use pkg_resources to access bundled files

* egg file can remain zipped
* see http://peak.telecommunity.com/DevCenter/PythonEggs#accessing-package-resources
  for details

propka/bonds.py

@@ -4,6 +4,7 @@ from __future__ import print_function
 
 import pickle,sys,os,math,propka.calculations
 
+import pkg_resources
 
 class bondmaker:
     def __init__(self):
@@ -26,8 +27,7 @@ class bondmaker:
         self.max_sq_distance = max(list(self.distances_squared.values())+[self.default_dist_squared])
 
         # protein bonding data
-        path = os.path.split(__file__)[0]
-        self.data_file_name = os.path.join(path,'protein_bonds.dat')
+        self.data_file_name = pkg_resources.resource_filename(__name__, 'protein_bonds.dat')
 
         data = open(self.data_file_name,'rb')
         self.protein_bonds = pickle.load(data)

propka/lib.py

@@ -1,23 +1,24 @@
-#!/usr/bin/python
-
 from __future__ import division
 from __future__ import print_function
 
 import string, sys, copy, math, os
 
+import pkg_resources
 
 #
 # file I/O
 #
 def open_file_for_reading(filename):
-    if not os.path.isfile(filename):
+    try:
+        f = open(filename,'r')
+    except:
         raise Exception('Cannot find file %s' %filename)
-    
-    return open(filename,'r')
+    return f
 
 def open_file_for_writing(filename):
-    res = open(filename,'w')
-    if not res:
+    try:
+        res = open(filename,'w')
+    except:
         raise Exception('Could not open %s'%filename)
     return res
 
@@ -102,8 +103,8 @@ def loadOptions():
            help="specifying mutation labels which is used to modify <filename> according to, e.g. N25R/N181D")
     parser.add_option("-v", "--version", dest="version_label", default="Jan15",
            help="specifying the sub-version of propka [Jan15/Dec19]")
-    parser.add_option("-p", "--parameters",dest="parameters", default="propka.cfg",
-                      help="set the parameter file")
+    parser.add_option("-p", "--parameters",dest="parameters", default=pkg_resources.resource_filename(__name__, "propka.cfg"),
+                      help="set the parameter file [%default]")
     parser.add_option("-z", "--verbose", dest="verbose", action="store_true", default=True,
            help="sleep during calculations")
     parser.add_option("-q", "--quiet", dest="verbose", action="store_false",

propka/parameters.py

@@ -6,6 +6,7 @@ import math
 import propka.lib as lib
 import sys, os
 
+import pkg_resources
 
 # names and types of all key words in configuration file
 matrices =            ['interaction_matrix']
@@ -57,8 +58,7 @@ class Parameters:
     def read_parameters(self, file):
         # try to locate the parameters file
         try:
-            path = os.path.dirname(__file__)
-            ifile = os.path.join(path,'../'+file)
+            ifile = pkg_resources.resource_filename(__name__, file)
             input = lib.open_file_for_reading(ifile)
         except:
             input = lib.open_file_for_reading(file)

setup.py

@@ -47,5 +47,5 @@ using the tutorial http://propka.ki.ku.dk/~luca/wiki/index.php/PROPKA_3.1_Tutori
             'propka31 = propka.run:main',
             ],
         },
-      zip_safe=False,
+      zip_safe=True,
 )