switch NFSim_test1 to python script for portability

NFsim_v1.11/CMakeLists.txt

@@ -94,7 +94,12 @@ enable_testing()
 add_executable(${exe_target} ${SRC_FILES})
 target_link_libraries(${exe_target} vcommons vcellmessaging)
 
-add_test(NAME ${exe_target}_test1 COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/tests/test1/test1.sh ${CMAKE_BINARY_DIR}/bin/${exe_target} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/tests/test1)
+# if windows then command is py test1.py, else it is test1.py
+set(test_command test1.py)
+if (WIN32)
+    set(test_command py test1.py)
+endif (WIN32)
+add_test(NAME ${exe_target}_test1 COMMAND ${test_command} ${CMAKE_BINARY_DIR}/bin/${exe_target} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/tests/test1)
 
 install(TARGETS ${exe_target} RUNTIME DESTINATION ${OPTION_EXE_DIRECTORY})
 

NFsim_v1.11/tests/test1/test1.py

@@ -0,0 +1,62 @@
+#!/usr/bin/env python3
+
+import os
+import subprocess
+import sys
+
+# get the directory of this script
+test_dir = os.path.dirname(os.path.realpath(__file__))
+
+exe = sys.argv[1]
+
+input_file = os.path.join(test_dir, "SimID_273069657_0_.nfsimInput")
+output = os.path.join(test_dir, "SimID_273069657_0_.gdat")
+expected_output = os.path.join(test_dir, "SimID_273069657_0_.gdat.expected")
+species = os.path.join(test_dir, "SimID_273069657_0_.species")
+expected_species = os.path.join(test_dir, "SimID_273069657_0_.species.expected")
+
+if not os.path.isfile(exe):
+    print(f"NFsim executable {exe} not found. Exiting...")
+    sys.exit(1)
+
+if not os.path.isfile(input_file):
+    print(f"Input file {input_file} not found. Exiting...")
+    sys.exit(1)
+
+if not os.path.isfile(expected_output):
+    print(f"Expected output file {expected_output} not found. Exiting...")
+    sys.exit(1)
+
+if not os.path.isfile(expected_species):
+    print(f"Expected species file {expected_species} not found. Exiting...")
+    sys.exit(1)
+
+command = [exe, "-seed", "505790288", "-vcell", "-xml", input_file, "-o", output, "-sim", "1.0", "-ss", species, "-oStep", "20", "-notf", "-utl", "1000", "-cb", "-pcmatch", "-tid", "0"]
+print(" ".join(command))
+
+try:
+    subprocess.check_call(command)
+except subprocess.CalledProcessError:
+    print("NFsim failed to run. Exiting...")
+    sys.exit(1)
+
+# verify that the output files exist
+if not os.path.isfile(output):
+    print(f"Output file {output} not found. Exiting...")
+    sys.exit(1)
+
+if not os.path.isfile(species):
+    print(f"Species file {species} not found. Exiting...")
+    sys.exit(1)
+
+# verify that the output files match the expected output files
+if open(output).read() != open(expected_output).read():
+    print(f"Output file {output} does not match expected output {expected_output}. Exiting...")
+    sys.exit(1)
+
+if open(species).read() != open(expected_species).read():
+    print(f"Species file {species} does not match expected species {expected_species}. Exiting...")
+    sys.exit(1)
+
+print("NFsim solver completed and solution matched expected output. Exiting...")
+sys.exit(0)