Added travis and coveralls

.coveragerc

@@ -0,0 +1,14 @@
+[run]
+branch = True
+source = MDAnalysis
+
+exclude_lines =
+    pragma: no cover
+
+[report]
+exclude_lines =
+    pragma: no cover
+
+    def __repr__
+    raise NotImplementedError
+    if __name__ == .__main__.: 

.travis.yml

@@ -0,0 +1,26 @@
+language: python
+python:
+  - "2.6"
+  - "2.7"
+# command to install dependencies
+before_install:
+  - sudo apt-get update -qq
+  - sudo apt-get install -q -y gfortran libhdf5-serial-dev libnetcdf-dev liblapack-dev libatlas-dev
+  - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
+  - chmod +x miniconda.sh
+  - ./miniconda.sh -b
+  - export PATH=/home/travis/miniconda/bin:$PATH
+  - conda update --yes conda
+install:
+  - if [[ $TRAVIS_PYTHON_VERSION == '2.6' ]]; then conda create --yes -q -n pyenv mkl python=2.6 numpy=1.6.2 scipy=0.11 nose=1.1; fi
+  - if [[ $TRAVIS_PYTHON_VERSION == '2.7' ]]; then conda create --yes -q -n pyenv mkl python=2.7 numpy=1.9.1 scipy=0.14.0 nose=1.3.4; fi
+  - source activate pyenv
+  - conda install --yes python=$TRAVIS_PYTHON_VERSION cython biopython matplotlib networkx netcdf4
+  - pip install package/
+  - pip install testsuite/
+  - pip install coveralls
+# command to run tests
+script:
+  - nosetests --with-coverage --cover-package MDAnalysis
+after_success:
+  coveralls 

README.rst

@@ -2,6 +2,8 @@
   MDAnalysis Repository README
 ================================
 
+|build| |cov|
+
 MDAnalysis_ is a Python toolkit to analyze molecular dynamics
 trajectories generated by CHARMM, Amber, NAMD, LAMMPS, or Gromacs.
 
@@ -34,3 +36,10 @@ MDAnalysis issue tracker.)
 .. _Issue 87: https://github.com/MDAnalysis/mdanalysis/issues/87
 .. _MDAnalysis: http://www.MDAnalysis.org
 .. _LICENSE: https://github.com/MDAnalysis/mdanalysis/blob/master/LICENSE
+
+.. |build| image:: https://travis-ci.org/richardjgowers/mdanalysis.svg?branch=develop
+    :alt: Build Status
+    :target: https://travis-ci.org/richardjgowers/mdanalysis
+.. |cov|   image:: https://coveralls.io/repos/richardjgowers/mdanalysis/badge.svg?branch=develop
+    :alt: Coverage Status
+    :target: https://coveralls.io/r/richardjgowers/mdanalysis?branch=develop

package/MDAnalysis/coordinates/DCD.py

@@ -250,7 +250,7 @@ def __init__(self, filename, numatoms, start=0, step=1,
                 self.step = 1
                 self.delta = MDAnalysis.core.units.convert(dt, 'ps', 'AKMA')
             else:
-                raise ValueError("DCDWriter: dt must be > 0, not {}".format(dt))
+                raise ValueError("DCDWriter: dt must be > 0, not {0}".format(dt))
         else:
             self.step = step
             self.delta = delta

package/MDAnalysis/coordinates/MOL2.py

@@ -117,9 +117,11 @@ def parse_block(self, block):
 
         atom_lines, bond_lines = sections["atom"], sections["bond"]
         if not len(atom_lines):
-            raise Exception("The mol2 (starting at line {}) block has no atoms".format(block["start_line"]))
+            raise Exception("The mol2 (starting at line {0}) block has no atoms"
+                            "".format(block["start_line"]))
         if not len(bond_lines):
-            raise Exception("The mol2 (starting at line {}) block has no bonds".format(block["start_line"]))
+            raise Exception("The mol2 (starting at line {0}) block has no bonds"
+                            "".format(block["start_line"]))
 
         coords = []
         for a in atom_lines:
@@ -284,8 +286,8 @@ def encode_block(self, obj):
         bonds = sorted([(bond[0].id, bond[1].id, bond.order) for bond in bonds])
         mapping = dict([(a.id, i) for i, a in enumerate(obj.atoms)])
 
-        atom_lines = ["{:>4} {:>4} {:>13.4f} {:>9.4f} {:>9.4f} {:>4} {} {} "
-                      "{:>7.4f}".format(mapping[a.id] + 1, a.name,
+        atom_lines = ["{0:>4} {1:>4} {2:>13.4f} {3:>9.4f} {4:>9.4f} {5:>4} {6} {7} "
+                      "{8:>7.4f}".format(mapping[a.id] + 1, a.name,
                                         float(a.pos[0]),
                                         float(a.pos[1]),
                                         float(a.pos[2]), a.type,
@@ -295,10 +297,11 @@ def encode_block(self, obj):
         atom_lines = "\n".join(atom_lines)
 
         bonds = [(atom1, atom2, order) for atom1, atom2, order in bonds if atom1 in mapping and atom2 in mapping]
-        bond_lines = ["{:>5} {:>5} {:>5} {:>2}".format(bid + 1,
-                                                       mapping[atom1] + 1,
-                                                       mapping[atom2] + 1,
-                                                       order) for bid, (atom1, atom2, order) in enumerate(bonds)]
+        bond_lines = ["{0:>5} {1:>5} {2:>5} {3:>2}"
+                      "".format(bid + 1,
+                                mapping[atom1] + 1,
+                                mapping[atom2] + 1,
+                                order) for bid, (atom1, atom2, order) in enumerate(bonds)]
         bond_lines = ["@<TRIPOS>BOND"] + bond_lines + ["\n"]
         bond_lines = "\n".join(bond_lines)
 
@@ -312,7 +315,7 @@ def encode_block(self, obj):
         molecule = traj.molecule[traj.frame]
         check_sums = molecule[1].split()
         check_sums[0], check_sums[1] = str(len(obj.atoms)), str(len(bonds))
-        molecule[1] = "{}\n".format(" ".join(check_sums))
+        molecule[1] = "{0}\n".format(" ".join(check_sums))
         molecule = ["@<TRIPOS>MOLECULE\n"] + molecule
 
         return "".join(molecule) + atom_lines + bond_lines + "".join(substructure)

package/MDAnalysis/coordinates/base.py

@@ -565,7 +565,7 @@ def __getitem__(self, frame):
 
     def _read_frame(self, frame):
         """Move to *frame* and fill timestep with data."""
-        raise TypeError("{} does not support direct frame indexing."
+        raise TypeError("{0} does not support direct frame indexing."
                         "".format(self.__class__.__name__))
         # Example implementation in the DCDReader:
         #self._jump_to_frame(frame)
@@ -589,7 +589,7 @@ def _iter(start=start, stop=stop, step=step):
                 for i in xrange(start, stop, step):
                     yield self[i]
             except TypeError:  # if _read_frame not implemented
-                raise TypeError("{} does not support slicing."
+                raise TypeError("{0} does not support slicing."
                                 "".format(self.__class__.__name__))
         return _iter()
 
@@ -996,7 +996,7 @@ class SingleFrameReader(Reader):
 
     .. versionadded:: 0.10.0
     """
-    _err = "{} only contains a single frame"
+    _err = "{0} only contains a single frame"
 
     def __init__(self, filename, convert_units=None, **kwargs):
         self.filename = filename

package/MDAnalysis/coordinates/xdrfile/core.py

@@ -422,8 +422,8 @@ def __init__(self, filename, convert_units=None, sub=None, **kwargs):
             if not isinstance(sub, numpy.ndarray) or len(sub.shape) != 1 or sub.dtype.kind != 'i':
                 raise TypeError("sub MUST be a single dimensional numpy array of integers")
             if len(sub) > self._trr_numatoms:
-                raise ValueError("sub MUST be less than or equal to the number of actual trr atoms, {} in this case".
-                                 format(self._trr_numatoms))
+                raise ValueError("sub MUST be less than or equal to the number of actual trr atoms,"
+                                 " {0} in this case".format(self._trr_numatoms))
             if numpy.max(sub) >= self._trr_numatoms or numpy.min(sub) < 0:
                 raise IndexError("sub contains out-of-range elements for the given trajectory")
             # sub appears to be valid
@@ -524,7 +524,7 @@ def delta(self):
 
     def _offset_filename(self):
         head, tail = os.path.split(self.filename)
-        return os.path.join(head, '.{}_offsets.pkl'.format(tail))
+        return os.path.join(head, '.{0}_offsets.pkl'.format(tail))
 
     def _store_offsets(self):
         """Stores offsets for trajectory as a hidden file in the same directory
@@ -638,7 +638,7 @@ def load_offsets(self, filename, check=False):
                 key = 'size'
                 conditions = (os.path.getsize(self.filename) == offsets[key]) and conditions
             except KeyError:
-                warnings.warn("Offsets in file '{}' not suitable; missing {}.".format(filename, key))
+                warnings.warn("Offsets in file '{0}' not suitable; missing {1}.".format(filename, key))
                 return
 
             # if conditions not met, abort immediately
@@ -650,7 +650,7 @@ def load_offsets(self, filename, check=False):
         try:
             self._offsets = offsets['offsets']
         except KeyError:
-            warnings.warn("Missing key 'offsets' in file '{}'; aborting load of offsets.".format(filename))
+            warnings.warn("Missing key 'offsets' in file '{0}'; aborting load of offsets.".format(filename))
             return
         self._numframes = len(self._offsets)
 

package/MDAnalysis/core/AtomGroup.py

@@ -470,7 +470,7 @@ def __repr__(self):
                     idx=self.number + 1, name=self.name, t=self.type,
                     rname=self.resname, rid=self.resid, sid=self.segid,
                     altloc="" if not self.altLoc
-                    else " and altloc {}".format(self.altLoc)))
+                    else " and altloc {0}".format(self.altLoc)))
 
     def __cmp__(self, other):
         return cmp(self.number, other.number)
@@ -483,7 +483,7 @@ def __hash__(self):
 
     def __add__(self, other):
         if not (isinstance(other, Atom) or isinstance(other, AtomGroup)):
-            raise TypeError('Can only concatenate Atoms (not "{}")'
+            raise TypeError('Can only concatenate Atoms (not "{0}")'
                             ' to AtomGroup'.format(other.__class__.__name__))
         if isinstance(other, Atom):
             return AtomGroup([self, other])
@@ -592,7 +592,7 @@ def universe(self):
             return self.__universe
         else:
             raise AttributeError(
-                "Atom {} is not assigned to a Universe".format(self.number))
+                "Atom {0} is not assigned to a Universe".format(self.number))
 
     @universe.setter
     def universe(self, universe):
@@ -957,7 +957,7 @@ def __contains__(self, other):
 
     def __add__(self, other):
         if not (isinstance(other, Atom) or isinstance(other, AtomGroup)):
-            raise TypeError('Can only concatenate AtomGroup (not "{}") to'
+            raise TypeError('Can only concatenate AtomGroup (not "{0}") to'
                             ' AtomGroup'.format(other.__class__.__name__))
         if isinstance(other, AtomGroup):
             return AtomGroup(self._atoms + other._atoms)
@@ -2441,7 +2441,7 @@ def wrap(self, compound="atoms", center="com", box=None):
         elif compound.lower() == 'fragments':
             objects = self.fragments
         else:
-            raise ValueError("Unrecognised compound definition: {}"
+            raise ValueError("Unrecognised compound definition: {0}"
                              "Please use one of 'group' 'residues' 'segments'"
                              "or 'fragments'".format(compound))
 
@@ -2450,7 +2450,7 @@ def wrap(self, compound="atoms", center="com", box=None):
         elif center.lower() in ('cog', 'centroid', 'centerofgeometry'):
             centers = numpy.vstack([o.centerOfGeometry() for o in objects])
         else:
-            raise ValueError("Unrecognised center definition: {}"
+            raise ValueError("Unrecognised center definition: {0}"
                              "Please use one of 'com' or 'cog'".format(center))
         centers = centers.astype(numpy.float32)
 
@@ -2589,7 +2589,7 @@ def write(self, filename=None, format="PDB",
             selection = True
 
         if not (coords or selection):
-            raise ValueError("No writer found for format: {}".format(filename))
+            raise ValueError("No writer found for format: {0}".format(filename))
         else:
             writer.write(self.atoms)
             if coords:  # only these writers have a close method
@@ -3130,7 +3130,8 @@ def __getattr__(self, attr):
         if len(seglist) == 0:
             return super(SegmentGroup, self).__getattr__(attr)
         if len(seglist) > 1:
-            warnings.warn("SegmentGroup: Multiple segments with the same name {}; a combined, NON-CONSECUTIVE "
+            warnings.warn("SegmentGroup: Multiple segments with the same name {0};"
+                          " a combined, NON-CONSECUTIVE "
                           "Segment is returned.".format(attr), category=SelectionWarning)
             #return Segment(sum([s.residues for s in seglist])) ### FIXME: not working yet, need __add__
             return seglist[0]
@@ -3341,13 +3342,13 @@ def __init__(self, *args, **kwargs):
             with parser(self.filename, universe=self) as p:
                 self._topology = p.parse()
         except IOError as err:
-            raise IOError("Failed to load from the topology file {}"
-                          " with parser {}.\n"
-                          "Error: {}".format(self.filename, parser, err))
+            raise IOError("Failed to load from the topology file {0}"
+                          " with parser {1}.\n"
+                          "Error: {2}".format(self.filename, parser, err))
         except ValueError as err:
-            raise ValueError("Failed to construct topology from file {}"
-                             " with parser {} \n"
-                             "Error: {}".format(self.filename, parser, err))
+            raise ValueError("Failed to construct topology from file {0}"
+                             " with parser {1} \n"
+                             "Error: {2}".format(self.filename, parser, err))
 
         # Generate atoms, residues and segments
         self._init_topology()
@@ -3549,7 +3550,7 @@ def add(self, other):
             def update(self, other):
                 self.ats.update(other.ats)
 
-        f = {a: None for a in self.atoms}  # each atom starts with its own list
+        f = dict.fromkeys(self.atoms, None)  # each atom starts with its own list
 
         for a1, a2 in bonds:  # Iterate through all bonds
             if not (f[a1] or f[a2]):  # New set made here
@@ -3565,10 +3566,10 @@ def update(self, other):
                 continue
             else:  # If they are both in different fragments, combine fragments
                 f[a1].update(f[a2])
-                f.update({a: f[a1] for a in f[a2]})
+                f.update(dict((a, f[a1]) for a in f[a2]))
 
                 # Lone atoms get their own fragment
-        f.update({a: _fragset((a,)) for a, val in f.items() if not val})
+        f.update(dict((a, _fragset((a,))) for a, val in f.items() if not val))
 
         # All the unique values in f are the fragments
         frags = tuple([AtomGroup(list(a.ats)) for a in set(f.values())])
@@ -3871,13 +3872,14 @@ def load_new(self, filename, **kwargs):
         kwargs['numatoms'] = self.atoms.numberOfAtoms()
         self.trajectory = reader(filename, **kwargs)    # unified trajectory API
         if self.trajectory.numatoms != self.atoms.numberOfAtoms():
-            raise ValueError("The topology and {} trajectory files don't"
+            raise ValueError("The topology and {form} trajectory files don't"
                              " have the same number of atoms!\n"
-                             "Topology number of atoms {}\n"
-                             "Trajectory: {} Number of atoms {}".format(
-                                 self.trajectory.format,
-                                 len(self.atoms),
-                                 filename, self.trajectory.numatoms))
+                             "Topology number of atoms {top_natoms}\n"
+                             "Trajectory: {fname} Number of atoms {trj_natoms}".format(
+                                 form=self.trajectory.format,
+                                 top_natoms=len(self.atoms),
+                                 fname=filename,
+                                 trj_natoms=self.trajectory.numatoms))
 
         return filename, self.trajectory.format
 
@@ -4032,7 +4034,7 @@ def selectAtoms(self, sel, *othersel, **selgroups):
     def __repr__(self):
         return "<Universe with {natoms} atoms{bonds}>".format(
             natoms=len(self.atoms),
-            bonds=" and {} bonds".format(len(self.bonds)) if self.bonds else "")
+            bonds=" and {0} bonds".format(len(self.bonds)) if self.bonds else "")
 
     def __getstate__(self):
         raise NotImplementedError

package/MDAnalysis/core/distances.py

@@ -108,10 +108,10 @@ def _check_array(coords, desc):
        float32 data
     """
     if (coords.ndim != 2 or coords.shape[1] != 3):
-        raise ValueError("{} must be a sequence of 3 dimensional coordinates"
+        raise ValueError("{0} must be a sequence of 3 dimensional coordinates"
                          "".format(desc))
     if coords.dtype != numpy.float32:
-        raise TypeError("{} must be of type float32".format(desc))
+        raise TypeError("{0} must be of type float32".format(desc))
 
 
 def _check_results_array(results, size):
@@ -123,7 +123,7 @@ def _check_results_array(results, size):
     """
     if results.shape != size:
         raise ValueError("Result array has incorrect size,"
-                         "should be {}, got {}".format(size, results.shape))
+                         "should be {0}, got {1}".format(size, results.shape))
     if results.dtype != numpy.float64:
         raise TypeError("Results array must be of type float64")
 
@@ -134,7 +134,7 @@ def _check_lengths_match(*arrays):
 
     if not all([a.shape == ref for a in arrays]):
         raise ValueError("Input arrays must all be same shape"
-                         "Got {}".format([a.shape for a in arrays]))
+                         "Got {0}".format([a.shape for a in arrays]))
 
 def distance_array(reference, configuration, box=None, result=None):
     """Calculate all distances between a reference set and another configuration.

package/MDAnalysis/core/util.py

@@ -302,7 +302,8 @@ def anyopen(datasource, mode='r', reset=True):
                     try:
                         stream.seek(0L)
                     except (AttributeError, IOError):
-                        warnings.warn("Stream {}: not guaranteed to be at the beginning.".format(filename),
+                        warnings.warn("Stream {0}: not guaranteed to be at the beginning."
+                                      "".format(filename),
                                       category=StreamWarning)
         else:
             stream = None
@@ -543,7 +544,8 @@ def reset(self):
             try:
                 self.stream.seek(0L)  # typical file objects
             except (AttributeError, IOError):
-                warnings.warn("NamedStream {}: not guaranteed to be at the beginning.".format(self.name),
+                warnings.warn("NamedStream {0}: not guaranteed to be at the beginning."
+                              "".format(self.name),
                               category=StreamWarning)
 
     # access the stream

package/MDAnalysis/topology/CRDParser.py

@@ -70,8 +70,8 @@ def parse(self):
                 try:
                     serial, TotRes, resName, name, x, y, z, chainID, resSeq, tempFactor = r.read(line)
                 except:
-                    raise ValueError("Check CRD format at line {}: {}".format(
-                        linenum, line.rstrip()))
+                    raise ValueError("Check CRD format at line {0}: {1}"
+                                     "".format(linenum, line.rstrip()))
 
                 atomtype = guess_atom_type(name)
                 mass = guess_atom_mass(name)