test some invalid cli options

tests/0505_CLIOptions/README.md

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+# 0505_CLIOptions
+
+tests various invalid command line options
+
+## tests
+
+- 1D, network, transport
+- appropriate warning for an empty network file
+- appropriate warning for a network file without edges
+- appropriate warning for test a network file with repeated edges
+- ensure that repeated edges are added exactly once to model
+- appropriate warning for a network file with non-numeric nodes

tests/0505_CLIOptions/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
+
+# test negative number of units
+../../sbmodelr -t G ../sources/GeneExpressionUnit.cps -2 > output 2>&1
+
+# check that the correct warning is issued
+if ! grep -q "sbmodelr: error: argument rows: -2 is an invalid negative value" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = 1"
+fi
+
+# test one unit only
+../../sbmodelr -t G ../sources/GeneExpressionUnit.cps 1 > output 2>&1
+
+# check that the correct warning is issued
+if ! grep -q "ERROR: Nothing to do, one copy only is the same as the original model!" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 2"
+fi
+
+# test one unit per dimension
+../../sbmodelr -t G ../sources/GeneExpressionUnit.cps 1 1 > output 2>&1
+
+# check that the correct warning is issued
+if ! grep -q "ERROR: Nothing to do, one copy only is the same as the original model!" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 4"
+fi
+
+# test one unit per dimension
+../../sbmodelr -t G ../sources/GeneExpressionUnit.cps 1 1 1 > output 2>&1
+
+# check that the correct warning is issued
+if ! grep -q "ERROR: Nothing to do, one copy only is the same as the original model!" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 8"
+fi
+
+# test negative kinetic constant value
+../../sbmodelr -t G -k -0.2 ../sources/GeneExpressionUnit.cps 2 > output 2>&1
+
+# check that the correct warning is issued
+if ! grep -q "sbmodelr: error: argument -k/--transport-k: -0.2 is an invalid negative value" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 16"
+fi
+
+# test negative noise level
+../../sbmodelr -t G --cn -0.3 uni ../sources/GeneExpressionUnit.cps 2 2 > output 2>&1
+
+# check that the correct warning is issued
+if ! grep -q "ERROR: 'level' must be a positive floating point number" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 32"
+fi
+
+# test integer noise level
+../../sbmodelr -t G --cn 3 uni ../sources/GeneExpressionUnit.cps 2 2 > output 2>&1
+
+# check that no warning is issued
+if grep -q "ERROR: 'level' must be a positive floating point number" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 64"
+fi
+
+# test invalid noise distribution
+../../sbmodelr -t G --cn 0.1 foo ../sources/GeneExpressionUnit.cps 2 2 > output 2>&1
+
+# check that the correct warning is issued
+if ! grep -q "ERROR: dist must be 'uni' or 'norm'" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 128"
+fi
+
+# we repeat error values matching those of--cn because we're testing more than 8 conditions
+
+# test negative noise level for --pn
+../../sbmodelr -t G --pn G -0.3 uni ../sources/GeneExpressionUnit.cps 2 2 > output 2>&1
+
+# check that the correct warning is issued
+if ! grep -q "ERROR: 'level' must be a positive floating point number" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 32"
+fi
+
+# test integer noise level
+../../sbmodelr -t G --pn G 3 uni ../sources/GeneExpressionUnit.cps 2 2 > output 2>&1
+
+# check that no warning is issued
+if grep -q "ERROR: 'level' must be a positive floating point number" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 64"
+fi
+
+# test invalid noise distribution
+../../sbmodelr -t G --pn G 0.1 foo ../sources/GeneExpressionUnit.cps 2 2 > output 2>&1
+
+# check that the correct warning is issued
+if ! grep -q "ERROR: dist must be 'uni' or 'norm'" output; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 128"
+fi
+
+if [ "$fail" = 0 ] ; then
+  printf 'PASS %s\n' "${test}"
+  rm output *.cps > /dev/null 2>&1
+fi
+
+exit $fail