tests ode compartment arrays diffusive connection

tests/0025_CompartmentArray/README.md

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+# 0025_CompartmentArray
+
+set of 27 units of model with compartment ODE connected by diffusive connections of *blob* 3x3x3
+
+## tests
+
+- 3D, 27 units, diffusive connection compartment ODE
+
+- SBML file reads well
+- network file reads well
+- checks that coupling constant exists and is set to default value
+- checks that there are 2 ODEs which contain the diffusive terms

tests/0025_CompartmentArray/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=/
+
+# run sbmodelr
+../../sbmodelr -d blob -c 0.05 --pn blob 0.9 uni ../sources/blob.cps 3 3 3 > output
+
+fail=0
+
+# 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 blob_3x3x3.cps >/dev/null
+if ! [[ $? = 0 ]]; then
+  printf 'FAIL %s\n' "${test}"
+  exit -1
+fi
+
+# check that the coupling constant has been defined with the correct value
+if ! grep -Pq "^k_blob_coupling\s+fixed\s+0.05" blob_3x3x3.summary.txt; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 2"
+fi
+
+# check that there are 27 compartments
+n=$(grep -Pc "^blob_[123],[123],[123]\s+ode" blob_3x3x3.summary.txt )
+if ((n != 27))  ; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 4"
+fi
+
+# check that the ode for blob_2,2,2 (the center unit) has 6 diffusive terms
+n=$(grep -P "^blob_2,2,2\s+ode" blob_3x3x3.summary.txt | grep -Po "\+ Values\[k_blob_coupling\] \* \("| wc -l)
+if ((n != 6))  ; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 8"
+fi
+
+# check that min and max of [blob]_0 are different (checks that --pn worked)
+n=$(grep -Po "^blob_[123],[123],[123]\s+ode\s+(.[0-9]+\.[0-9]+\s)" blob_3x3x3.summary.txt | awk '(NR==1){Min=$3;Max=$3};(NR>=2){if(Min>$3) Min=$3;if(Max<$3) Max=$3} END {if(Min == Max) {print 1} else {print 0} }')
+if ((n != 0)) ; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 16"
+fi
+
+# validate the model with CopasiSE
+../CopasiSE -c . --nologo --validate blob_3x3x3.cps > cpsout 2>&1
+if ! [[ $? = 0 ]]; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 32"
+fi
+
+if [ "$fail" = 0 ] ; then
+  printf 'PASS %s\n' "${test}"
+  rm blob_3x3x3.* cpsout output
+fi
+
+exit $fail

tests/0025_CompartmentArray/target_stdout

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+Processing ../sources/blob.cps
+  Reactions:         0
+  Species:           0	(Reactions: 0, Fixed: 0, Assignment: 0, ODE: 0)
+  Compartments:      1	(Fixed: 0, Assignment: 0, ODE: 1)
+  Global quantities: 0	(Fixed: 0, Assignment: 0, ODE: 0)
+  Events:            0	(Only time-dependent: 0, variable-dependent: 0)
+created new model blob_3x3x3.cps with a 3D set of 27 replicas (3x3x3) of ../sources/blob.cps
+