Support for NumPy 2.0 in Neo Core

.github/workflows/core-test.yml

@@ -22,21 +22,36 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     strategy:
-      fail-fast: true
+      fail-fast: false # change back before MERGE
       matrix:
         os: ["ubuntu-latest", "windows-latest"]
         # "macos-latest",
-        python-version: ['3.9', '3.10', '3.11', '3.12']
-        numpy-version: ['1.22.4', '1.23.5', '1.24.1', '1.25.1', '1.26.4']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
+        numpy-version: ['1.22.4', '1.23.5', '1.24.4', '1.25.1', '1.26.4', '2.0.2','2.1']
         exclude:
+           - python-version: '3.9'
+             numpy-version: '2.1'
            - python-version: '3.12'
              numpy-version: '1.22.4'
            - python-version: '3.12'
              numpy-version: '1.23.5'
            - python-version: '3.12'
-             numpy-version: '1.24.1'
+             numpy-version: '1.24.4'
            - python-version: '3.12'
              numpy-version: '1.25.1'
+           - python-version: '3.13'
+             numpy-version: '1.22.4'
+           - python-version: '3.13'
+             numpy-version: '1.23.5'
+           - python-version: '3.13'
+             numpy-version: '1.24.4'
+           - python-version: '3.13'
+             numpy-version: '1.25.1'
+           - python-version: '3.13'
+             numpy-version: '1.26.4'
+           - python-version: '3.13'
+             numpy-version: '2.0.2'
+
     steps:
         - name: Set up Python ${{ matrix.python-version }}
           uses: actions/setup-python@v4

.github/workflows/io-test.yml

@@ -18,7 +18,8 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ['3.9', '3.11.9']
+        python-version: ['3.9', '3.12']
+        numpy-version: ["1.26.4"]
     defaults:
       # by default run in bash mode (required for conda usage)
       run:
@@ -90,9 +91,13 @@ jobs:
       - name: Install neo including dependencies
         # installation with dependencies is only required if no cache was found
         # restore-key hits should result in `cache-hit` == 'false'
+        # in the run we don't do upgrade to prevent forced numpy 2.0. when ready
+        # change to pip install --upgrade -e . instead.
         if: steps.cache-conda-env.outputs.cache-hit != 'true'
         run: |
-          pip install --upgrade -e .
+          pip install -e .
+          pip uninstall numpy -y
+          pip install numpy==1.26.4 -y
           pip install .[test]
 
       - name: Install neo without dependencies

environment_testing.yml

@@ -4,3 +4,6 @@ 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/core/spiketrain.py

@@ -975,7 +975,7 @@ def _merge_array_annotations(self, others, sorting=None):
 
         omitted_keys_other = [
             key
-            for key in np.unique([key for other in others for key in other.array_annotations])
+            for key in set([key for other in others for key in other.array_annotations])
             if key not in self.array_annotations
         ]
 

neo/test/coretest/test_spiketrain.py

@@ -315,6 +315,10 @@ def test__create_from_quantity_array(self):
 
     def test__create_from_quantity_array_with_dtype(self):
         times = np.arange(10, dtype="f4") * pq.ms
+        # this step is required for NumPy 2.0 which now casts to float64 in the case either value/array
+        # is float64 even if not necessary
+        # https://numpy.org/devdocs/numpy_2_0_migration_guide.html
+        times = times.astype(dtype="f4")
         t_start = 0.0 * pq.s
         t_stop = 12.0 * pq.ms
         train1 = SpikeTrain(times, t_start=t_start, t_stop=t_stop)
@@ -346,6 +350,10 @@ def test__create_from_quantity_array_no_start_stop_units(self):
 
     def test__create_from_quantity_array_no_start_stop_units_with_dtype(self):
         times = np.arange(10, dtype="f4") * pq.ms
+        # this step is required for NumPy 2.0 which now casts to float64 in the case either value/array
+        # is float64 even if not necessary
+        # https://numpy.org/devdocs/numpy_2_0_migration_guide.html
+        times = times.astype(dtype="f4")
         t_start = 0.0
         t_stop = 12.0
         train1 = SpikeTrain(times, t_start=t_start, t_stop=t_stop)
@@ -1147,7 +1155,7 @@ def test_merge_multiple(self):
         expected *= time_unit
         sorting = np.argsort(expected)
         expected = expected[sorting]
-        np.testing.assert_array_equal(result.times, expected)
+        np.testing.assert_array_equal(result.times.magnitude, expected.magnitude)
 
         # Make sure array annotations are merged correctly
         self.assertTrue("label" not in result.array_annotations)

pyproject.toml

@@ -23,7 +23,7 @@ classifiers = [
 
 dependencies = [
     "packaging",
-    "numpy>=1.22.4,<2.0.0",
+    "numpy>=1.22.4",
     "quantities>=0.16.1"
 ]