add deprecation tests

testsuite/MDAnalysisTests/analysis/test_align.py

@@ -20,6 +20,8 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 from __future__ import absolute_import, print_function
+import warnings
+import os.path
 
 import MDAnalysis
 import MDAnalysis.analysis.align as align
@@ -33,11 +35,13 @@
 import numpy as np
 from nose.plugins.attrib import attr
 
-import os.path
-
 from MDAnalysisTests.datafiles import PSF, DCD, FASTA
 from MDAnalysisTests import executable_not_found, parser_not_found, tempdir
 
+# I want to catch all warnings in the tests. If this is not set at the start it
+# could cause test that check for warnings to fail.
+warnings.simplefilter('always')
+
 
 class TestRotationMatrix(object):
     def __init__(self):
@@ -119,6 +123,17 @@ def test_rmsd(self):
                                    center=True, superposition=True)
         assert_almost_equal(rmsd[1], rmsd_sup_weight, 6)
 
+    def test_rmsd_deprecated(self):
+        last_atoms_weight = self.universe.atoms.masses
+        A = self.universe.trajectory[0]
+        B = self.reference.trajectory[-1]
+        with warnings.catch_warnings(record=True) as warn:
+            warnings.simplefilter('always')
+            rmsd = align.alignto(self.universe, self.reference, mass_weighted=True)
+        assert_equal(len(warn), 1)
+        rmsd_sup_weight = rms.rmsd(A, B,  weights=last_atoms_weight,
+                                   center=True, superposition=True)
+        assert_almost_equal(rmsd[1], rmsd_sup_weight, 6)
 
     @dec.slow
     @attr('issue')
@@ -187,6 +202,21 @@ def test_AlignTraj_weighted(self):
         self._assert_rmsd(fitted, -1, 6.929083032629219,
                           weights=self.universe.atoms.masses)
 
+    def test_AlignTraj_weigts_deprecated(self):
+        with warnings.catch_warnings(record=True) as warn:
+            warnings.simplefilter('always')
+            x = align.AlignTraj(self.universe, self.reference,
+                                filename=self.outfile, mass_weighted=True).run()
+        assert_equal(len(warn), 1)
+        fitted = MDAnalysis.Universe(PSF, self.outfile)
+        assert_almost_equal(x.rmsd[0], 0,  decimal=3)
+        assert_almost_equal(x.rmsd[-1], 6.9033, decimal=3)
+
+        self._assert_rmsd(fitted, 0, 0.0,
+                          weights=self.universe.atoms.masses)
+        self._assert_rmsd(fitted, -1, 6.929083032629219,
+                          weights=self.universe.atoms.masses)
+
     def test_AlignTraj_partial_fit(self):
         # fitting on a partial selection should still write the whole topology
         align.AlignTraj(self.universe, self.reference, select='resid 1-20',

testsuite/MDAnalysisTests/analysis/test_rms.py

@@ -20,9 +20,12 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 from __future__ import print_function
-
 from six.moves import range
 
+import warnings
+import os
+import sys
+
 import MDAnalysis
 import MDAnalysis as mda
 from MDAnalysis.analysis import rms, align
@@ -33,13 +36,14 @@
 
 import numpy as np
 
-import os
-import sys
-
 from MDAnalysis.exceptions import SelectionError, NoDataError
 from MDAnalysisTests.datafiles import GRO, XTC, rmsfArray, PSF, DCD
 from MDAnalysisTests import tempdir, parser_not_found
 
+# I want to catch all warnings in the tests. If this is not set at the start it
+# could cause test that check for warnings to fail.
+warnings.simplefilter('always')
+
 
 class Testrmsd(object):
     def __init__(self):
@@ -191,6 +195,18 @@ def test_mass_weighted_and_save(self):
                                   err_msg="error: rmsd profile should match " +
                                           "test values")
 
+    def test_mass_weighted_and_save_deprecated(self):
+        with warnings.catch_warnings(record=True) as warn:
+            warnings.simplefilter('always')
+            RMSD = MDAnalysis.analysis.rms.RMSD(self.universe, select='name CA',
+                                                step=49, mass_weighted=True).run()
+        assert(len(warn), 1)
+        RMSD.save(self.outfile)
+        saved = np.loadtxt(self.outfile)
+        assert_array_almost_equal(RMSD.rmsd, saved, 4,
+                                  err_msg="error: rmsd profile should match " +
+                                          "test values")
+
     def test_rmsd_group_selections(self):
         RMSD = MDAnalysis.analysis.rms.RMSD(self.universe,
                                             groupselections=