def get_model_file_list(
             lems_def_dir = get_model_file_list(inc, filelist, rootdir, lems_def_dir)
 
     elif rootfile.endswith(".sedml"):
+        import libsedml
         if pathlib.Path(rootfile).is_absolute():
             rootdoc = libsedml.readSedMLFromFile(rootfile)
         else:

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = pyNeuroML
-version = 1.2.9
+version = 1.2.10
 author = Padraig Gleeson
 author_email = [email protected]
 url = https://github.com/NeuroML/pyNeuroML
@@ -31,6 +31,7 @@ install_requires =
     graphviz
     typing; python_version<"3.5"
     lxml
+    sympy
     ppft[dill]
 
 packages = find:

test-ghactions.sh

@@ -68,6 +68,16 @@ echo "##   Multi-validate with jNeuroML"
 pynml -validate *.channel.nml
 
 
+echo
+echo "################################################"
+echo "##   Test XPP"
+
+pynml-xpp test_data/xppaut/fhn.ode
+pynml-xpp test_data/xppaut/fhn.ode -xpp
+pynml-xpp test_data/xppaut/fhn.ode -lems -run
+pynml-xpp test_data/xppaut/wc.ode -lems -run
+pynml-xpp test_data/xppaut/nca.ode -lems -run
+
 echo
 echo "################################################"
 echo "##   Test some conversions"
@@ -200,9 +210,9 @@ if [ "$run_neuron_examples" == true ]; then
             python tunePyr.py -tune -nogui
         popd
 
-    echo
-    echo "################################################"
-    echo "##   Finished all tests! "
-    echo "################################################"
-
 fi
+
+echo
+echo "################################################"
+echo "##   Finished all tests! "
+echo "################################################"