renamed

tests/0502_GvSelfTransport/README.md

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+# 0502_GvSelfTransport
+
+tries to create a set of 2 units of the Selkov-Wolf-Heinrich model where the graphviz file has a self connection
+
+## tests
+
+- 1D, network, directed
+- file reads well
+- gv file reads well
+- issues a warning that the slef connection will be ignored
+- produces no other warning or error (ignores bad node)
+- tests -o option to name output file
+- checks that the self connection was ignored

tests/0502_GvSelfTransport/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 -t X -n ../sources/self.gv -o ISC.cps ../sources/Selkov-Wolf-Heinrich.cps 2 > output
+
+fail=0
+
+# compare output and target
+difference=$(diff output target_stdout)
+if [[ $difference ]]; then
+  printf 'FAIL %s\n' "${test}"
+  fail=1
+fi
+
+# test -o option by checking if output file was created
+if ! [ -f ISC.cps ]; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 2"
+fi
+
+# create model summary
+../model_report.py ISC.cps >/dev/null
+if ! [[ $? = 0 ]]; then
+  printf 'FAIL %s\n' "${test}"
+  exit -1
+fi
+
+# check that there is a transport reaction 1->2
+if ! grep -Pq "t_X_1-2\s+X_1 -> X_2" ISC.summary.txt; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 2"
+fi
+
+# check that there is no transport reaction 2->2
+if grep -Pq "t_X_2-2\s+X_2 -> X_2" ISC.summary.txt; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 4"
+fi
+
+# check that there is only one transport constant
+n=$(grep -Pc "^k_.+_transport\s+fixed" ISC.summary.txt )
+if ((n != 1))  ; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 8"
+fi
+
+if [ "$fail" = 0 ] ; then
+  printf 'PASS %s\n' "${test}"
+  rm ISC.summary.txt output *.cps
+fi
+
+exit $fail

tests/0502_GvSelfTransport/target_stdout

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+Processing ../sources/Selkov-Wolf-Heinrich.cps
+  Reactions:         3
+  Species:           2	(Reactions: 2, Fixed: 0, Assignment: 0, ODE: 0)
+  Compartments:      1	(Fixed: 1, Assignment: 0, ODE: 0)
+  Global quantities: 2	(Fixed: 2, Assignment: 0, ODE: 0)
+  Events:            0	(Only time-dependent: 0, variable-dependent: 0)
+  Network:           directed	(Nodes: 2, Edges: 2)
+ Warning: transport on the same unit not allowed, ignoring 2 -> 2
+created new model ISC.cps with a set of 2 replicas of ../sources/Selkov-Wolf-Heinrich.cps
+