create test/tutorial via cli, always install tests

CMakeLists.txt

@@ -17,9 +17,6 @@ set (CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${SIMEX_CMAKE_DIR})
 
 option (DEVELOPER_INSTALL "Install modules only, do not install SimEx files" OFF)
 
-CMAKE_DEPENDENT_OPTION(INSTALL_TESTS "Install test files" ON
-                       "NOT DEVELOPER_INSTALL" OFF)
-
 set (LIBDIR     lib)
 set (INCLUDEDIR include)
 set (BINDIR     bin)
@@ -35,15 +32,12 @@ endif()
 if (DEVELOPER_INSTALL)
   set (FRAMEWORK_DIR ${SIMEX_SOURCE_DIR}/Sources)
   set (UNITTESTS_DIR ${FRAMEWORK_DIR}/unittest/)
-  set (TESTFILES_DIR ${UNITTESTS_DIR}/TestFiles/)
   set (UTILITIES_DIR ${FRAMEWORK_DIR}/python/SimEx/Utilities/)
   set (CALCULATORS_DIR ${FRAMEWORK_DIR}/python/SimEx/Calculators/)
 else()
   set (UTILITIES_DIR ${PYPATH}/SimEx/Utilities/)
   set (CALCULATORS_DIR ${PYPATH}/SimEx/Calculators/)
-  if (INSTALL_TESTS)
-     add_subdirectory (Tests)
-  endif()
+  add_subdirectory (Tests)
   add_subdirectory (Sources)
 endif()
 

Modules/Others/s2e/CMakeLists.txt

@@ -12,13 +12,6 @@ INSTALL_COMMAND ""
 
 ExternalProject_Get_Property(s2e SOURCE_DIR)
 
-#if (DEVELOPER_INSTALL)
-#install(FILES ${SOURCE_DIR}/data/sim_example/diffr/s2e.beam
-#              ${SOURCE_DIR}/data/sim_example/diffr/s2e.geom
-#              ${SOURCE_DIR}/data/sim_example/sample/sample.h5
-#        DESTINATION  ${TESTFILES_DIR})
-#endif()
-
 install(FILES ${SOURCE_DIR}/modules/diffr/prepHDF5.py
         DESTINATION  ${PYPATH})
 

Sources/python/SimEx/CLI/commands/modules.py

@@ -19,8 +19,7 @@ def set_arguments(parser):
 #enable module    
     parser_enable = subparsers.add_parser('enable', help='enable module(s)')
     parser_enable.set_defaults(func=enable_module.process_args_enable)
-
-
+
 #disable module
     parser_disable = subparsers.add_parser('disable', help='disable module(s)')
     parser_disable.set_defaults(func=enable_module.process_args_disable)    

Sources/python/SimEx/CLI/commands/modules_commands/set_param.py

@@ -1,5 +1,5 @@
 from SimEx.CLI.utilities import parse_modules,parse_classes,parse_settings,module_files
-
+import os
 
 def process_args(args):
 	set_parameters(args.name,args.parameters)
@@ -11,9 +11,10 @@ def getFromDict(dataDict, mapList):
 		raise Exception		
 	return vals
 
+
 def setInDict(dataDict, mapList, value):
-	getFromDict(dataDict, mapList) # to check if parameter exists
-	getFromDict(dataDict, mapList[:-1])[mapList[-1]] = value
+	old_value = getFromDict(dataDict, mapList) # to check if parameter exists
+	getFromDict(dataDict, mapList[:-1])[mapList[-1]] = type(old_value)(value)
 
 def set_param(param,module):
 	try:
@@ -39,7 +40,12 @@ def set_parameters(name,params):
 		return
 
 	paramfile = name+'_params'
+
 	module = __import__(paramfile)
+
+	picfile = name+'_params.pyc'
+	os.remove(picfile)
+
 
 	to_write = False
 	for param in params:

Sources/python/SimEx/CLI/commands/project.py

@@ -1,10 +1,12 @@
-from project_commands import create_project
+from project_commands import create_project,create_test_project
 
 
 def set_arguments(parser):
     subparsers = parser.add_subparsers(title='project commands',help='')
     parser = subparsers.add_parser('create', help='create project')
     parser.add_argument('name',metavar='<name>',nargs=1,help='Project name')
     parser.set_defaults(func=create_project.process_args)
+    parser = subparsers.add_parser('create-test', help='create test project')
+    parser.set_defaults(func=create_test_project.process_args)
 
 

Sources/python/SimEx/CLI/commands/project_commands/create_test_project.py

@@ -0,0 +1,62 @@
+
+import json
+import os
+
+import create_project 
+
+
+def process_args(args):
+	create_test_project()
+
+def prGreen(prt,newline=True):
+	if (newline):
+		print("\033[92m{}\033[00m" .format(prt))
+	else:
+		print("\033[92m{}\033[00m" .format(prt)),
+
+def prCyan(prt,newline=True):
+	if (newline):
+		print("\033[96m{}\033[00m" .format(prt))
+	else:
+		print("\033[96m{}\033[00m" .format(prt)),
+
+
+def runCommented(cmd,comment):
+	prCyan('*'*80)
+	prCyan(comment+':')
+	prGreen(cmd)
+	prCyan('*'*80)	
+	os.system(cmd)
+
+
+def create_test_project():
+	if os.listdir('.'):
+		print('Cannot create test project, directory is not empty') 
+		return
+
+	modules_to_test = ["XFELPhotonSource","XFELPhotonPropagator","XMDYNDemoPhotonMatterInteractor",
+					   "SingFELPhotonDiffractor","PerfectPhotonDetector","S2EReconstruction"]
+
+	filestocopy = ["$SIMEX_TESTS/python/unittest/TestFiles/s2e.*","$SIMEX_TESTS/python/unittest/TestFiles/sample.h5",
+				   "$SIMEX_TESTS/python/unittest/TestFiles/FELsource_out.h5"]
+
+	commands = [
+				["create project","simex project create test"],
+				["print available modules","simex module avail"],
+				["add modules to the project","simex module add "+' '.join(modules_to_test)],
+				["print project modules","simex module list"],
+				["make input dir and copy necessary files (not simex command)",
+					"mkdir -p input/FELsource && cp "+ ' '.join(filestocopy)+" input" + \
+					" && mv input/FELsource_out.h5 input/FELsource"],
+				["set module parameter","simex module set XFELPhotonSource input_path=input/FELsource"],
+				["set another module parameter","simex module set S2EReconstruction EMC_Parameters:max_number_of_iterations=2"],
+			   ]
+
+	for cmd in commands:
+		runCommented(cmd[1],cmd[0])
+
+	prCyan("Type",False),prGreen("simex run",False),prCyan("to start simulations")	
+
+if __name__ == "__main__":
+	import sys
+	create_test_project()

Sources/python/SimEx/CLI/utilities/module_files.py

@@ -23,6 +23,6 @@ def write_module_parameters(moduleName,module):
     s=pprint.pformat(module.parameters)
     print>>modfile,'parameters = ',s
 
-    modfile.close
+    modfile.close()
 
 

Sources/python/SimEx/CLI/utilities/project_files.py

@@ -33,11 +33,11 @@ def create_modulecall_code(moduleName,prevModule,nextModule):
                                     input_path=${ModuleName}_params.input_path,
                                     output_path=${ModuleName}_params.output_path
                                     )
-print "-"*80
-print ("Running ${ModuleName} ...")                                  
+prCyan("-"*80)
+prCyan ("Running ${ModuleName} ...")                                  
 module_time=time.time()                                    
 ${ModuleName}_inst.backengine()
-print "Done in "+str(datetime.timedelta(seconds=time.time()-start_time))
+prCyan ("Done in "+str(datetime.timedelta(seconds=time.time()-module_time)))
                        """
     prevpath = """
 if (${ModuleName}_params.input_path == 'default'):
@@ -64,7 +64,7 @@ def update_main_file():
         shutil.copy(src,dest)
         for line in fileinput.FileInput(dest, inplace=1):
             line=line.replace('${PROJECT_NAME}',fname)
-            print line.strip()        
+            print line.rstrip()
     except shutil.Error as e:
         print('Error: %s' % e)
     # eg. source or destination doesn't exist
@@ -86,4 +86,4 @@ def update_main_file():
 
     for line in fileinput.FileInput(dest, inplace=1):
             line=line.replace('# modules will be added here',string)
-            print line.strip()        
+            print line.rstrip()        

Sources/python/SimEx/Calculators/RegisteredCalculators/S2EReconstruction_ParamTemplate.py

@@ -24,21 +24,21 @@
 output_path = 'default'
 
 
-emc_parameters = {'initial_number_of_quaternions' : 1,
+EMC_Parameters = {'initial_number_of_quaternions' : 1,
                   'max_number_of_quaternions'     : 9,
                   'max_number_of_iterations'      : 3,
                   'min_error'                     : 1.0e-8,
                   'beamstop'                      : 1.0e-5,
                   'detailed_output'               : False
                  }
 
-dm_parameters = {'number_of_trials'        : 5,
+DM_Parameters = {'number_of_trials'        : 5,
                  'number_of_iterations'    : 2,
                  'averaging_start'         : 15,
                  'leash'                   : 0.2,
                  'number_of_shrink_cycles' : 2,
                 }
 
-parameters = {'EMC_Parameters' : emc_parameters, 'DM_Parameters' : dm_parameters}
+parameters = {'EMC_Parameters' : EMC_Parameters, 'DM_Parameters' : DM_Parameters}
 
 

Sources/python/SimEx/Templates/main.py

@@ -22,18 +22,22 @@
 
 import time,datetime,os
 
-
-
+def prGreen(prt,newline=True):
+	print ("\033[92m{}\033[00m" .format(prt))
+
+def prCyan(prt,newline=True):
+	print ("\033[96m{}\033[00m" .format(prt))
+
 start_time=time.time()
-print "="*80
-print "Simex platform. Copyright (C) 2016."
-print "Running project ${PROJECT_NAME}"
-print "-"*80
+prCyan("="*80)
+prCyan("Simex platform. Copyright (C) 2016.")
+prCyan("Running project ${PROJECT_NAME}")
+prCyan("-"*80)
 
 # modules will be added here
 
 
-print "-"*80
+prCyan("-"*80)
 
-print "Finished in "+str(datetime.timedelta(seconds=time.time()-start_time))
+prCyan("Simex finished in "+str(datetime.timedelta(seconds=time.time()-start_time)))
 

simex_vars.sh.in

@@ -2,3 +2,4 @@
 
 export PATH=${CMAKE_INSTALL_PREFIX}/${BINDIR}:$PATH
 export PYTHONPATH=${CMAKE_INSTALL_PREFIX}/${PYPATH}:$PYTHONPATH
+export SIMEX_TESTS=${CMAKE_INSTALL_PREFIX}/${TESTSDIR}

simex_vars_dev.sh.in

@@ -2,3 +2,5 @@
 
 export PATH=${CMAKE_INSTALL_PREFIX}/${BINDIR}:$PATH
 export PYTHONPATH=${FRAMEWORK_DIR}/python:${CMAKE_INSTALL_PREFIX}/${PYPATH}:$PYTHONPATH
+export SIMEX_TESTS=${SIMEX_SOURCE_DIR}/${TESTSDIR}
+