From 61bb87524818f1c24b48b9a737ba044fefce2a91 Mon Sep 17 00:00:00 2001
From: Mike Beachy <mike.beachy@schrodinger.com>
Date: Sat, 22 Feb 2014 17:33:18 -0500
Subject: [PATCH] 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/__init__.py     |  0
 Tests/pkacalc_test.py | 68 +++++++++++++++++++++++++++++++++++++++++++
 Tests/runtest.py      | 64 +++++++++++++++++++---------------------
 setup.py              |  1 +
 4 files changed, 99 insertions(+), 34 deletions(-)
 create mode 100644 Tests/__init__.py
 create mode 100644 Tests/pkacalc_test.py

diff --git a/Tests/__init__.py b/Tests/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/Tests/pkacalc_test.py b/Tests/pkacalc_test.py
new file mode 100644
index 0000000..04f896e
--- /dev/null
+++ b/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))
diff --git a/Tests/runtest.py b/Tests/runtest.py
index e73517a..3ea030c 100755
--- a/Tests/runtest.py
+++ b/Tests/runtest.py
@@ -9,43 +9,39 @@ from subprocess import call
 import os, re
 import sys
 
-pdbs = ['1FTJ-Chain-A',
-        '1HPX',
-        '4DFR']
-
-for pdb in pdbs:
-  print('')
-  print('RUNNING '+pdb)
-
-  # Run pka calculation
-  call([sys.executable, '../scripts/propka31.py','pdb/'+pdb+'.pdb'], stdout = open(pdb+'.out', 'w+'))
-
-  # Test pka predictiona
-  result = open('results/'+pdb+'.dat','r')
-  atpka = False
-  for line in open(pdb+'.pka', 'r').readlines():
-    if not atpka:
-      if "model-pKa" in line:
-        # test pka
-        atpka = True
-        continue
-      else:
-        continue
-    if "-" in line:
-      # done testing
-      atpka = False
-      continue
-
-    r = float(result.readline())
-    m = re.search('([0-9]+\.[0-9]+)', line)
-
-    if(float(m.group(0)) != r):
-      print(" ERR:")
-      print(line)
-      print(" "+"should be: "+str(r))
+if __name__ == "__main__":
+    pdbs = ['1FTJ-Chain-A',
+            '1HPX',
+            '4DFR']
 
+    for pdb in pdbs:
+        print('')
+        print('RUNNING '+pdb)
 
+        # Run pka calculation
+        call([sys.executable, '../scripts/propka31.py','pdb/'+pdb+'.pdb'], stdout = open(pdb+'.out', 'w+'))
 
+        # Test pka predictiona
+        result = open('results/'+pdb+'.dat','r')
+        atpka = False
+        for line in open(pdb+'.pka', 'r').readlines():
+            if not atpka:
+                if "model-pKa" in line:
+                    # test pka
+                    atpka = True
+                    continue
+                else:
+                    continue
+            if "-" in line:
+                # done testing
+                atpka = False
+                continue
 
+            r = float(result.readline())
+            m = re.search('([0-9]+\.[0-9]+)', line)
 
+            if(float(m.group(0)) != r):
+                print(" ERR:")
+                print(line)
+                print(" "+"should be: "+str(r))
 
diff --git a/setup.py b/setup.py
index 1bee359..94e7ea4 100644
--- a/setup.py
+++ b/setup.py
@@ -48,4 +48,5 @@ using the tutorial http://propka.ki.ku.dk/~luca/wiki/index.php/PROPKA_3.1_Tutori
             ],
         },
       zip_safe=True,
+      test_suite="Tests",
 )