Convert libmdaxdr test

package/CHANGELOG

@@ -39,6 +39,9 @@ Changes
   * use fast scipy.io.netcdf pure python implementation for reading of Amber
     netcdf3 trajctories instead of netCDF4 but use netCDF4 for fast
     writing (if available) or fall back to netcdf (see also Issue #506)
+  * libmdaxdr classes now accept more argument types for a write (PR #1442)
+  * libmdaxdr classes now raise EOFError when accessing another frame after
+  the end of the file. Used to raise IOError.
 
 
 mm/dd/17 richardjgowers, rathann, jbarnoud, orbeckst, utkbansal

package/MDAnalysis/lib/formats/libmdaxdr.pyx

@@ -227,7 +227,7 @@ cdef class _XDRFile:
             opening_mode = b'w'
         else:
             raise IOError('mode must be one of "r" or "w", you '
-                             'supplied {}'.format(mode))
+                          'supplied {}'.format(mode))
         self.mode = mode
 
         if self.mode == 'r':
@@ -293,9 +293,11 @@ cdef class _XDRFile:
         cdef int64_t offset
         if frame == 0:
             offset = 0
+        elif frame < 0:
+            raise IOError("Can't seek to negative frame")
         else:
             if frame >= self.offsets.size:
-                raise IOError('Trying to seek over max number of frames')
+                raise EOFError('Trying to seek over max number of frames')
             offset = self.offsets[frame]
         self.reached_eof = False
         ok = xdr_seek(self.xfp, offset, SEEK_SET)
@@ -446,7 +448,7 @@ cdef class TRRFile(_XDRFile):
         IOError
         """
         if self.reached_eof:
-            raise IOError('Reached last frame in TRR, seek to 0')
+            raise EOFError('Reached last frame in TRR, seek to 0')
         if not self.is_open:
             raise IOError('No file opened')
         if self.mode != 'r':
@@ -502,9 +504,13 @@ cdef class TRRFile(_XDRFile):
 
         Parameters
         ----------
-        xyz : ndarray, shape=(`n_atoms`, 3)
-            cartesion coordinates
-        box : ndarray, shape=(3, 3)
+        xyz : array_like, shape=(`n_atoms`, 3), optional
+            cartesion coordinates. Only written if not ``None``.
+        velocity : array_like, shape=(`n_atoms`, 3), optional
+            cartesion velocities. Only written if not ``None``.
+        forces : array_like, shape=(`n_atoms`, 3), optional
+            cartesion forces. Only written if not ``None``.
+        box : array_like, shape=(3, 3)
             Box vectors for this frame
         step : int
             current step number, 1 indexed
@@ -536,15 +542,19 @@ cdef class TRRFile(_XDRFile):
         cdef np.ndarray forces_helper
 
         if xyz is not None:
+            xyz = np.asarray(xyz)
             xyz_helper = np.ascontiguousarray(xyz, dtype=DTYPE)
             xyz_ptr = <float*>xyz_helper.data
         if velocity is not None:
+            velocity = np.asarray(velocity)
             velocity_helper = np.ascontiguousarray(velocity, dtype=DTYPE)
             velocity_ptr = <float*>velocity_helper.data
         if forces is not None:
+            forces = np.asarray(forces)
             forces_helper = np.ascontiguousarray(forces, dtype=DTYPE)
             forces_ptr = <float*>forces_helper.data
 
+        box = np.asarray(box)
         cdef np.ndarray box_helper = np.ascontiguousarray(box, dtype=DTYPE)
         cdef float* box_ptr = <float*>box_helper.data
 
@@ -651,7 +661,7 @@ cdef class XTCFile(_XDRFile):
         IOError
         """
         if self.reached_eof:
-            raise IOError('Reached last frame in XTC, seek to 0')
+            raise EOFError('Reached last frame in XTC, seek to 0')
         if not self.is_open:
             raise IOError('No file opened')
         if self.mode != 'r':
@@ -685,9 +695,9 @@ cdef class XTCFile(_XDRFile):
 
         Parameters
         ----------
-        xyz : ndarray, shape=(`n_atoms`, 3)
+        xyz : array_like, shape=(`n_atoms`, 3)
             cartesion coordinates
-        box : ndarray, shape=(3, 3)
+        box : array_like, shape=(3, 3)
             Box vectors for this frame
         step : int
             current step number, 1 indexed
@@ -712,6 +722,9 @@ cdef class XTCFile(_XDRFile):
             raise IOError('File opened in mode: {}. Writing only allow '
                           'in mode "w"'.format('self.mode'))
 
+        xyz = np.asarray(xyz)
+        box = np.asarray(box)
+
         cdef DTYPE_T[:, ::1] xyz_view = np.ascontiguousarray(xyz, dtype=DTYPE)
         cdef DTYPE_T[:, ::1] box_view = np.ascontiguousarray(box, dtype=DTYPE)
 

testsuite/MDAnalysisTests/datafiles.py

@@ -103,9 +103,7 @@
     "CONECT",  # HIV Reverse Transcriptase with inhibitor
     "TRZ", "TRZ_psf",
     "TRIC",
-    "XTC_single_frame",
     "XTC_multi_frame",
-    "TRR_single_frame",
     "TRR_multi_frame",
     "merge_protein", "merge_ligand", "merge_water",
     "mol2_molecules", "mol2_molecule", "mol2_broken_molecule",
@@ -235,13 +233,9 @@
 XTC_sub_sol = resource_filename(__name__, 'data/cobrotoxin.xtc')
 PDB_sub_sol = resource_filename(__name__, 'data/cobrotoxin.pdb')
 PDB_xlserial = resource_filename(__name__, 'data/xl_serial.pdb')
-XTC_single_frame = resource_filename(
-    __name__, 'data/xtc_test_only_single_frame_10_atoms.xtc')
 XTC_multi_frame = resource_filename(
     __name__, 'data/xtc_test_only_10_frame_10_atoms.xtc'
 )
-TRR_single_frame = resource_filename(
-    __name__, 'data/trr_test_only_single_frame_10_atoms.trr')
 TRR_multi_frame = resource_filename(
     __name__, 'data/trr_test_only_10_frame_10_atoms.trr'
 )