Support for NumPy 2.0 in Neo Core

.github/workflows/core-test.yml

@@ -25,28 +25,43 @@ jobs:
       fail-fast: true
       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']
         # numpy 1.22: 3.10, 1.23: 3.11, 1.24: 3.11, 1.25: 3.11, 1.26: 3.12
         exclude:
+           - python-version: '3.9'
+             numpy-version: '2.1'
            - python-version: '3.11'
              numpy-version: '1.22.4'
            - 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
+          uses: actions/setup-python@v5
           with:
             python-version: ${{ matrix.python-version }}
 
         - name: Checkout repository
-          uses: actions/checkout@v3
+          uses: actions/checkout@v4
 
         - name: Install numpy ${{ matrix.numpy-version }}
           run: |

.github/workflows/io-test.yml

@@ -18,15 +18,15 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ['3.9', '3.11.9']
+        python-version: ['3.9', '3.12']
     defaults:
       # by default run in bash mode (required for conda usage)
       run:
         shell: bash -l {0}
     steps:
 
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Get current year-month
         id: date
@@ -38,7 +38,7 @@ jobs:
         run: |
           echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
 
-      - uses: actions/cache/restore@v3
+      - uses: actions/cache/restore@v4
         # Loading cache of ephys_testing_dataset
         id: cache-datasets
         with:

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

@@ -979,7 +979,7 @@ 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

@@ -313,6 +313,10 @@ 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)
@@ -343,6 +347,10 @@ 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)
@@ -1143,7 +1151,7 @@ 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

@@ -4,7 +4,7 @@ version = "0.14.0.dev0"
 authors = [{name = "Neo authors and contributors"}]
 description = "Neo is a package for representing electrophysiology data in Python, together with support for reading a wide range of neurophysiology file formats"
 readme = "README.rst"
-requires-python = ">=3.9,<3.13" # 3.13 will require NumPy > 2.0 (Windows issue in CI)
+requires-python = ">=3.9"
 license = {text = "BSD 3-Clause License"}
 classifiers = [
     "Development Status :: 4 - Beta",
@@ -23,7 +23,7 @@ classifiers = [
 
 dependencies = [
     "packaging",
-    "numpy>=1.22.4,<2.0.0",
+    "numpy>=1.22.4",
     "quantities>=0.16.1"
 ]
 
@@ -45,7 +45,7 @@ iocache = [
 ]
 
 test = [
-    "dhn_med_py<2.0", # ci failing with 2.0 test future version when stable
+    # "dhn_med_py<2.0", # ci failing with 2.0 test future version when stable
     "pytest",
     "pytest-cov",
     # datalad   # this dependency is covered by conda (environment_testing.yml)
@@ -105,7 +105,7 @@ plexon2 = ["zugbruecke>=0.2; sys_platform!='win32'", "wenv; sys_platform!='win32
 all = [
     "coverage",
     "coveralls",
-    "dhn_med_py<2.0", # ci failing with 2.0 test future version when stable
+    # "dhn_med_py<2.0", # ci failing with 2.0 test future version when stable
     "h5py",
     "igor2",
     "ipython",