Merge pull request #1361 from apdavison/fix-local-test-failures

Fix some tests that fail when running locally

Author: samuelgarcia

neo/test/coretest/test_analogsignal.py

@@ -286,7 +286,7 @@ def test__repr(self):
     def test__pretty(self):
         for i, signal in enumerate(self.signals):
             prepr = pretty(signal)
-            targ = (('AnalogSignal with %d channels of length %d; units %s; datatype %s \n'
+            targ = (('AnalogSignal with %d channels of length %d; units %s; datatype %s\n'
                      '' % (signal.shape[1], signal.shape[0],
                            signal.units.dimensionality.unicode, signal.dtype))
                     + ('annotations: %s\n' % signal.annotations)

neo/test/coretest/test_irregularysampledsignal.py

@@ -806,7 +806,7 @@ def test__divide_signal_by_const_should_preserve_data_complement(self):
     def test__pretty(self):
         res = pretty(self.signal1)
         signal = self.signal1
-        targ = (("IrregularlySampledSignal with %d channels of length %d; units %s; datatype %s \n"
+        targ = (("IrregularlySampledSignal with %d channels of length %d; units %s; datatype %s\n"
                  "" % (signal.shape[1], signal.shape[0], signal.units.dimensionality.unicode,
                        signal.dtype))
                 + ("name: '{}'\ndescription: '{}'\n".format(signal.name, signal.description))

neo/test/iotest/test_bci2000.py neo/test/iotest/test_bci2000io.pyneo/test/iotest/test_bci2000.py renamed to neo/test/iotest/test_bci2000io.py

@@ -5,18 +5,21 @@
 import pathlib
 import unittest
 
+import quantities as pq
+import numpy as np
+
 from neo.io.medio import MedIO
 from neo.test.iotest.common_io_test import BaseTestIO
-from neo.test.iotest.tools import get_test_file_full_path
-from neo.io.proxyobjects import (AnalogSignalProxy,
-                SpikeTrainProxy, EventProxy, EpochProxy)
-from neo import (AnalogSignal, SpikeTrain)
 
-import quantities as pq
-import numpy as np
+try:
+    import dhn_med_py
+    HAVE_DHN_MED = True
+except ImportError:
+    HAVE_DHN_MED = False
 
 
-# This run standard tests, this is mandatory for all IOs
+# This runs standard tests, this is mandatory for all IOs
+@unittest.skipUnless(HAVE_DHN_MED, "requires dhn_med_py package and all its dependencies")
 class TestMedIO(BaseTestIO, unittest.TestCase, ):
     ioclass = MedIO
     entities_to_download = ['med']
@@ -31,22 +34,22 @@ def setUp(self):
         self.dirname = self.get_local_path('med/sine_waves.medd')
         self.dirname2 = self.get_local_path('med/test.medd')
         self.password = 'L2_password'
-                
+
     def test_read_segment_lazy(self):
-    
+
         r = MedIO(self.dirname, self.password)
         seg = r.read_segment(lazy=False)
-        
+
         # There will only be one analogsignal in this reading
         self.assertEqual(len(seg.analogsignals), 1)
         # Test that the correct number of samples are read, 5760000 samps for 3 channels
         self.assertEqual(seg.analogsignals[0].shape[0], 5760000)
         self.assertEqual(seg.analogsignals[0].shape[1], 3)
-        
+
         # Test the first sample value of all 3 channels, which are
         # known to be [-1, -4, -4]
         np.testing.assert_array_equal(seg.analogsignals[0][0][:3], [-1, -4, -4])
-        
+
         for anasig in seg.analogsignals:
             self.assertNotEqual(anasig.size, 0)
         for st in seg.spiketrains:
@@ -61,61 +64,61 @@ def test_read_segment_lazy(self):
             assert ev.name is not None
         for ep in seg.epochs:
             assert ep.name is not None
-          
+
         r.close()
 
     def test_read_block(self):
-  
+
         r = MedIO(self.dirname, self.password)
         bl = r.read_block(lazy=True)
         self.assertTrue(bl.annotations)
-        
+
         for count, seg in enumerate(bl.segments):
             assert seg.name == 'Seg #' + str(count) + ' Block #0'
-            
+
         for anasig in seg.analogsignals:
                 assert anasig.name is not None
-                
+
         # Verify that the block annotations from the MED session are
         # read properly.  There are a lot of annotations, so we'll just
         # spot-check a couple of them.
         assert(bl.annotations['metadata']['recording_country'] == 'United States')
         assert(bl.annotations['metadata']['AC_line_frequency'] == 60.0)
-        
+
         r.close()
-        
+
     def test_read_segment_with_time_slice(self):
         """
         Test loading of a time slice and check resulting times
         """
         r = MedIO(self.dirname, self.password)
         seg = r.read_segment(time_slice=None)
-        
+
         # spike and epoch timestamps are not being read
         self.assertEqual(len(seg.spiketrains), 0)
         self.assertEqual(len(seg.epochs), 1)
         self.assertEqual(len(seg.epochs[0]), 0)
-        
+
         # Test for 180 events (1 per second for 3 minute recording)
         self.assertEqual(len(seg.events), 1)
         self.assertEqual(len(seg.events[0]), 180)
-        
+
         for asig in seg.analogsignals:
             self.assertEqual(asig.shape[0], 5760000)
         n_channels = sum(a.shape[-1] for a in seg.analogsignals)
         self.assertEqual(n_channels, 3)
-            
+
         t_start, t_stop = 500 * pq.ms, 800 * pq.ms
         seg = r.read_segment(time_slice=(t_start, t_stop))
-        
+
         # Test that 300 ms were read, which at 32 kHz, is 9600 samples
         self.assertAlmostEqual(seg.analogsignals[0].shape[0], 9600, delta=1.)
         # Test that it read from 3 channels
         self.assertEqual(seg.analogsignals[0].shape[1], 3)
-            
+
         self.assertAlmostEqual(seg.t_start.rescale(t_start.units), t_start, delta=5.)
         self.assertAlmostEqual(seg.t_stop.rescale(t_stop.units), t_stop, delta=5.)
-            
+
         r.close()
 
 

neo/test/iotest/test_medio.py

@@ -10,6 +10,14 @@
 from neo.test.rawiotest.test_plexon2rawio import TestPlexon2RawIO
 
 
+try:
+    from neo.rawio.plexon2rawio.pypl2 import pypl2lib
+    HAVE_PYPL2 = True
+except (ImportError, TimeoutError):
+    HAVE_PYPL2 = False
+
+
+@unittest.skipUnless(HAVE_PYPL2, "requires pypl package and all its dependencies")
 class TestPlexon2IO(BaseTestIO, unittest.TestCase):
     entities_to_download = TestPlexon2RawIO.entities_to_download
     entities_to_test = TestPlexon2RawIO.entities_to_test

neo/test/iotest/test_plexon2io.py

@@ -4,6 +4,15 @@
 
 from neo.test.rawiotest.common_rawio_test import BaseTestRawIO
 
+try:
+    import sonpy
+    HAVE_SONPY = True
+except ImportError:
+    HAVE_SONPY = False
+
+
+# This runs standard tests, this is mandatory for all IOs
+@unittest.skipUnless(HAVE_SONPY, "requires sonpy package and all its dependencies")
 
 class TestCedRawIO(BaseTestRawIO, unittest.TestCase, ):
     rawioclass = CedRawIO