cleanup related to BioPDB removal (#777)

- Changed tests to eliminate known failures caused by BioPython
- Updated CHANGELOGs and fixed wrong version number in AtomGroup.py,
- fixed indentation issue in PDB.py
- Fixed doc references to version strings and the permissive flags,
- got rid of extraneous text in PrimitivePDBParser, fixed scope of warnings
- Used boolean property of collections as suggested by QC

package/MDAnalysis/coordinates/PDB.py

@@ -56,15 +56,13 @@
 Implementations
 ---------------
 
-PDB I/O is available in the form of the":ref:`permissive<permissive>`"
-Reader/Writers.
+PDB I/O is available in the form of the Simple PDB Reader/Writers.
 
-..deprecated:: 0.14.1
-Only available in the form of the ":ref:":ref:`permissive<permissive>`"
-Readers and Writers, see below
+..deprecated:: 0.15.0
+Readers amd writers solely available in the form of
+Simple Readers and Writers, see below.
 
-.. _permissive:
-Simple (permissive) PDB Reader and Writer
+Simple PDB Reader and Writer
 -----------------------------------------
 A pure-Python implementation for PDB files commonly encountered in MD
 simulations comes under the names :class:`PDBReader` and
@@ -132,7 +130,7 @@
    :members:
 
 
-..deprecated:: 0.14.1
+..deprecated:: 0.15.0
     Setting the flag "permissive_pdb_reader" in :data:`MDAnalysis.core.flags`
     (see :ref:`flags-label`) to ``False``::
 
@@ -262,7 +260,7 @@ def __init__(self, filename, **kwargs):
         with util.openany(filename, 'rt') as pdbfile:
             for i, line in enumerate(pdbfile):
                 line = line.strip()  # Remove extra spaces
-                if len(line) == 0:  # Skip line if empty
+                if not line:  # Skip line if empty
                     continue
                 record = line[:6].strip()
 
@@ -326,7 +324,7 @@ def __init__(self, filename, **kwargs):
             self.convert_pos_from_native(self.ts._unitcell[:3])  # in-place ! (only lengths)
 
         # No 'MODEL' entries
-        if len(frames) == 0:
+        if not frames:
             frames[0] = 0
 
         self.frames = frames
@@ -736,12 +734,12 @@ def _update_frame(self, obj):
 
         Attributes initialized/updated:
 
-        * :attr:`PrimitivePDBWriter.obj` (the entity that provides topology information *and*
+        * :attr:`PDBWriter.obj` (the entity that provides topology information *and*
           coordinates, either a :class:`~MDAnalysis.core.AtomGroup.AtomGroup` or a whole
           :class:`~MDAnalysis.core.AtomGroup.Universe`)
-        * :attr:`PrimitivePDBWriter.trajectory` (the underlying trajectory
+        * :attr:`PDBWriter.trajectory` (the underlying trajectory
           :class:`~MDAnalysis.coordinates.base.Reader`)
-        * :attr:`PrimitivePDBWriter.timestep` (the underlying trajectory
+        * :attr:`PDBWriter.timestep` (the underlying trajectory
           :class:`~MDAnalysis.coordinates.base.Timestep`)
 
         Before calling :meth:`write_next_timestep` this method **must** be
@@ -855,14 +853,14 @@ def write_next_timestep(self, ts=None, **kwargs):
         :Keywords:
           *ts*
              :class:`base.Timestep` object containing coordinates to be written to trajectory file;
-             if ``None`` then :attr:`PrimitivePDBWriter.ts`` is tried.
+             if ``None`` then :attr:`PDBWriter.ts`` is tried.
           *multiframe*
              ``False``: write a single frame (default); ``True`` behave as a trajectory writer
 
         .. Note::
 
            Before using this method with another :class:`base.Timestep` in the *ts*
-           argument, :meth:`PrimitivePDBWriter._update_frame` *must* be called
+           argument, :meth:`PDBWriter._update_frame` *must* be called
            with the :class:`~MDAnalysis.core.AtomGroup.AtomGroup.Universe` as
            its argument so that topology information can be gathered.
         '''
@@ -1027,7 +1025,7 @@ def END(self):
         Only a single END record is written. Calling END multiple times has no
         effect. Because :meth:`~PDBWriter.close` also calls this
         method right before closing the file it is recommended to *not* call
-        :meth:`~PrimitivePDBWriter.END` explicitly.
+        :meth:`~PDBWriter.END` explicitly.
 
         .. _END: http://www.wwpdb.org/documentation/format32/sect11.html#END
 
@@ -1055,16 +1053,23 @@ def CONECT(self, conect):
         conect = "".join(conect)
         self.pdbfile.write(self.fmt['CONECT'].format(conect))
 
-warnings.warn('PrimitivePDBReader is identical to the PDBReader,'
-              'it is deprecated in favor of the shorter name',
-              category=DeprecationWarning)
+
 class PrimitivePDBReader(PDBReader):
+    def __init__(self, filename, *args, **kwargs):
+        warnings.warn('PrimitivePDBReader is identical to the PDBReader,'
+                  ' it is deprecated in favor of the shorter name'
+                  ' removal targeted for version 0.16.0',
+                  category=DeprecationWarning)
+        super(PrimitivePDBReader, self).__init__(filename, *args, **kwargs)
     format = 'Permissive_PDB'
 
-warnings.warn('PrimitivePDBWriter is now identical to the PDBWriter,'
-              'it is deprecated in favor of the shorter name',
-              category=DeprecationWarning)
 class PrimitivePDBWriter(PDBWriter):
+    def __init__(self, filename, *args, **kwargs):
+        warnings.warn('PrimitivePDBWriter is identical to the Writer,'
+                      'it is deprecated in favor of the shorter name'
+                      ' removal targeted for version 0.16.0',
+                      category=DeprecationWarning)
+        super(PrimitivePDBWriter, self).__init__(filename, *args, **kwargs)
     format = 'Permissive_PDB'
 
 class ExtendedPDBReader(PDBReader):

package/MDAnalysis/core/AtomGroup.py

@@ -1429,7 +1429,7 @@ def ids(self):
 
         """
         out = np.array([atom.serial for atom in self._atoms])
-        
+
         if not any(out):
             out = np.array([atom.id for atom in self._atoms])
 
@@ -3334,7 +3334,7 @@ def split(self, level):
             return [AtomGroup([a]) for a in self]
 
         if level in ('resid', 'segid'):
-            warnings.warn("'resid' or 'segid' are no longer allowed levels " 
+            warnings.warn("'resid' or 'segid' are no longer allowed levels "
                           "in version 0.16.0; instead give "
                           "'residue' or 'segment', respectively.",
                           DeprecationWarning)
@@ -4196,8 +4196,12 @@ def __init__(self, *args, **kwargs):
 
           *permissive*
              currently only relevant to PDBs, Readers and Writers and Parsers
-             returned by setting ::permisive = False are depecrated in favor
+             returned by setting ::permisive = False are deprecated in favor
              of their ::permissive = True counterparts
+             ..deprecated:: 0.15.0
+             Readers amd writers solely available in the form of
+             Simple Readers and Writers, see below. Permissive flag
+             will soon be removed.
 
           *topology_format*
              provide the file format of the topology file; ``None`` guesses it from the file
@@ -4260,7 +4264,7 @@ def __init__(self, *args, **kwargs):
         .. versionchanged:: 0.11.0
            Added the *is_anchor* and *anchor_name* keywords for finer behavior
            control when unpickling instances of :class:`MDAnalysis.core.AtomGroup.AtomGroup`.
-        .. versionchanged:: 0.14.1
+        .. versionchanged:: 0.15.0
            *permissive* set to ``True`` and set to ``False`` both yield permissive
            PDB readers, writers and parsers
         """

package/MDAnalysis/topology/PDBParser.py

@@ -100,7 +100,7 @@ def _parseatoms(self):
             resid_prev = 0  # resid looping hack
             for i, line in enumerate(f):
                 line = line.strip()  # Remove extra spaces
-                if len(line) == 0:  # Skip line if empty
+                if not line:  # Skip line if empty
                     continue
                 record = line[:6].strip()
 

package/MDAnalysis/topology/PrimitivePDBParser.py

@@ -45,9 +45,8 @@
    :members:
    :inherited-members:
 
-..deprecated:: 0.14.1
-    PrimitivePDBParser now has the same behavior as PDBParser, and will be
-    absent from future versions
+..deprecated:: 0.15.0
+    PDBParser has been replaced with PrimitivePDBParser.
 """
 
 from __future__ import absolute_import, print_function
@@ -62,17 +61,17 @@
 from .base import TopologyReader
 
 
-warnings.warn('PrimitivePDBParser is identical to the PDBParser,'
-              'it is deprecated in favor of the shorter name',
-              category=DeprecationWarning)
+
 class PrimitivePDBParser(PDBParser.PDBParser):
+    def __init__(self, *args, **kwargs):
+        warnings.warn('PrimitivePDBParser is identical to the PDBParser,'
+                    ' it is deprecated in favor of the shorter name',
+                    category=DeprecationWarning)
+        super(PDBParser.PDBParser, self).__init__(*args, **kwargs)
     format = 'Permissive_PDB'
 
-warnings.warn('PrimitivePDBParser is identical to the PDBParser,'
-              'it is deprecated in favor of the shorter name,'
-              'please use the parse_conect function of that class',
-              category=DeprecationWarning)
 def _parse_conect(conect):
+
     """parse a CONECT record from pdbs
 
     Parameters

testsuite/CHANGELOG

@@ -16,6 +16,7 @@ and https://github.com/MDAnalysis/mdanalysis/wiki/UnitTests
 ??/??/16 orbeckst, jbarnoud, pedrishi, fiona-naughton, jdetle
   * 0.15.0
     - Added test for weighted rmsd (issue #814)
+    - removed biopython PDB parser for coordinates and topology (Issue #777)
     - metadata update: link download_url to GitHub releases so that
       Depsy recognizes contributors (issue #749) and added
       @richardjgowers as maintainer

testsuite/MDAnalysisTests/coordinates/test_pdb.py

@@ -30,18 +30,19 @@ def setUp(self):
         # http://www.wwpdb.org/documentation/format32/sect9.html#ATOM
         self.prec = 3
 
-    def test_uses_Biopython(self):
+
+    def test_uses_PDBReader(self):
         from MDAnalysis.coordinates.PDB import PDBReader
 
         assert_(isinstance(self.universe.trajectory, PDBReader),
-                "failed to choose Biopython PDBReader")
+                "failed to choose PDBReader")
+
 
-    @knownfailure("Biopython PDB reader does not parse CRYST1", AssertionError)
     def test_dimensions(self):
         assert_almost_equal(
             self.universe.trajectory.ts.dimensions, RefAdKSmall.ref_unitcell,
             self.prec,
-            "Biopython reader failed to get unitcell dimensions from CRYST1")
+            "PDBReader failed to get unitcell dimensions from CRYST1")
 
 
 class _PDBMetadata(TestCase, Ref4e43):
@@ -712,11 +713,11 @@ def setUp(self):
         # http://www.wwpdb.org/documentation/format32/sect9.html#ATOM
         self.prec = 3
 
-    def test_uses_Biopython(self):
+    def test_uses_PDBReader(self):
         from MDAnalysis.coordinates.PDB import PDBReader
 
         assert_(isinstance(self.universe.trajectory, PDBReader),
-                "failed to choose Biopython PDBReader")
+                "failed to choose PDBReader")
 
 
 class TestPDBWriterOccupancies(object):

testsuite/MDAnalysisTests/test_streamio.py

@@ -333,7 +333,7 @@ def test_PrimitivePDBReader(self):
         u = MDAnalysis.Universe(streamData.as_NamedStream('PDB'))
         assert_equal(u.atoms.n_atoms, self.ref_n_atoms)
 
-    @knownfailure()
+
     def test_PDBReader(self):
         try:
             u = MDAnalysis.Universe(streamData.as_NamedStream('PDB'), permissive=False)