NeuralEnsemble · apdavison · Jul 4, 2019 · Jan 29, 2019 · May 23, 2019 · May 15, 2019
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -23,11 +23,11 @@ jobs:
       - checkout
 
       # Download and cache dependencies
-      - restore_cache:
-          keys:
-          - v1-dependencies-{{ checksum "requirements.txt" }}
-          # fallback to using the latest cache if no exact match is found
-          - v1-dependencies-
+      #- restore_cache:
+      #    keys:
+      #    - v1-dependencies-{{ checksum "requirements.txt" }}
+      #    # fallback to using the latest cache if no exact match is found
+      #    - v1-dependencies-
 
       - restore-cache:
           keys:
@@ -82,11 +82,11 @@ jobs:
       - checkout
 
       # Download and cache dependencies
-      - restore_cache:
-          keys:
-          - v1-py2-dependencies-{{ checksum "requirements.txt" }}
-          # fallback to using the latest cache if no exact match is found
-          - v1-py2-dependencies-
+      #- restore_cache:
+      #    keys:
+      #    - v1-py2-dependencies-{{ checksum "requirements.txt" }}
+      #    # fallback to using the latest cache if no exact match is found
+      #    - v1-py2-dependencies-
 
       - restore-cache:
           keys:

diff --git a/neo/core/basesignal.py b/neo/core/basesignal.py
@@ -255,7 +255,7 @@ def merge(self, other):
                 raise MergeError("Cannot merge a lazy object with a real object.")
         if other.units != self.units:
             other = other.rescale(self.units)
-        stack = np.hstack(map(np.array, (self, other)))
+        stack = np.hstack((self.magnitude, other.magnitude))
         kwargs = {}
         for name in ("name", "description", "file_origin"):
             attr_self = getattr(self, name)

diff --git a/neo/core/irregularlysampledsignal.py b/neo/core/irregularlysampledsignal.py
@@ -436,7 +436,7 @@ def merge(self, other):
                 raise MergeError("Cannot merge a lazy object with a real object.")
         if other.units != self.units:
             other = other.rescale(self.units)
-        stack = np.hstack(map(np.array, (self, other)))
+        stack = np.hstack((self.magnitude, other.magnitude))
         kwargs = {}
         for name in ("name", "description", "file_origin"):
             attr_self = getattr(self, name)

diff --git a/neo/io/klustakwikio.py b/neo/io/klustakwikio.py
@@ -203,8 +203,8 @@ def _load_spike_times(self, fetfilename):
             names = ['fet%d' % n for n in range(nbFeatures)]
             names.append('spike_time')
 
-            # Load into recarray
-            data = mlab.csv2rec(f, names=names, skiprows=1, delimiter=' ')
+        # Load into recarray
+        data = np.recfromtxt(fetfilename, names=names, skip_header=1, delimiter=' ')
 
         # get features
         features = np.array([data['fet%d' % n] for n in range(nbFeatures)])

diff --git a/neo/test/generate_datasets.py b/neo/test/generate_datasets.py
@@ -52,7 +52,8 @@ def generate_one_simple_segment(seg_name='segment 0', supported_objects=[], nb_a
 
                                 epoch_types={'animal state': ['Sleep', 'Freeze', 'Escape'],
                                              'light': ['dark', 'lighted']},
-                                epoch_duration_range=[.5, 3.],
+                                epoch_duration_range=[.5, 3.],  
+                                # this should be multiplied by pq.s, no?
 
                                 array_annotations={'valid': np.array([True, False]),
                                                    'number': np.array(range(5))}
@@ -107,7 +108,7 @@ def generate_one_simple_segment(seg_name='segment 0', supported_objects=[], nb_a
             durations = []
             while t < duration:
                 times.append(t)
-                dur = rand() * np.diff(epoch_duration_range)
+                dur = rand() * (epoch_duration_range[1] - epoch_duration_range[0])
                 dur += epoch_duration_range[0]
                 durations.append(dur)
                 t = t + dur
@@ -116,8 +117,9 @@ def generate_one_simple_segment(seg_name='segment 0', supported_objects=[], nb_a
             assert len(times) == len(durations)
             assert len(times) == len(labels)
             epc = Epoch(times=pq.Quantity(times, units=pq.s),
-                        durations=pq.Quantity([x[0] for x in durations], units=pq.s),
-                        labels=labels, )
+                        durations=pq.Quantity(durations, units=pq.s),
+                        labels=labels,)
+            assert epc.times.dtype == 'float'
             # Randomly generate array_annotations from given options
             arr_ann = {key: value[(rand(len(times)) * len(value)).astype('i')] for (key, value) in
                        array_annotations.items()}
@@ -406,8 +408,8 @@ def fake_neo(obj_type="Block", cascade=True, seed=None, n=1):
             # if we are creating a block and this is the object's primary
             # parent, don't create the object, we will import it from secondary
             # containers later
-            if (cascade == 'block' and len(child._parent_objects) > 0 and obj_type !=
-                    child._parent_objects[-1]):
+            if (cascade == 'block' and len(child._parent_objects) > 0 
+                    and obj_type != child._parent_objects[-1]):
                 continue
             getattr(obj, _container_name(childname)).append(child)
 

diff --git a/neo/test/iotest/test_brainwaredamio.py b/neo/test/iotest/test_brainwaredamio.py
@@ -44,7 +44,7 @@ def proc_dam(filename):
     example: filename = 'file1_dam_py2.npz'
              dam file name = 'file1.dam'
     '''
-    with np.load(filename) as damobj:
+    with np.load(filename, allow_pickle=True) as damobj:
         damfile = list(damobj.items())[0][1].flatten()
 
     filename = os.path.basename(filename[:-12] + '.dam')

diff --git a/neo/test/iotest/test_brainwaref32io.py b/neo/test/iotest/test_brainwaref32io.py
@@ -58,7 +58,7 @@ def proc_f32(filename):
     chx.units.append(unit)
 
     try:
-        with np.load(filename) as f32obj:
+        with np.load(filename, allow_pickle=True) as f32obj:
             f32file = list(f32obj.items())[0][1].flatten()
     except IOError as exc:
         if 'as a pickle' in exc.message:

diff --git a/neo/test/iotest/test_brainwaresrcio.py b/neo/test/iotest/test_brainwaresrcio.py
@@ -67,7 +67,7 @@ def proc_src(filename):
     example: filename = 'file1_src_py2.npz'
              src file name = 'file1.src'
     '''
-    with np.load(filename) as srcobj:
+    with np.load(filename, allow_pickle=True) as srcobj:
         srcfile = list(srcobj.items())[0][1]
 
     filename = os.path.basename(filename[:-12] + '.src')

diff --git a/requirements.txt b/requirements.txt
@@ -1,5 +1,5 @@
 # essential
-numpy>=1.7.1
+numpy>=1.7.1,!=1.16.0
 quantities>=0.9.0
 # for running tests
 nose>=1.1.2