Added exception and unittest for dist_mat_to_vec of analysis/psa.py (…

…Part of MDAnalysis#597)

package/AUTHORS

@@ -81,6 +81,7 @@ Chronological list of authors
   - Shantanu Srivastava
  2017
   - Utkarsh Bansal
+  - Vedant Rathore
 
 External code
 -------------

package/CHANGELOG

@@ -15,7 +15,7 @@ The rules for this file:
 ------------------------------------------------------------------------------
 ??/??/16 kain88-de, fiona-naughton, richardjgowers, tyler.je.reddy, jdetle
          euhruska, orbeckst, rbrtdlg, jbarnoud, wouterboomsma, shanmbic,
-         dotsdl, manuel.nuno.melo, utkbansal
+         dotsdl, manuel.nuno.melo, utkbansal, vedantrathore
 
   * 0.16.0
 
@@ -61,6 +61,7 @@ Enhancements
   * Added groupby method to Group objects. (PR #1112)
 
 Fixes
+  * Argument validation of dist_mat_to_vec is fixed (#597 PR #1183)
   * Give correct error when the topology file format is not recognized (Issue #982)
   * Give correct error when file doesn't exist/ has bad permissions (Issue #981)
   * Improvement of analysis/waterdynamics module (Issue #935)

package/MDAnalysis/analysis/psa.py

@@ -212,6 +212,7 @@
 from six.moves import range, cPickle
 
 import numpy as np
+import warnings
 
 import MDAnalysis
 import MDAnalysis.analysis.align
@@ -581,7 +582,7 @@ def dist_mat_to_vec(N, i, j):
         error_str = "Matrix indices are invalid; i and j must be greater than 0 and N must be greater the 2"
         raise ValueError(error_str)
 
-    if i > N or j > N:
+    if (j > i and (i > N - 1 or j > N)) or (j < i and (i > N or j > N - 1)):
         err_str = "Matrix indices are out of range; i and j must be less than"  \
                 + " N = {0:d}".format(N)
         raise ValueError(err_str)
@@ -591,7 +592,7 @@ def dist_mat_to_vec(N, i, j):
         warn_str = "Column index entered (j = {:d} is smaller than row index"   \
                  + " (i = {:d}). Using symmetric element in upper triangle of"  \
                  + " distance matrix instead: i --> j, j --> i"
-        warnings.warn(war_str.format(j, i))
+        warnings.warn(warn_str.format(j, i))
         return (N*j) + i - (j+2)*(j+1)/2
     else:
         err_str = "Error in processing matrix indices; i and j must be integers"\

testsuite/AUTHORS

@@ -73,7 +73,7 @@ Chronological list of authors
 
 2017
   - Utkarsh Bansal
-
+  - Vedant Rathore
 
 External code
 -------------

testsuite/CHANGELOG

@@ -14,7 +14,7 @@ and https://github.com/MDAnalysis/mdanalysis/wiki/UnitTests
 
 ------------------------------------------------------------------------------
 ??/??/16 jbarnoud, orbeckst, fiona-naughton, manuel.nuno.melo, richardjgowers
-         tyler.je.reddy, utkbansal
+         tyler.je.reddy, utkbansal, vedantrathore
 
   * 0.16
     - added two unit tests for MDAnalysis.analysis.polymer

testsuite/MDAnalysisTests/analysis/test_psa.py

@@ -144,7 +144,7 @@ def test_dist_mat_to_vec_func_out_of_bounds(self):
         with self.assertRaises(ValueError):
             PSA.dist_mat_to_vec(5, -1, 2)
 
-        # Check if i is negative
+        # Check if j is negative
         with self.assertRaises(ValueError):
             PSA.dist_mat_to_vec(5, 1, -2)