Merge pull request #121 from OpenSourceBrain/test_xpp

Add XPP to engines; to v0.2.21

Author: pgleeson

.github/workflows/ci.yml

@@ -51,6 +51,7 @@ jobs:
           - pyNeuroML_validate_sbml
           - jNeuroML_Moose
           - MOOSE:3.1.5
+          - XPP
 
     steps:
     - uses: actions/checkout@v4

omv/common/inout.py

@@ -121,8 +121,8 @@ def check_output(cmds, cwd=".", shell=False, verbosity=0, env=None):
 
     except sp.CalledProcessError as err:
         inform(
-            "Error running commands: %s in %s (return code: %s)"
-            % (cmds, cwd, err.returncode),
+            "CalledProcessError running commands: %s in %s (return code: %s), output:\n%s"
+            % (cmds, cwd, err.returncode, err.output),
             indent=2,
             verbosity=verbosity,
         )

omv/engines/__init__.py

@@ -23,6 +23,7 @@
 # from omv.engines.brian1 import Brian1Engine
 from omv.engines.brian2_ import Brian2Engine
 from omv.engines.arbor_ import ArborEngine
+from omv.engines.xpp import XppEngine
 from omv.engines.eden_ import EdenEngine
 from omv.engines.nestsli import NestEngine
 from omv.engines.pynest import PyNestEngine

omv/engines/getxpp.py

@@ -0,0 +1,83 @@
+import os
+from omv.common.inout import inform, check_output
+
+from omv.engines.utils.wdir import working_dir
+from sysconfig import get_paths
+import sys
+        
+import fileinput
+
+
+def install_xpp(version='latest'):
+
+    if version is None: 
+        version='latest'
+    elif not version=='latest':
+        raise Exception('Can currently only install the latest XPP version')
+
+    inform("Installing XPP", indent=2, verbosity=1)
+    xppinstallpath = os.path.join(os.environ["HOME"])
+    xpphomepath = os.path.join(xppinstallpath, 'xppaut')
+
+    inform(
+        "Installing XPP to: %s" % (xpphomepath),
+        indent=2,
+        verbosity=1,
+    )
+    pypaths = get_paths()
+    inform("Python lib info: %s" % (pypaths), indent=2, verbosity=1)
+
+
+    with working_dir(xppinstallpath):
+        print(
+            check_output(
+                [
+                    "git",
+                    "clone",
+                    "https://github.com/NeuroML/xppaut"
+                ]
+            )
+        )
+
+    with working_dir(xpphomepath):
+        print(
+            check_output(
+                [
+                    "ls",
+                    "-alth"
+                ]
+            )
+        )
+
+        makefile = os.path.join(xpphomepath, 'Makefile')
+                
+        print(' - Replacing text in %s'%makefile)
+        with open(makefile, 'r') as file:
+            filedata = file.read()
+
+        # Replace the target string
+        filedata = filedata.replace("/usr/local/", "%s/"%xpphomepath)
+
+        # Write the file out again
+        with open(makefile, 'w') as file:
+            file.write(filedata)
+
+        print(
+            check_output(
+                [
+                    "make", "-j4"
+                ]
+            )
+        )
+        print(
+            check_output(
+                [
+                    "make", "install"
+                ]
+            )
+        )
+
+
+
+if __name__ == "__main__":
+    install_nest()

omv/engines/xpp.py

@@ -0,0 +1,82 @@
+import os
+import sys
+
+import subprocess as sp
+
+from omv.common.inout import inform, trim_path, check_output, is_verbose
+from omv.engines.engine import OMVEngine, EngineExecutionError
+
+
+class XppEngine(OMVEngine):
+    name = "XPP"
+
+    @staticmethod
+    def get_xpp_environment():
+
+        # Default, if it was installed by omv...
+        xpppath = os.path.join(os.environ["HOME"], "xppaut/bin")
+
+        if "XPP_HOME" in os.environ:
+            xpppath = os.environ["XPP_HOME"] + "/"
+
+        environment_vars = {
+            "XPP_HOME": xpppath,
+        }
+
+        return environment_vars
+
+    @staticmethod
+    def is_installed():
+        ret = True
+        environment_vars = XppEngine.get_xpp_environment()
+        try:
+            FNULL = open(os.devnull, "w")
+
+            r = check_output(
+                [environment_vars["XPP_HOME"] + "/xppaut", "-version"], verbosity=2
+            )
+            if "Problem" in r:
+                ret = 'v???'
+
+            else:
+                ret = "%s" % r.split()[2]
+                if not "v" in ret:
+                    ret = "v%s" % ret
+
+            inform("XPP %s is correctly installed..." % ret, indent=2, verbosity=1)
+
+        except OSError as err:
+            if is_verbose():
+                inform("Couldn't execute XPP: ", err, indent=1)
+            ret = False
+        return ret
+
+    @staticmethod
+    def install(version):
+        from omv.engines.getxpp import install_xpp
+
+        install_xpp(version)
+        inform("Done...", indent=2)
+
+    def run(self):
+        self.environment_vars = XppEngine.get_xpp_environment()
+        self.set_environment()
+
+        try:
+            inform(
+                "Running file %s with %s" % (trim_path(self.modelpath), self.name),
+                indent=1,
+            )
+            self.stdout = check_output(
+                [self.environment_vars["XPP_HOME"] + "/xppaut", self.modelpath, '-silent'],
+                cwd=os.path.dirname(self.modelpath),
+            )
+            self.returncode = 0
+        except sp.CalledProcessError as err:
+            self.returncode = err.returncode
+            self.stdout = err.output
+            raise EngineExecutionError
+        except Exception as err:
+            inform("Another error with running %s: " % self.name, err, indent=1)
+            self.returncode = -1
+            self.stdout = "???"

omv/omv_util.py

@@ -279,6 +279,16 @@ def _install_engine(eng):
 
                 install_arbor(engine_version)
 
+        elif eng.lower() == "XPP".lower():
+            from omv.engines.xpp import XppEngine as ee
+
+            if ee.is_installed():
+                already_installed = True
+            else:
+                from omv.engines.getxpp import install_xpp
+
+                install_xpp(engine_version)
+
         elif eng.lower() == "EDEN".lower():
             from omv.engines.eden_ import EdenEngine as ee
 

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = OSBModelValidation
-version = 0.2.20
+version = 0.2.21
 author = Boris Marin, Padraig Gleeson
 author_email = [email protected]
 url = https://github.com/OpenSourceBrain/osb-model-validation
@@ -18,6 +18,7 @@ classifiers=
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
     Topic :: Scientific/Engineering
 
 [options]

utilities/tests/.test.xpp.mep

@@ -0,0 +1,7 @@
+system: Test XPP
+
+experiments:
+    spikes:
+        expected:
+            spike times: [32.25, 60.400002, 156.60001, 256.45001, 356.10001, 455.79999]
+

utilities/tests/.test.xpp.omt

@@ -0,0 +1,17 @@
+target: nca.ode
+engine: XPP
+
+mep: .test.xpp.mep
+experiments:
+  spikes:
+    observables:
+      spike times:
+        file: 
+          path: output.dat
+          columns: [0,1]
+          scaling: [1, 1]
+        spike detection: 
+          method: threshold
+          threshold: 0
+        tolerance: 0.00
+

utilities/tests/nca.ode

@@ -0,0 +1,82 @@
+# 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
+#if(t<=3.0)then(Iapp)else(0.0)
+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