Changed tests to eliminate known failures

caused by BioPython, updated CHANGELOG.

package/MDAnalysis/coordinates/PDB.py

@@ -1055,16 +1055,19 @@ 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):
+    warnings.warn('PrimitivePDBReader is identical to the PDBReader,'
+                  'it is deprecated in favor of the shorter name'
+                  'removal targeted for version 0.15.0',
+                  category=DeprecationWarning)
     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):
+        warnings.warn('PrimitivePDBWriter is identical to the Writer,'
+                      'it is deprecated in favor of the shorter name'
+                      'removal targeted for version 0.15.0',
+                      category=DeprecationWarning)
     format = 'Permissive_PDB'
 
 class ExtendedPDBReader(PDBReader):

package/MDAnalysis/topology/PrimitivePDBParser.py

@@ -62,17 +62,18 @@
 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):
+    warnings.warn('PrimitivePDBParser is identical to the PDBParser,'
+                  'it is deprecated in favor of the shorter name',
+                  category=DeprecationWarning)
     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):
+    warnings.warn('PrimitivePDBParser module is identical to the PDBParser,'
+                  'module, it is deprecated in favor of the shorter name,'
+                  'please use the parse_conect function of that class',
+                  category=DeprecationWarning)
     """parse a CONECT record from pdbs
 
     Parameters

testsuite/CHANGELOG

@@ -13,9 +13,9 @@ Also see https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysisTests
 and https://github.com/MDAnalysis/mdanalysis/wiki/UnitTests
 
 ------------------------------------------------------------------------------
-??/??/16 orbeckst, jbarnoud, pedrishi, fiona-naughton
+??/??/16 jdetle, orbeckst, jbarnoud, pedrishi, fiona-naughton
   * 0.15.0
-
+    - removed known failures from BioPython
     - 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

@@ -31,18 +31,19 @@ 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):
@@ -247,7 +248,7 @@ def test_check_coordinate_limits_max(self):
     def test_check_header_title_multiframe(self):
         """Check whether HEADER and TITLE are written just once in a multi-
         frame PDB file (Issue 741)"""
-        u = mda.Universe(PSF,DCD, permissive=True) 
+        u = mda.Universe(PSF,DCD, permissive=True)
         pdb = mda.Writer(self.outfile, multiframe=True)
         protein = u.select_atoms("protein and name CA")
         for ts in u.trajectory[:5]:
@@ -713,11 +714,11 @@ 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

@@ -334,7 +334,7 @@ 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)