Added setup processing to the APBS tester Python script to support adding the protein RNA tests. Closes issues #149.

examples/protein-rna/apbs_unix_dx.py

@@ -0,0 +1,23 @@
+#!/bin/python
+
+my_list = ('0.025', '0.050', '0.075', '0.100', '0.125', '0.150', '0.175', '0.200', '0.225', '0.250', '0.275', '0.300', '0.325', '0.400', '0.500', '0.600', '0.700', '0.800')
+
+with open("template.txt", "r") as temp:  
+	template_text = temp.read()
+
+for item in my_list:  
+	input_txt = template_text.replace("IONSTR", item)
+	file_name = "apbs-" + item + ".in"  
+	print "Creating file now:", file_name  
+	with open(file_name, "w") as temp:  
+		temp.write(input_txt)
+
+with open("dxmath.txt", "r") as temp:
+	template_2_text = temp.read()
+
+for item in my_list:
+	input_2_txt = template_2_text.replace("IONSTR", item)
+	file_2_name = "dxmath-" + item + ".in"
+	print "Creating file_2 now:", file_2_name
+	with open(file_2_name, "w") as temp:
+		temp.write(input_2_txt)

examples/protein-rna/apbs_win_dx.py

@@ -1,25 +1,25 @@
 from subprocess import call
 
-my_list = (0.025, 0.05, 0.075, 0.1, 0.125, 0.15, 0.175, 0.225, 0.275,
-0.325, 0.4, 0.5, 0.6, 0.7, 0.8)
+my_list = ('0.025', '0.050', '0.075', '0.100', '0.125', '0.150', '0.175', '0.200', '0.225', '0.250', '0.275', '0.300', '0.325', '0.400', '0.500', '0.600', '0.700', '0.800')
+
 with open("template.txt", "r") as temp:  
 	template_text = temp.read()
 
 for item in my_list:  
-	input_txt = template_text.replace("IONSTR",str(item))  
-	file_name = "apbs-" + str(item) + ".in"  
+	input_txt = template_text.replace("IONSTR", item)  
+	file_name = "apbs-" + item + ".in"  
 	print "Creating file now:", file_name  
 	with open(file_name, "w") as temp:  
 		temp.write(input_txt)
-	call(["apbs", "apbs-" + str(item) + ".in"])
+	call(["apbs", "apbs-" + item + ".in"])
 
 with open("dxmath.txt", "r") as temp:
 	template_2_text = temp.read()
 
 for item in my_list:
-	input_2_txt = template_2_text.replace("IONSTR",str(item))
-	file_2_name = "dxmath-" + str(item) + ".in"
+	input_2_txt = template_2_text.replace("IONSTR", item)
+	file_2_name = "dxmath-" + item + ".in"
 	print "Creating file_2 now:", file_2_name
 	with open(file_2_name, "w") as temp:
 		temp.write(input_2_txt)
-	call(["dxmath", "dxmath-" + str(item) + ".in"])
+	call(["dxmath", "dxmath-" + item + ".in"])

tests/apbs_tester.py

@@ -6,7 +6,7 @@ Provides utility for testing apbs against examples and known results
 
 import sys, os, re, datetime, subprocess, operator
 from optparse import OptionParser
-from ConfigParser import ConfigParser
+from ConfigParser import ConfigParser, NoOptionError
 
 # The inputgen utility needs to be accessible, so we add its path
 sys.path.insert( 0, "../tools/manip" )
@@ -115,7 +115,7 @@ def process_parallel( binary, input_file, procs, logger ):
 
 
 
-def run_test( binary, test_files, test_name, test_directory, logger, ocd ):
+def run_test( binary, test_files, test_name, test_directory, setup, logger, ocd ):
     """
     Runs a given test from the test cases file
     """
@@ -131,6 +131,10 @@ def run_test( binary, test_files, test_name, test_directory, logger, ocd ):
     # Change the current working directory to the test directory
     os.chdir( test_directory )
 
+    # Run the setup, if any
+    if setup:
+        subprocess.call(setup.split())
+
     for ( base_name, expected_results ) in test_files:
 
         # Get the name of the input file from the base name
@@ -281,13 +285,21 @@ def main():
             print "  " + test_name + " section not found in " + options.test_config
             print "  skipping..."
             continue
-            
-        # As each test runs, remove the value so it can't be run twice
+
+        # Grab the test directory
         test_directory = config.get( test_name, 'input_dir' )
         config.remove_option( test_name, 'input_dir' )
         
+        # Check if there is a setup step.
+        test_setup = None
+        try:
+            test_setup = config.get(test_name, 'setup')
+            config.remove_option(test_name, 'setup')
+        except NoOptionError:
+            pass
+
         # Run the test!
-        run_test( binary, config.items( test_name ), test_name, test_directory, logger, options.ocd )
+        run_test( binary, config.items( test_name ), test_name, test_directory, test_setup, logger, options.ocd )
 
 
 

tests/test_cases.cfg

@@ -73,4 +73,26 @@ apbs-smol          : -3.757593797629E+01 -3.912388198513E+02 -3.536628818750E+02
 
 [geoflow]
 input_dir   : ../examples/geoflow
-geoflow     : -1.04893133E+01 5.417419E-01
+imidazole   : -1.030222099963E+01 5.417419E-01
+
+[protein-rna]
+input_dir  : ../examples/protein-rna
+setup      : python apbs_unix_dx.py
+apbs-0.025 : 8.674116429353E+01
+apbs-0.050 : 9.606836713866E+01
+apbs-0.075 : 1.011537214883E+02
+apbs-0.100 : 1.046142116108E+02
+apbs-0.125 : 1.072226817610E+02
+apbs-0.150 : 1.093084123761E+02
+apbs-0.175 : 1.110412443877E+02
+apbs-0.200 : 1.125199716537E+02
+apbs-0.225 : 1.138070465620E+02
+apbs-0.250 : 1.149444369078E+02
+apbs-0.275 : 1.159616972338E+02
+apbs-0.300 : 1.168804254687E+02
+apbs-0.325 : 1.177168854906E+02
+apbs-0.400 : 1.198456038803E+02
+apbs-0.500 : 1.220607673699E+02
+apbs-0.600 : 1.238080564885E+02
+apbs-0.700 : 1.252364090878E+02
+apbs-0.800 : 1.264340604647E+02