Fix deprecation warnings in tests

Author: rossant

phylib/io/model.py

@@ -1048,6 +1048,8 @@ def get_depths(self):
             features = self.sparse_features.data[ispi, :, 0]
             features = np.maximum(features, 0) ** 2  # takes only positive values into account
             ichannels = self.sparse_features.cols[self.spike_clusters[ispi]].astype(np.uint32)
+            # features = np.square(self.sparse_features.data[ispi, :, 0])
+            # ichannels = self.sparse_features.cols[self.spike_templates[ispi]].astype(np.int64)
             ypos = self.channel_positions[ichannels, 1]
             with np.errstate(divide='ignore'):
                 spikes_depths[ispi] = (np.sum(np.transpose(ypos * features) /
@@ -1088,7 +1090,7 @@ def get_amplitudes_true(self, sample2unit=1.):
         templates_amps_au = np.max(templates_ch_amps, axis=1)
         spike_amps = templates_amps_au[self.spike_templates] * self.amplitudes
 
-        with np.errstate(divide='ignore'):
+        with np.errstate(divide='ignore', invalid='ignore'):
             # take the average spike amplitude per template
             templates_amps_v = (np.bincount(self.spike_templates, weights=spike_amps) /
                                 np.bincount(self.spike_templates))

phylib/io/tests/test_datasets.py

@@ -46,15 +46,15 @@ def _add_mock_response(url, body, file_type='binary'):
 
 @yield_fixture
 def mock_url():
-    _add_mock_response(_URL, _DATA.tostring())
+    _add_mock_response(_URL, _DATA.tobytes())
     _add_mock_response(_URL + '.md5', _CHECKSUM + '  ' + Path(_URL).name)
     yield _URL
     responses.reset()
 
 
 @yield_fixture(params=product((True, False), repeat=4))
 def mock_urls(request):
-    data = _DATA.tostring()
+    data = _DATA.tobytes()
     checksum = _CHECKSUM
     url_data = _URL
     url_checksum = _URL + '.md5'
@@ -128,7 +128,7 @@ def test_download_already_exists_valid(tempdir, mock_url):
         path = Path(tempdir) / 'test'
         # Create valid file.
         with open(path, 'ab') as f:
-            f.write(_DATA.tostring())
+            f.write(_DATA.tobytes())
         _check(_dl(path))
     assert 'skip' in buf.getvalue()
 
@@ -144,7 +144,7 @@ def test_download_file(tempdir, mock_urls):
                         (not(checksum_here) and checksum_valid)))
 
     download_succeeds = (assert_succeeds or (data_here and
-                         (not(data_valid) and not(checksum_here))))
+                                             (not(data_valid) and not(checksum_here))))
 
     if download_succeeds:
         data = _dl(path)

phylib/io/tests/test_merge.py

@@ -101,7 +101,7 @@ def test_merged_single(merged, merged_original_amps=None):
         assert np.all(merged_original_amps[spike_probes == 0] <= 15)
         assert np.all(merged_original_amps[spike_probes == 1] >= 20)
 
-        np.all(merged.sparse_templates.data[:64, :, 0:32] == single.sparse_templates.data)
+        # np.all(merged.sparse_templates.data[:64, :, 0:32] == single.sparse_templates.data)
 
     # Convert into ALF and load.
     alf = EphysAlfCreator(merged).convert(tempdir / 'alf')

phylib/io/traces.py

@@ -459,6 +459,7 @@ def _get_ephys_constructor(obj, **kwargs):
             return None, None, {}
         assert path.exists()
         ext = path.suffix
+        assert ext, "No extension found in file `%s`" % path
         # Mtscomp file
         if ext == '.cbin':
             reader = mtscomp.Reader(n_threads=mp.cpu_count() // 2)
@@ -471,7 +472,7 @@ def _get_ephys_constructor(obj, **kwargs):
             return (NpyEphysReader, obj, kwargs)
             # TODO: other standard binary formats
         else:  # pragma: no cover
-            raise IOError("Unknown file extension: %s.", ext)
+            raise IOError("Unknown file extension: `%s`." % ext)
     elif isinstance(obj, (tuple, list)):
         if obj:
             # Concatenate the main argument to the constructor.