Improved Exception handling

.gitignore

@@ -38,3 +38,5 @@ MDAnalysis.log
 authors.py
 # Ignore the .DS_Store file in the osx file system
 *.DS_Store
+# ignore files from tests
+.hypothesis/

package/AUTHORS

@@ -124,6 +124,7 @@ Chronological list of authors
   - Rocco Meli
   - Lily Wang
   - Matthijs Tadema
+  - Joao Miguel Correia Teixeira
 
 External code
 -------------

package/CHANGELOG

@@ -13,7 +13,8 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-mm/dd/yy richardjgowers, kain88-de, lilyminium, p-j-smith, bdice
+
+mm/dd/yy richardjgowers, kain88-de, lilyminium, p-j-smith, bdice, joaomcteixeira
 
   * 0.21.0
 
@@ -25,6 +26,9 @@ Fixes
   * PDBQTParser now gives icode TopologyAttrs (Issue #2361)
 
 Enhancements
+  * Uniforms exception handling between Python 2.7 and Python 3: raised exceptions
+    do not contain previous exceptions traceback. Uses six package to handle
+    py27 and py3 compatibility (PR #2357)
   * Expanded selection wildcards to the start and middle of strings (Issue #2370)
   * Added type checking and conversion to Connection TopologyAttrs (Issue #2373)
   * New analysis.hydrogenbonds.HydrogenBondAnalysis class for the analysis of

package/MDAnalysis/analysis/align.py

@@ -190,7 +190,7 @@
 import logging
 
 from six.moves import range, zip, zip_longest
-from six import string_types
+from six import raise_from, string_types
 
 import numpy as np
 
@@ -507,8 +507,12 @@ def alignto(mobile, reference, select="all", weights=None,
             # treat subselection as AtomGroup
             mobile_atoms = subselection.atoms
         except AttributeError:
-            raise TypeError("subselection must be a selection string, an"
-                            " AtomGroup or Universe or None")
+            raise_from(
+                TypeError(
+                    "subselection must be a selection string, an"
+                    " AtomGroup or Universe or None"
+                    ),
+                None)
 
     # _fit_to DOES subtract center of mass, will provide proper min_rmsd
     mobile_atoms, new_rmsd = _fit_to(mobile_coordinates, ref_coordinates,
@@ -1167,7 +1171,7 @@ def get_atoms_byres(g, match_mask=np.logical_not(mismatch_mask)):
                   "Try to improve your selections for mobile and reference.").format(
                       ag1.n_atoms, ag2.n_atoms)
         logger.error(errmsg)
-        raise SelectionError(errmsg)
+        raise_from(SelectionError(errmsg), None)
 
     if np.any(mass_mismatches):
         # Test 2 failed.

package/MDAnalysis/analysis/density.py

@@ -161,7 +161,7 @@
 
 from __future__ import print_function, division, absolute_import
 from six.moves import range, zip
-from six import string_types
+from six import raise_from, string_types
 
 import numpy as np
 import sys
@@ -373,11 +373,14 @@ def _check_set_unit(self, u):
                     units.conversion_factor[unit_type][value]
                     self.units[unit_type] = value
                 except KeyError:
-                    raise ValueError('Unit ' + str(value) + ' of type ' + str(unit_type) + ' is not recognized.')
+                    raise_from(
+                        ValueError('Unit ' + str(value) + ' of type ' + str(unit_type) + ' is not recognized.'),
+                        None,
+                        )
         except AttributeError:
             errmsg = '"unit" must be a dictionary with keys "length" and "density.'
             logger.fatal(errmsg)
-            raise ValueError(errmsg)
+            raise_from(ValueError(errmsg), None)
         # need at least length and density (can be None)
         if 'length' not in self.units:
             raise ValueError('"unit" must contain a unit for "length".')
@@ -486,7 +489,10 @@ def convert_density(self, unit='Angstrom'):
             self.grid *= units.get_conversion_factor('density',
                                                      self.units['density'], unit)
         except KeyError:
-            raise ValueError("The name of the unit ({0!r} supplied) must be one of:\n{1!r}".format(unit, units.conversion_factor['density'].keys()))
+            raise_from(
+                ValueError("The name of the unit ({0!r} supplied) must be one of:\n{1!r}".format(unit, units.conversion_factor['density'].keys())),
+                None,
+                )
         self.units['density'] = unit
 
     def __repr__(self):
@@ -527,13 +533,13 @@ def _set_user_grid(gridcenter, xdim, ydim, zdim, smin, smax):
     try:
         gridcenter = np.asarray(gridcenter, dtype=np.float32)
     except ValueError:
-        raise ValueError("Non-number values assigned to gridcenter")
+        raise_from(ValueError("Non-number values assigned to gridcenter"), None)
     if gridcenter.shape != (3,):
         raise ValueError("gridcenter must be a 3D coordinate")
     try:
         xyzdim = np.array([xdim, ydim, zdim], dtype=np.float32)
     except ValueError:
-        raise ValueError("xdim, ydim, and zdim must be numbers")
+        raise_from(ValueError("xdim, ydim, and zdim must be numbers"), None)
 
     # Set min/max by shifting by half the edge length of each dimension
     umin = gridcenter - xyzdim/2

package/MDAnalysis/analysis/hbonds/hbond_autocorrel.py

@@ -206,6 +206,7 @@
 """
 from __future__ import division, absolute_import
 from six.moves import zip
+from six import raise_from
 
 import numpy as np
 import scipy.optimize
@@ -300,8 +301,8 @@ def __init__(self, universe,
         # check that slicing is possible
         try:
             self.u.trajectory[0]
-        except:
-            raise ValueError("Trajectory must support slicing")
+        except Exception:
+            raise_from(ValueError("Trajectory must support slicing"), None)
 
         self.h = hydrogens
         self.a = acceptors

package/MDAnalysis/analysis/hole.py

@@ -1030,7 +1030,7 @@ def create_vmd_surface(self, filename="hole.vmd", **kwargs):
         except subprocess.CalledProcessError as err:
             os.unlink(tmp_sos)
             logger.fatal("sph_process failed ({0})".format(err.returncode))
-            raise OSError(err.returncode, "sph_process failed")
+            six.raise_from(OSError(err.returncode, "sph_process failed"), None)
         except:
             os.unlink(tmp_sos)
             raise
@@ -1045,7 +1045,7 @@ def create_vmd_surface(self, filename="hole.vmd", **kwargs):
                     stderr=FNULL)
         except subprocess.CalledProcessError as err:
             logger.fatal("sos_triangle failed ({0})".format(err.returncode))
-            raise OSError(err.returncode, "sos_triangle failed")
+            six.raise_from(OSError(err.returncode, "sos_triangle failed"), None)
         finally:
             os.unlink(tmp_sos)
 

package/MDAnalysis/analysis/nuclinfo.py

@@ -107,6 +107,7 @@
 
 import numpy as np
 from math import pi, sin, cos, atan2, sqrt, pow
+from six import raise_from
 
 from MDAnalysis.lib import mdamath
 
@@ -711,8 +712,15 @@ def hydroxyl(universe, seg, i):
     try:
         hydr = h.dihedral.value() % 360
     except ValueError:
-        raise ValueError("Resid {0} does not contain atoms C1', C2', O2', H2' but atoms {1}"
-                         .format(i, str(list(h.atoms))))
+        raise_from(
+            ValueError(
+                (
+                    "Resid {0} does not contain atoms C1', C2', O2', H2' "
+                    "but atoms {1}"
+                    ).format(i, str(list(h.atoms)))
+                ),
+            None)
+
     return hydr
 
 

package/MDAnalysis/analysis/polymer.py

@@ -62,6 +62,7 @@
 """
 from __future__ import division, absolute_import
 from six.moves import range
+from six import raise_from
 
 import numpy as np
 import scipy.optimize
@@ -248,7 +249,7 @@ def _perform_fit(self):
         try:
             self.results
         except AttributeError:
-            raise NoDataError("Use the run method first")
+            raise_from(NoDataError("Use the run method first"), None)
         self.x = np.arange(len(self.results)) * self.lb
 
         self.lp = fit_exponential_decay(self.x, self.results)

package/MDAnalysis/analysis/psa.py

@@ -215,7 +215,7 @@
 
 import six
 from six.moves import range, cPickle, zip
-from six import string_types
+from six import raise_from, string_types
 
 import os
 import warnings
@@ -266,9 +266,14 @@ def get_path_metric_func(name):
     try:
         return path_metrics[name]
     except KeyError as key:
-        raise KeyError('Path metric "{}" not found. Valid selections: {}'
-                       ''.format(key, " ".join('"{}"'.format(n)
-                                               for n in path_metrics.keys())))
+        raise_from(
+            KeyError(
+                'Path metric "{}" not found. Valid selections: {}'.format(
+                    key,
+                    " ".join('"{}"'.format(n) for n in path_metrics.keys())
+                    )
+                ),
+            None)
 
 
 def sqnorm(v, axis=None):
@@ -1865,7 +1870,7 @@ def plot_annotated_heatmap(self, filename=None, linkage='ward',             \
         try:
             import seaborn.apionly as sns
         except ImportError:
-            raise ImportError(
+            raise_from(ImportError(
                 """ERROR --- The seaborn package cannot be found!
 
                 The seaborn API could not be imported. Please install it first.
@@ -1880,7 +1885,9 @@ def plot_annotated_heatmap(self, filename=None, linkage='ward',             \
 
                 and install in the usual manner.
                 """
-            )
+                ),
+                None,
+                )
 
         if self.D is None:
             raise ValueError(
@@ -1974,7 +1981,7 @@ def plot_nearest_neighbors(self, filename=None, idx=0,                      \
         try:
             import seaborn.apionly as sns
         except ImportError:
-            raise ImportError(
+            raise_from(ImportError(
                 """ERROR --- The seaborn package cannot be found!
 
                 The seaborn API could not be imported. Please install it first.
@@ -1989,7 +1996,9 @@ def plot_nearest_neighbors(self, filename=None, idx=0,                      \
 
                 and install in the usual manner.
                 """
-            )
+                ),
+                None,
+                )
 
         colors = sns.xkcd_palette(["cherry", "windows blue"])
 

package/MDAnalysis/analysis/rms.py

@@ -136,7 +136,7 @@
 from __future__ import division, absolute_import
 
 from six.moves import zip
-from six import string_types
+from six import raise_from, string_types
 
 import numpy as np
 
@@ -287,16 +287,24 @@ def process_selection(select):
         try:
             select = {'mobile': select[0], 'reference': select[1]}
         except IndexError:
-            raise IndexError("select must contain two selection strings "
-                             "(reference, mobile)")
+            raise_from(IndexError(
+                "select must contain two selection strings "
+                "(reference, mobile)"),
+                None,
+                )
     elif type(select) is dict:
         # compatability hack to use new nomenclature
         try:
             select['mobile']
             select['reference']
         except KeyError:
-            raise KeyError("select dictionary must contain entries for keys "
-                           "'mobile' and 'reference'.")
+            raise_from(
+                KeyError(
+                    "select dictionary must contain entries for keys "
+                    "'mobile' and 'reference'."
+                    ),
+                None,
+                )
     else:
         raise TypeError("'select' must be either a string, 2-tuple, or dict")
     select['mobile'] = asiterable(select['mobile'])

package/MDAnalysis/auxiliary/XVG.py

@@ -69,6 +69,7 @@
 from __future__ import absolute_import
 
 from six.moves import range
+from six import raise_from
 
 import numbers
 import os
@@ -149,8 +150,13 @@ def _select_data(self, key):
             try:
                 return self._data[key]
             except IndexError:
-                raise ValueError('{} not a valid index for data with {} '
-                                 'columns'.format(key, len(self._data)))
+                raise_from(
+                    ValueError(
+                        '{} not a valid index for data with {} '
+                        'columns'.format(key, len(self._data))
+                        ),
+                    None
+                    )
         else:
             return np.array([self._select_data(i) for i in key])
 

package/MDAnalysis/auxiliary/core.py

@@ -30,7 +30,7 @@
 """
 from __future__ import absolute_import
 
-from six import string_types
+from six import raise_from, string_types
 
 from . import _AUXREADERS
 from ..lib import util
@@ -75,13 +75,19 @@ def get_auxreader_for(auxdata=None, format=None):
         try:
             return _AUXREADERS[format]
         except KeyError:
-            raise ValueError("Unknown auxiliary data format for auxdata: "
-                             "{0}".format(auxdata))
+            raise_from(
+                ValueError(
+                    "Unknown auxiliary data format for auxdata: "
+                    "{0}".format(auxdata)),
+                None
+                )
     else:
         try:
             return _AUXREADERS[format]
         except KeyError:
-            raise ValueError("Unknown auxiliary data format {0}".format(format))
+            raise_from(
+                ValueError("Unknown auxiliary data format {0}".format(format)),
+                None)
 
 def auxreader(auxdata, format=None, **kwargs):
     """ Return an auxiliary reader instance for *auxdata*.

package/MDAnalysis/coordinates/CRD.py

@@ -32,6 +32,7 @@
 from __future__ import absolute_import
 
 from six.moves import zip, range
+from six import raise_from
 
 import itertools
 import numpy as np
@@ -80,9 +81,13 @@ def _read_first_frame(self):
                         coords_list.append(np.array(line[45:100].split()[0:3], dtype=float))
                     else:
                         coords_list.append(np.array(line[20:50].split()[0:3], dtype=float))
-                except:
-                    raise ValueError("Check CRD format at line {0}: {1}"
-                                     "".format(linenum, line.rstrip()))
+                except Exception:
+                    raise_from(
+                        ValueError(
+                            "Check CRD format at line {0}: {1}"
+                            "".format(linenum, line.rstrip())),
+                        None
+                        )
 
         self.n_atoms = len(coords_list)