add test framework

- add the ability to run tests from the top level directory via
  'python setup.py test'
- translate runtest.py into a test that runs under this framework
- add a __main__ section to Tests/runtest.py and change its indent to 4
  spaces; make no other changes to this script

Tests/pkacalc_test.py

@@ -0,0 +1,68 @@
+
+import os
+import re
+from subprocess import call
+import sys
+import unittest
+
+# Setting this up as a direct translation of the original runtest.py script
+# that will be run as part of 'python setup.py test'. This takes on the
+# order of 30s to run.
+
+class SystemTest(unittest.TestCase):
+    """
+    Run the program and compare against reference results.
+    """
+    def test_pka_calc(self):
+        pdbs = ['1FTJ-Chain-A',
+                '1HPX',
+                '4DFR']
+
+        test_dir = os.path.dirname(__file__)
+        base_dir = os.path.dirname(test_dir)
+
+        executable = os.path.join(base_dir, "scripts", "propka31.py")
+
+        env = { "PYTHONPATH" : base_dir }
+
+        for pdb in pdbs:
+            input_filename = os.path.join(test_dir, "pdb", pdb + ".pdb")
+            output_filename = os.path.join(test_dir, pdb + ".out")
+
+            output_file = open(output_filename, "w")
+            call([sys.executable, executable, input_filename],
+                    stdout=output_file, env=env)
+            output_file.close()
+
+            # Check pka predictions.
+            ref = open(os.path.join(test_dir, "results", pdb + ".dat"))
+            output = open(output_filename)
+
+            atpka = False
+            errors = []
+            for line in output:
+                if not atpka:
+                    # Start testing pka values.
+                    if "model-pKa" in line:
+                        atpka = True
+                    continue
+
+                m = re.search('([0-9]+\.[0-9]+)', line)
+                if not m:
+                    break
+
+                expected_value = float(ref.readline())
+                value = float(m.group(0))
+
+                if(value != expected_value):
+                    identity = line[:m.start()].strip()
+                    errors.append("%12s  %8.2f    %8.2f" %
+                            (identity, expected_value, value))
+
+            ref.close()
+            output.close()
+
+            if errors:
+                error_header = "       Group  Expected  Calculated\n"
+                self.Fail("Unexpected pKa values:\n" + error_header +
+                          "\n".join(errors))