first commit, tests for noise on synapses

tests/0029_SynapseNoise/README.md

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+# 0029_SynapseNoise
+
+three replicates of IzhikevichBurstingNeuron.cps connected by chemical synapses by ODE *v* adding noise
+
+## tests
+
+- 1D, 3 units, network, synaptic connection global quantity ODE, noise
+- cps file reads well
+- network file reads well
+- checks that there are two ODEs for br_i_j (the post-synaptic bound receptor)
+- checks that there are two Vsyn parameters
+- checks that there are two tau_r parameters
+- checks that there are two tau_d parameters
+- running the model through COPASI produces output

tests/0029_SynapseNoise/run.sh

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+#!/bin/bash
+
+# work out our folder name
+test=${PWD##*/}          # to assign to a variable
+test=${test:-/}          # to correct for the case where PWD=/
+
+fail=0
+
+# run sbmodelr
+../../sbmodelr -s v -n ../sources/1to2to3.gv --cn 0.1 uni -o IzNoise.cps ../sources/IzhikevichBurstingNeuron.cps 3 1> output 2> /dev/null
+
+# compare output and target
+difference=$(diff output target_stdout)
+if [[ $difference ]]; then
+  printf 'FAIL %s\n' "${test}"
+  fail=1
+fi
+
+# create model summary
+../model_report.py IzNoise.cps >/dev/null
+if ! [[ $? = 0 ]]; then
+  printf 'FAIL %s\n' "${test}"
+  exit -1
+fi
+
+# check that there are two ODEs for br_i_j (the post-synaptic bound receptor)
+n=$(grep -Pc "br_v_([12])\,([23])\s+ode" IzNoise.summary.txt)
+if ((n != 2))  ; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 2"
+fi
+
+# check that there are two Vsyn parameters
+n=$(grep -Pc "^Vsyn_v_synapse_[12]-[23]\s+fixed" IzNoise.summary.txt)
+if ((n != 2))  ; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 4"
+fi
+
+# check that there are two tau_r parameters
+n=$(grep -Pc "^tau_r_v_synapse_[12]-[23]\s+fixed" IzNoise.summary.txt)
+if ((n != 2))  ; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 8"
+fi
+
+# check that there are two tau_d parameters
+n=$(grep -Pc "^tau_d_v_synapse_[12]-[23]\s+fixed" IzNoise.summary.txt)
+if ((n != 2))  ; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 8"
+fi
+
+# run the model with CopasiSE
+../CopasiSE -c . --nologo IzNoise.cps > cpsout 2>&1
+if ! [[ $? = 0 ]]; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 16"
+fi
+
+# check that the output was created and contains last time point
+n=$(tail -n 3 I-tc.txt | grep -Pc "^300\s+")
+if ((n != 1))  ; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 32"
+fi
+
+if [ "$fail" = 0 ] ; then
+  printf 'PASS %s\n' "${test}"
+  rm IzNoise.summary.txt I-tc.txt cpsout output *.cps
+fi
+
+exit $fail

tests/0029_SynapseNoise/target_stdout

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+Processing ../sources/IzhikevichBurstingNeuron.cps
+  Reactions:         0
+  Species:           0	(Reactions: 0, Fixed: 0, Assignment: 0, ODE: 0)
+  Compartments:      1	(Fixed: 1, Assignment: 0, ODE: 0)
+  Global quantities: 8	(Fixed: 6, Assignment: 0, ODE: 2)
+  Events:            2	(Only time-dependent: 1, variable-dependent: 1)
+  Network:           directed	(Nodes: 3, Edges: 2)
+
+created new model IzNoise.cps with a set of 3 replicas of ../sources/IzhikevichBurstingNeuron.cps
+