Issue 1940 pickle chain reader

testsuite/MDAnalysisTests/coordinates/base.py

@@ -24,6 +24,7 @@
 import numpy as np
 import pytest
 from six.moves import zip, range
+from six.moves import cPickle as pickle
 from unittest import TestCase
 from numpy.testing import (assert_equal, assert_almost_equal,
                            assert_array_almost_equal, assert_allclose)
@@ -100,8 +101,8 @@ def test_coordinates(self):
                             err_msg="wrong coordinates for A10:CA")
 
     def test_distances(self):
-        NTERM = self.universe.atoms.N[0]
-        CTERM = self.universe.atoms.C[-1]
+        NTERM = self.universe.select_atoms("name N")[0]
+        CTERM = self.universe.select_atoms("name C")[-1]
         d = mda.lib.mdamath.norm(NTERM.position - CTERM.position)
         assert_almost_equal(d,
                             self.ref_distances['endtoend'],
@@ -424,6 +425,16 @@ def test_add_another_transformations_raises_ValueError(self, transformed):
         with pytest.raises(ValueError):
             transformed.add_transformations(translate([2,2,2]))
 
+    @pytest.mark.parametrize("protocol", range(1, pickle.HIGHEST_PROTOCOL+1))
+    def test_pickle(self, reader, protocol):
+        try:
+            s = pickle.dumps(reader, protocol=protocol)
+        except TypeError as err:
+            pytest.fail("Reader cannot be pickled with protocol={}\n{}".format(
+                protocol, err))
+        assert len(s) > 1000
+
+
 class MultiframeReaderTest(BaseReaderTest):
     def test_last_frame(self, ref, reader):
         ts = reader[-1]

testsuite/MDAnalysisTests/coordinates/test_chainreader.py

@@ -21,6 +21,7 @@
 #
 from __future__ import division, absolute_import
 from six.moves import zip
+from six.moves import cPickle as pickle
 
 import numpy as np
 import os
@@ -119,8 +120,8 @@ def test_write_dcd(self, universe, tmpdir):
                 ts_new._pos,
                 self.prec,
                 err_msg="Coordinates disagree at frame {0:d}".format(
-                    ts_orig.frame))       
-    
+                    ts_orig.frame))
+
     def test_transform_iteration(self, universe, transformed):
         vector = np.float32([10,10,10])
         # # Are the transformations applied and
@@ -135,15 +136,15 @@ def test_transform_iteration(self, universe, transformed):
             frame = ts.frame
             ref = universe.trajectory[frame].positions + vector
             assert_almost_equal(ts.positions, ref, decimal = 6)
-    
+
     def test_transform_slice(self, universe, transformed):
         vector = np.float32([10,10,10])
         # what happens when we slice the trajectory?
         for ts in transformed.trajectory[5:17:3]:
             frame = ts.frame
             ref = universe.trajectory[frame].positions + vector
             assert_almost_equal(ts.positions, ref, decimal = 6)
-    
+
     def test_transform_switch(self, universe, transformed):
         vector = np.float32([10,10,10])
         # grab a frame:
@@ -154,13 +155,22 @@ def test_transform_switch(self, universe, transformed):
         assert_almost_equal(transformed.trajectory[10].positions, newref, decimal = 6)
         # what happens when we comeback to the previous frame?
         assert_almost_equal(transformed.trajectory[2].positions, ref, decimal = 6)
-    
+
     def test_transfrom_rewind(self, universe, transformed):
         vector = np.float32([10,10,10])
         ref = universe.trajectory[0].positions + vector
         transformed.trajectory.rewind()
         assert_almost_equal(transformed.trajectory.ts.positions, ref, decimal = 6)
 
+    @pytest.mark.parametrize("protocol", range(1, pickle.HIGHEST_PROTOCOL+1))
+    def test_pickle(self, universe, protocol):
+        try:
+            s = pickle.dumps(universe.trajectory, protocol=protocol)
+        except TypeError as err:
+            pytest.fail("ChainReader cannot be pickled with protocol={}\n{}".format(
+                protocol, err))
+        assert len(s) > 1000
+
 class TestChainReaderCommonDt(object):
     common_dt = 100.0
     prec = 3

testsuite/MDAnalysisTests/coordinates/test_crd.py

@@ -29,10 +29,61 @@
     assert_equal,
 )
 
+import numpy as np
+
 import MDAnalysis as mda
+from MDAnalysis.coordinates.CRD import CRDReader, CRDWriter
+from MDAnalysis.coordinates.base import Timestep
 
-from MDAnalysisTests.datafiles import CRD
+from MDAnalysisTests.datafiles import PSF, CRD, COORDINATES_ADK
 from MDAnalysisTests import make_Universe
+from MDAnalysisTests.coordinates.base import (
+    BaseReference, BaseReaderTest, BaseWriterTest,
+)
+
+
+class CRDReference(BaseReference):
+    def __init__(self):
+        super(CRDReference, self).__init__()
+        self.trajectory = CRD
+        self.topology = PSF
+        self.reader = CRDReader
+        self.writer = CRDWriter
+        self.ext = 'crd'
+        self.n_frames = 1
+        self.totaltime = 0
+        self.n_atoms = 3341
+        self.container_format = True
+        self.dimensions = np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0])
+        self.volume = 0.0
+
+        self.first_frame = Timestep(self.n_atoms)
+        self.first_frame.positions = np.loadtxt(COORDINATES_ADK, delimiter=',',
+                                                dtype=np.float32)
+        self.first_frame.frame = 0
+        self.first_frame.aux.lowf = self.aux_lowf_data[0]
+        self.first_frame.aux.highf = self.aux_highf_data[0]
+
+        self.last_frame = self.first_frame.copy()
+
+
+class TestCRDReader(BaseReaderTest):
+    @staticmethod
+    @pytest.fixture(scope='class')
+    def ref():
+        return CRDReference()
+
+    def test_time(self, ref, reader):
+        u = mda.Universe(ref.topology, ref.trajectory)
+        assert_equal(u.trajectory.time, 0.0,
+                     "wrong time of the frame")
+
+    def test_full_slice(self, ref, reader):
+        u = mda.Universe(ref.topology, ref.trajectory)
+        trj_iter = u.trajectory[:]
+        frames = [ts.frame for ts in trj_iter]
+        assert_equal(frames, np.arange(u.trajectory.n_frames))
+
 
 
 class TestCRDWriter(object):

testsuite/MDAnalysisTests/data/coordinates/test_topology.pdb

@@ -1,8 +1,8 @@
 MODEL
 CRYST1 80.000   80.000   80.000  60.00  60.00  90.00
-ATOM      1 CA   MET     1      00.000  00.000  00.000  1.00 84.71
-ATOM      2 CA   ARG     2      01.000  01.000  01.000  1.00 68.59
-ATOM      3 CA   ILE     3      02.000  02.000  02.000  1.00 48.30
-ATOM      4 CA   LYS     4      03.000  03.000  03.000  1.00 49.38
-ATOM      5 CA   LEU     5      04.000  04.000  04.000  1.00 42.10
+ATOM      1 CA   MET     1       0.000   0.000   0.000  1.00 84.71
+ATOM      2 CA   ARG     2       1.000   1.000   1.000  1.00 68.59
+ATOM      3 CA   ILE     3       2.000   2.000   2.000  1.00 48.30
+ATOM      4 CA   LYS     4       3.000   3.000   3.000  1.00 49.38
+ATOM      5 CA   LEU     5       4.000   4.000   4.000  1.00 42.10
 END

testsuite/MDAnalysisTests/datafiles.py

@@ -37,6 +37,8 @@
 from __future__ import absolute_import
 
 __all__ = [
+    "COORDINATES_ADK", # numpy/csv file with 3341 coordinates from CRD
+                       # np.savetxt("data/adk_positions.csv.gz", u.atoms.positions, delimiter=",")
     "PSF", "DCD", "CRD",  # CHARMM (AdK example, DIMS trajectory from JMB 2009 paper)
     "DCD2", # CHARMM (AdK example, DIMS trajectory from PLOS Comput Biol paper)
     "PSF_notop", "PSF_BAD",  # Same as PSF but no bonds etc, malformed version of previous
@@ -67,7 +69,6 @@
     "PDB_chainidrepeat",  # Issue #1107
     "PDB", "GRO", "XTC", "TRR", "TPR", "GRO_velocity",  # Gromacs (AdK)
     "GRO_incomplete_vels",
-    "COORDINATES_GRO_BZ2",
     "GRO_large", #atom number truncation at > 100,000 particles, Issue 550
     "GRO_residwrap",  # resids wrapping because of 5 digit field (Issue #728)
     "GRO_residwrap_0base",  # corner case of #728 with resid=0 for first atom
@@ -136,6 +137,7 @@
     "COORDINATES_XYZ_BZ2",
     "COORDINATES_GRO",
     "COORDINATES_GRO_INCOMPLETE_VELOCITY",
+    "COORDINATES_GRO_BZ2",
     "Martini_membrane_gro", # for testing the leaflet finder
     "COORDINATES_XTC",
     "COORDINATES_TRR",
@@ -185,6 +187,8 @@
 COORDINATES_DCD = resource_filename(__name__, 'data/coordinates/test.dcd')
 COORDINATES_TOPOLOGY = resource_filename(__name__, 'data/coordinates/test_topology.pdb')
 
+COORDINATES_ADK = resource_filename(__name__, 'data/adk_positions.csv.gz')
+
 PSF = resource_filename(__name__, 'data/adk.psf')
 PSF_notop = resource_filename(__name__, 'data/adk_notop.psf')
 PSF_BAD = resource_filename(__name__, 'data/adk_notop_BAD.psf')