Merge pull request #3683 from alejoe91/python-3.13

Test Python 3.13

Author: alejoe91

.github/workflows/all-tests.yml

@@ -25,7 +25,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.12"]  # Lower and higher versions we support
+        python-version: ["3.9", "3.13"]  # Lower and higher versions we support
         os: [macos-latest, windows-latest, ubuntu-latest]
     steps:
       - uses: actions/checkout@v4

pyproject.toml

@@ -7,7 +7,7 @@ authors = [
 ]
 description = "Python toolkit for analysis, visualization, and comparison of spike sorting output"
 readme = "README.md"
-requires-python = ">=3.9,<3.13"
+requires-python = ">=3.9,<3.14"
 classifiers = [
     "Programming Language :: Python :: 3 :: Only",
     "License :: OSI Approved :: MIT License",
@@ -20,7 +20,8 @@ classifiers = [
 
 
 dependencies = [
-    "numpy>=1.20",
+    "numpy>=1.20;python_version<'3.13'",
+    "numpy>=2.0.0;python_version>='3.13'",
     "threadpoolctl>=3.0.0",
     "tqdm",
     "zarr>=2.18,<3",
@@ -164,15 +165,6 @@ test = [
     # for sortingview backend
     "sortingview",
 
-
-    ## install tridesclous for testing ##
-    "tridesclous>=1.6.8",
-
-    ## sliding_nn
-    "pymde",
-    "torch",
-    "pynndescent",
-
     # curation
     "skops",
     "huggingface_hub",

src/spikeinterface/extractors/phykilosortextractors.py

@@ -56,7 +56,7 @@ def __init__(
         spike_clusters = np.atleast_1d(spike_clusters.squeeze())
 
         clust_id = np.unique(spike_clusters)
-        unique_unit_ids = list(clust_id)
+        unique_unit_ids = [int(c) for c in clust_id]
         params = read_python(str(phy_folder / "params.py"))
         sampling_frequency = params["sample_rate"]
 

src/spikeinterface/sorters/tests/test_runsorter.py

@@ -29,10 +29,10 @@ def test_run_sorter_local(generate_recording, create_cache_folder):
     recording = generate_recording
     cache_folder = create_cache_folder
 
-    sorter_params = {"detect_threshold": 4.9}
+    sorter_params = {"detection": {"detect_threshold": 4.9}}
 
     sorting = run_sorter(
-        "tridesclous",
+        "tridesclous2",
         recording,
         output_folder=cache_folder / "sorting_tdc_local",
         remove_existing_folder=True,