Merge pull request #1625 from alejoe91/final-2.0-fixes

Fix failing tests due to Numpy 2.0

Author: samuelgarcia

.github/workflows/io-test.yml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ['3.9', '3.12']
+        python-version: ['3.9', '3.13']
     defaults:
       # by default run in bash mode (required for conda usage)
       run:

environment_testing.yml

@@ -4,6 +4,3 @@ channels:
 dependencies:
   - datalad
   - pip
-  # temporary have this here for IO testing while we decide how to deal with
-  # external packages not 2.0 ready
-  - numpy=1.26.4

neo/io/klustakwikio.py

@@ -197,7 +197,7 @@ def _load_spike_times(self, fetfilename):
             names.append("spike_time")
 
         # Load into recarray
-        data = np.recfromtxt(fetfilename, names=names, skip_header=1, delimiter=" ")
+        data = np.genfromtxt(fetfilename, names=names, skip_header=1, delimiter=" ")
 
         # get features
         features = np.array([data[f"fet{n}"] for n in range(nbFeatures)])

neo/rawio/blackrockrawio.py

@@ -1365,7 +1365,7 @@ def __match_nsx_and_nev_segment_ids(self, nsx_nb):
 
                     # Show warning if spikes do not fit any segment (+- 1 sampling 'tick')
                     # Spike should belong to segment before
-                    mask_outside = (ev_ids == i) & (data["timestamp"] < int(seg["timestamp"]) - nsx_offset - nsx_period)
+                    mask_outside = (ev_ids == i) & (data["timestamp"] < int(seg["timestamp"]) - int(nsx_offset) - int(nsx_period))
 
                     if len(data[mask_outside]) > 0:
                         warnings.warn(f"Spikes outside any segment. Detected on segment #{i}")
@@ -1995,6 +1995,7 @@ def __get_nsx_param_variant_a(self, nsx_nb):
         else:
             units = "uV"
 
+        
         nsx_parameters = {
             "nb_data_points": int(
                 (self.__get_file_size(filename) - bytes_in_headers)
@@ -2003,8 +2004,8 @@ def __get_nsx_param_variant_a(self, nsx_nb):
             ),
             "labels": labels,
             "units": np.array([units] * self.__nsx_basic_header[nsx_nb]["channel_count"]),
-            "min_analog_val": -1 * np.array(dig_factor),
-            "max_analog_val": np.array(dig_factor),
+            "min_analog_val": -1 * np.array(dig_factor, dtype="float"),
+            "max_analog_val": np.array(dig_factor, dtype="float"),
             "min_digital_val": np.array([-1000] * self.__nsx_basic_header[nsx_nb]["channel_count"]),
             "max_digital_val": np.array([1000] * self.__nsx_basic_header[nsx_nb]["channel_count"]),
             "timestamp_resolution": 30000,

neo/test/iotest/test_asciisignalio.py

@@ -166,10 +166,10 @@ def test_skiprows(self):
         self.assertEqual(signal.units, pq.V)
         assert_array_equal(signal.times, [0.0, 1.0, 2.0, 3.0] * pq.s)
         assert_array_equal(signal.times.magnitude, [0.0, 1.0, 2.0, 3.0])
-        assert_array_equal(signal[0].magnitude, -64.8)
-        assert_array_equal(signal[1].magnitude, -64.6)
-        assert_array_equal(signal[2].magnitude, -64.3)
-        assert_array_equal(signal[3].magnitude, -66)
+        assert_array_almost_equal(signal[0].magnitude, -64.8, decimal=5)
+        assert_array_almost_equal(signal[1].magnitude, -64.6, decimal=5)
+        assert_array_almost_equal(signal[2].magnitude, -64.3, decimal=5)
+        assert_array_almost_equal(signal[3].magnitude, -66, decimal=5)
         assert_array_almost_equal(np.asarray(signal).flatten(), np.array([-64.8, -64.6, -64.3, -66]), decimal=5)
 
         os.remove(filename)
@@ -195,11 +195,11 @@ def test_usecols(self):
         self.assertEqual(signal.units, pq.V)
         assert_array_equal(signal.times, [0.0, 1.0, 2.0, 3.0, 4.0] * pq.s)
         assert_array_equal(signal.times.magnitude, [0.0, 1.0, 2.0, 3.0, 4.0])
-        assert_array_equal(signal[0].magnitude, 0.5)
-        assert_array_equal(signal[1].magnitude, 0.6)
-        assert_array_equal(signal[2].magnitude, 0.7)
-        assert_array_equal(signal[3].magnitude, 0.8)
-        assert_array_equal(signal[4].magnitude, 1.4)
+        assert_array_almost_equal(signal[0].magnitude, 0.5, decimal=5)
+        assert_array_almost_equal(signal[1].magnitude, 0.6, decimal=5)
+        assert_array_almost_equal(signal[2].magnitude, 0.7, decimal=5)
+        assert_array_almost_equal(signal[3].magnitude, 0.8, decimal=5)
+        assert_array_almost_equal(signal[4].magnitude, 1.4, decimal=5)
         assert_array_almost_equal(np.asarray(signal).flatten(), np.array([0.5, 0.6, 0.7, 0.8, 1.4]), decimal=5)
 
         os.remove(filename)

neo/test/iotest/test_axographio.py

@@ -9,7 +9,7 @@
 from neo.test.iotest.common_io_test import BaseTestIO
 
 import numpy as np
-from numpy.testing import assert_equal
+from numpy.testing import assert_equal, assert_almost_equal
 import quantities as pq
 from neo.test.rawiotest.test_axographrawio import TestAxographRawIO
 
@@ -35,9 +35,9 @@ def test_version_1(self):
         target = np.array([[-5.5078130], [-3.1171880], [+1.6640626], [+1.6640626], [+4.0546880]], dtype=np.float32)
         assert_equal(arr, target)
 
-        assert_equal(sig.t_start, 0.0005000000237487257 * pq.s)
+        assert_almost_equal(sig.t_start, 0.0005000000237487257 * pq.s, decimal=9)
 
-        assert_equal(sig.sampling_period, 0.0005000010132789612 * pq.s)
+        assert_almost_equal(sig.sampling_period, 0.0005000010132789612 * pq.s, decimal=9)
 
     def test_version_2(self):
         """Test reading a version 2 AxoGraph file"""
@@ -87,9 +87,9 @@ def test_version_2(self):
         target = np.array([[0.3125], [9.6875], [9.6875], [9.6875], [9.3750]], dtype=np.float32)
         assert_equal(arr, target)
 
-        assert_equal(sig.t_start, 0.00009999999747378752 * pq.s)
+        assert_almost_equal(sig.t_start, 0.00009999999747378752 * pq.s, decimal=9)
 
-        assert_equal(sig.sampling_period, 0.00009999999747378750 * pq.s)
+        assert_almost_equal(sig.sampling_period, 0.00009999999747378750 * pq.s, decimal=9)
 
     def test_version_5(self):
         """Test reading a version 5 AxoGraph file"""
@@ -169,7 +169,7 @@ def test_file_written_by_axographio_package_without_linearsequence(self):
 
         assert_equal(sig.t_start, 0 * pq.s)
 
-        assert_equal(sig.sampling_period, 0.009999999999999787 * pq.s)
+        assert_almost_equal(sig.sampling_period, 0.009999999999999787 * pq.s, decimal=9)
 
     def test_file_with_corrupt_comment(self):
         """Test reading a file with a corrupt comment"""

pyproject.toml

@@ -81,7 +81,7 @@ docs = [
     "nixio",
     "pynwb",
     "igor2",
-    "numpy<2.0" # https://github.com/NeuralEnsemble/python-neo/pull/1612
+    "numpy>=2.0"
 ]
 
 dev = [