Improved target and target behavior of makefile for example simulation

- new target "clean_example" to delete output and input artifacts of the example simulation

- targets that run the example simulation gain the "-r" option which automatically renames the domain template file in nc-mode

makefile

@@ -76,6 +76,7 @@
 #                  does not clean artifacts from code coverage or documentation
 # make clean_bin   delete 'bin/' (binary and test executables and library)
 # make clean_build delete binary executable build artifacts
+# make clean_example delete output and input artifacts of example simulation
 # make clean_test  delete test executable build artifacts
 # make clean_cov   delete code coverage artifacts
 # make clean_doc   delete documentation
@@ -509,7 +510,7 @@ $(dir_bin) $(dir_build_sw2) $(dir_build_test):
 #--- Convenience targets for testing
 .PHONY : bin_run
 bin_run : all
-		$(bin_sw2) -d ./tests/example -f files.in
+		$(bin_sw2) -d ./tests/example -f files.in -r
 
 .PHONY : test_run
 test_run : test
@@ -590,6 +591,13 @@ clean_build:
 		-@$(RM) -r $(dir_build_sw2)
 		-@$(RM) -f $(bin_sw2) $(lib_sw2) $(lib_rsw2)
 
+.PHONY : clean_example
+clean_example:
+		-@$(RM) -r tests/example/Output
+		-@$(RM) -f tests/example/Input_nc/domain_template.nc
+		-@$(RM) -f tests/example/Input_nc/domain.nc
+		-@$(RM) -f tests/example/Input_nc/progress.nc
+
 .PHONY : clean_test
 clean_test:
 		-@$(RM) -r $(dir_build_test)

tools/check_functionality.sh

@@ -21,17 +21,6 @@ exists() {
   command -v "$1" > /dev/null 2>&1
 }
 
-#--- Function to clean example inputs
-clean_example_inputs() {
-  rm tests/example/Input_nc/progress.nc
-  rm tests/example/Input_nc/domain.nc
-  rm tests/example/Input_nc/domain_template.nc
-}
-
-#--- Function to delete example output
-clean_example_outputs() {
-  rm -r tests/example/Output
-}
 
 #--- Function to run example SOILWAT2 simulation with fresh inputs
 # $1 Compiler, e.g., CC=clang, CXX=g++, or (if not specify a compiler) CC=
@@ -59,8 +48,7 @@ run_fresh_sw2() {
     mflags+=("CPPFLAGS=-DSWNC")
   fi
 
-  clean_example_inputs > /dev/null 2>&1
-  clean_example_outputs > /dev/null 2>&1
+  res=$(make clean_example)
 
   res=$(make "${mflags[@]}" clean "${target}" 2>&1)
   status=$?

tools/check_outputModes.sh

@@ -34,7 +34,7 @@ if [[ "${res}" == *"make failed"* ]]; then
 else
     cp -R tests/example/Output tests/example/Output_comps-nc > /dev/null 2>&1
 fi
-clean_example_inputs > /dev/null 2>&1
+res=$(make clean_example)
 
 unset noflags
 

tools/run_bin_leaks.sh

@@ -6,4 +6,4 @@
 # or via makefile
 # run as `CC=clang make clean bin_leaks`
 
-MallocStackLogging=1 MallocStackLoggingNoCompact=1 MallocScribble=1 MallocPreScribble=1 MallocCheckHeapStart=0 MallocCheckHeapEach=0 leaks -quiet -atExit -- bin/SOILWAT2 -d ./tests/example -f files.in
+MallocStackLogging=1 MallocStackLoggingNoCompact=1 MallocScribble=1 MallocPreScribble=1 MallocCheckHeapStart=0 MallocCheckHeapEach=0 leaks -quiet -atExit -- bin/SOILWAT2 -d ./tests/example -f files.in -r

tools/run_bin_sanitizer.sh

@@ -35,4 +35,4 @@ instr_flags_severe="\
 
 
 # Note: # Apple clang does not support "AddressSanitizer: detect_leaks" (at least as of clang-1200.0.32.29)
-ASAN_OPTIONS=detect_leaks=1:strict_string_checks=1:detect_stack_use_after_return=1:check_initialization_order=1:strict_init_order=1 LSAN_OPTIONS=suppressions=../.LSAN_suppr.txt SW2_FLAGS=""$debug_flags" "$warning_flags_severe_cc" "$instr_flags_severe"" make bin_run
+ASAN_OPTIONS=detect_leaks=1:strict_string_checks=1:detect_stack_use_after_return=1:check_initialization_order=1:strict_init_order=1 LSAN_OPTIONS=suppressions=../.LSAN_suppr.txt SW2_FLAGS=""$debug_flags" "$warning_flags_severe_cc" "$instr_flags_severe"" make bin_run -r