Fixes for numpy 2.0

.github/workflows/python-package.yml

@@ -13,19 +13,20 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.10"]
+        python-version: ["3.10", "3.12"]
     steps:
-      - uses: actions/checkout@v2
-      - uses: s-weigand/setup-conda@v1
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Which conda/python
+      - name: Which python
         run: |
-          conda --version
           python --version
       - name: Install dependencies
         run: |
           pip install .[templates,test]
+          pip install "zarr<3.0.0"
       - name: pip list
         run: |
           pip list

.github/workflows/python-publish.yml

@@ -14,13 +14,14 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
-      - uses: s-weigand/setup-conda@v1
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
       - name: Which python
         run: |
-          conda --version
+          python --version
       - name: Install dependencies
         run: |
           pip install .[templates,test]

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "MEArec"
-version = "1.9.1"
+version = "1.9.2"
 authors = [
   { name="Alessio Buccino", email="[email protected]" },
 ]

readthedocs.yml

@@ -1,5 +1,9 @@
 version: 2
 
+sphinx:
+  # Path to your Sphinx configuration file.
+  configuration: docs/conf.py
+
 build:
   os: ubuntu-22.04
   tools:

src/MEArec/generators/spiketraingenerator.py

@@ -1,7 +1,5 @@
 from copy import deepcopy
 
-import elephant.spike_train_generation as stg
-import elephant.statistics as stat
 import neo
 import numpy as np
 import quantities as pq
@@ -129,6 +127,9 @@ def generate_spikes(self):
         Generate spike trains based on default_params of the SpikeTrainGenerator class.
         self.spiketrains contains the newly generated spike trains
         """
+        import elephant.spike_train_generation as stg
+        import elephant.statistics as stat
+
         if not self._has_spiketrains:
             self.spiketrains = []
             idx = 0

src/MEArec/tests/test_generators.py

@@ -4,7 +4,6 @@
 from copy import deepcopy
 from pathlib import Path
 
-import elephant.statistics as stat
 import numpy as np
 import yaml
 from click.testing import CliRunner
@@ -198,6 +197,8 @@ def test_gen_templates_beta_distr(self):
         assert tempgen_drift_beta.templates.shape[0] == self.tempgen_drift.templates.shape[0]
 
     def test_gen_spiketrains(self):
+        import elephant.statistics as stat
+
         print("Test spike train generation")
         rec_params = mr.get_default_recordings_params()
         sp_params = rec_params["spiketrains"]

src/MEArec/tools.py

@@ -777,7 +777,7 @@ def clean_dict(d):
 def _clean_numpy_scalar(v):
     if isinstance(v, np.bool_):
         v = bool(v)
-    if isinstance(v, np.float_):
+    if isinstance(v, np.float64):
         v = float(v)
     if isinstance(v, np.int_):
         v = int(v)