more PSA tests

- additional tests
- pylint fix in PSA code
- tests for load() still xfail

package/MDAnalysis/analysis/psa.py

@@ -214,7 +214,7 @@
 from __future__ import division, absolute_import, print_function
 
 import six
-from six.moves import range, cPickle
+from six.moves import range, cPickle, zip
 from six import string_types
 
 import os
@@ -1353,10 +1353,10 @@ def __init__(self, universes, reference=None, ref_select='name CA',
 
         # Set default directory names for storing topology/reference structures,
         # fitted trajectories, paths, distance matrices, and plots
-        self.datadirs = {'fitted_trajs' : '/fitted_trajs',
-                         'paths' : '/paths',
-                         'distance_matrices' : '/distance_matrices',
-                         'plots' : '/plots'}
+        self.datadirs = {'fitted_trajs' : 'fitted_trajs',
+                         'paths' : 'paths',
+                         'distance_matrices' : 'distance_matrices',
+                         'plots' : 'plots'}
         for dir_name, directory in six.iteritems(self.datadirs):
             try:
                 full_dir_name = os.path.join(self.targetdir, dir_name)
@@ -1465,7 +1465,7 @@ def generate_paths(self, align=False, filename='fitted', infix='', weights=None,
         for i, u in enumerate(self.universes):
             p = Path(u, self.u_reference, ref_select=self.ref_select,
                      path_select=self.path_select, ref_frame=ref_frame)
-            trj_dir = self.targetdir + self.datadirs['fitted_trajs']
+            trj_dir = os.path.join(self.targetdir, self.datadirs['fitted_trajs'])
             postfix = '{0}{1}{2:03n}'.format(infix, '_psa', i+1)
             top_name, fit_trj_name = p.run(align=align, filename=filename,
                                            postfix=postfix,
@@ -1635,7 +1635,7 @@ def save_result(self, filename=None):
 
         """
         filename = filename or 'psa_distances'
-        head = self.targetdir + self.datadirs['distance_matrices']
+        head = os.path.join(self.targetdir, self.datadirs['distance_matrices'])
         outfile = os.path.join(head, filename)
         if self.D is None:
             raise NoDataError("Distance matrix has not been calculated yet")
@@ -1661,9 +1661,13 @@ def save_paths(self, filename=None):
         -------
         filename : str
 
+        See Also
+        --------
+        load
+
         """
         filename = filename or 'path_psa'
-        head = self.targetdir + self.datadirs['paths']
+        head = os.path.join(self.targetdir, self.datadirs['paths'])
         outfile = os.path.join(head, filename)
         if self.paths is None:
             raise NoDataError("Paths have not been calculated yet")
@@ -1682,6 +1686,13 @@ def save_paths(self, filename=None):
     def load(self):
         """Load fitted paths specified by 'psa_path-names.pkl' in
         :attr:`PSAnalysis.targetdir`.
+
+        All filenames are determined by :class:`PSAnalysis`.
+
+        See Also
+        --------
+        save_paths
+
         """
         if not os.path.exists(self._paths_pkl):
             raise NoDataError("Fitted trajectories cannot be loaded; save file" +
@@ -1690,7 +1701,7 @@ def load(self):
         self.paths = [np.load(pname) for pname in self.path_names]
         if os.path.exists(self._labels_pkl):
             self.labels = np.load(self._labels_pkl)
-        print("Loaded paths from " + self._paths_pkl)
+        logger.info("Loaded paths from %r", self._paths_pkl)
 
 
     def plot(self, filename=None, linkage='ward', count_sort=False,
@@ -1796,7 +1807,7 @@ def plot(self, filename=None, linkage='ward', count_sort=False,
             tic.tick1On = tic.tick2On = False
 
         if filename is not None:
-            head = self.targetdir + self.datadirs['plots']
+            head = os.path.join(self.targetdir, self.datadirs['plots'])
             outfile = os.path.join(head, filename)
             savefig(outfile, dpi=300, bbox_inches='tight')
 
@@ -1907,7 +1918,7 @@ def plot_annotated_heatmap(self, filename=None, linkage='ward',             \
             tic.tick1On = tic.tick2On = False
 
         if filename is not None:
-            head = self.targetdir + self.datadirs['plots']
+            head = os.path.join(self.targetdir, self.datadirs['plots'])
             outfile = os.path.join(head, filename)
             savefig(outfile, dpi=600, bbox_inches='tight')
 
@@ -2011,7 +2022,7 @@ def plot_nearest_neighbors(self, filename=None, idx=0,                      \
         tight_layout()
 
         if filename is not None:
-            head = self.targetdir + self.datadirs['plots']
+            head = os.path.join(self.targetdir, self.datadirs['plots'])
             outfile = os.path.join(head, filename)
             savefig(outfile, dpi=300, bbox_inches='tight')
 

testsuite/MDAnalysisTests/analysis/test_psa.py

@@ -135,6 +135,54 @@ def test_reversal_frechet(self, frech_matrix):
         err_msg = "Frechet distances did not increase after path reversal"
         assert frech_matrix[1,2] >= frech_matrix[0,1], err_msg
 
+    def test_get_num_paths(self, psa):
+        assert psa.get_num_paths() == 3
+
+    def test_get_paths(self, psa):
+        paths = psa.get_paths()
+        assert len(paths) == 3
+        assert isinstance(paths, list)
+
+    def test_psa_pairs_ValueError(self, psa):
+        with pytest.raises(ValueError):
+            psa.psa_pairs
+
+    def test_psa_pairs(self, psa):
+        psa.run_pairs_analysis()
+        assert len(psa.psa_pairs) == 3
+
+    def test_hausdorff_pairs_ValueError(self, psa):
+        with pytest.raises(ValueError):
+            psa.hausdorff_pairs
+
+    def test_hausdorff_pairs(self, psa):
+        psa.run_pairs_analysis(hausdorff_pairs=True)
+        assert len(psa.hausdorff_pairs) == 3
+
+    def test_nearest_neighbors_ValueError(self, psa):
+        with pytest.raises(ValueError):
+            psa.nearest_neighbors
+
+    def test_nearest_neighbors(self, psa):
+        psa.run_pairs_analysis(neighbors=True)
+        assert len(psa.nearest_neighbors) == 3
+
+    @pytest.mark.xfail
+    def test_load(self, psa):
+        """Test that the automatically saved files can be loaded"""
+        expected_path_names = psa.path_names[:]
+        expected_paths = [p.copy() for p in psa.paths]
+        psa.save_paths()
+        psa.load()
+        assert psa.path_names == expected_path_names
+        # manually compare paths because
+        #         assert_almost_equal(psa.paths, expected_paths, decimal=6)
+        # raises a ValueError in the assertion code itself
+        assert len(psa.paths) == len(expected_paths)
+        for ipath, (observed, expected) in enumerate(zip(psa.paths, expected_paths)):
+            assert_almost_equal(observed, expected, decimal=6,
+                                err_msg="loaded path {} does not agree with input".format(ipath))
+
     def test_dendrogram_produced(self, plot_data):
         """Test whether Dendrogram dictionary object was produced"""
         err_msg = "Dendrogram dictionary object was not produced"