Merge branch 'main' into total_memory

Author: samuelgarcia

.github/workflows/all-tests.yml

@@ -23,7 +23,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.13"]  # Lower and higher versions we support
+        python-version: ["3.9", "3.13.3"]  # Lower and higher versions we support, bug in 3.13.4 adjust when fixed
         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,<3.14"
+requires-python = ">=3.9,<3.13.4" # limit until Windows bug is fixed.
 classifiers = [
     "Programming Language :: Python :: 3 :: Only",
     "License :: OSI Approved :: MIT License",

src/spikeinterface/benchmark/benchmark_plot_tools.py

@@ -432,6 +432,8 @@ def plot_performances_vs_snr(
     levels_to_keep=None,
     orientation="vertical",
     show_legend=True,
+    with_sigmoid_fit=True,
+    show_average_by_bin=False,
     axs=None,
 ):
     """
@@ -455,6 +457,10 @@ def plot_performances_vs_snr(
         The orientation of the plot.
     show_legend : bool, default True
         Show legend or not
+    show_sigmoid_fit : bool, default True
+        Show sigmoid that fit the performances.
+    show_average_by_bin : bool, default False
+        Instead of the sigmoid an average by bins can be plotted.
     axs : matplotlib.axes.Axes | None, default: None
         The axs to use for plotting. Should be the same size as len(performance_names).
 
@@ -478,7 +484,12 @@ def plot_performances_vs_snr(
         raise ValueError("orientation must be 'vertical' or 'horizontal'")
 
     if axs is None:
-        fig, axs = plt.subplots(ncols=ncols, nrows=nrows, figsize=figsize, squeeze=True)
+        fig, axs = plt.subplots(ncols=ncols, nrows=nrows, figsize=figsize, squeeze=False)
+        if orientation == "vertical":
+            axs = axs[:, 0]
+        else:
+            axs = axs[0, :]
+
     else:
         assert len(axs) == len(performance_names), "axs should have the same number of axes as performance_names"
         fig = axs[0].get_figure()
@@ -512,8 +523,12 @@ def plot_performances_vs_snr(
                     analyzer = study.get_sorting_analyzer(dataset_key=snr_dataset_reference)
 
                 quality_metrics = analyzer.get_extension("quality_metrics").get_data()
-                x = quality_metrics["snr"].values
-                y = study.get_result(sub_key)["gt_comparison"].get_performance()[performance_name].values
+                x = quality_metrics["snr"].to_numpy(dtype="float64")
+                y = (
+                    study.get_result(sub_key)["gt_comparison"]
+                    .get_performance()[performance_name]
+                    .to_numpy(dtype="float64")
+                )
                 all_xs.append(x)
                 all_ys.append(y)
 
@@ -524,9 +539,17 @@ def plot_performances_vs_snr(
             ax.scatter(all_xs, all_ys, marker=".", label=label, color=color)
             ax.set_ylabel(performance_name)
 
-            popt = fit_sigmoid(all_xs, all_ys, p0=None)
-            xfit = np.linspace(0, max(x), 100)
-            ax.plot(xfit, sigmoid(xfit, *popt), color=color)
+            if with_sigmoid_fit:
+                popt = fit_sigmoid(all_xs, all_ys, p0=None)
+                xfit = np.linspace(0, max(x), 100)
+                ax.plot(xfit, sigmoid(xfit, *popt), color=color)
+
+            if show_average_by_bin:
+                from scipy.stats import binned_statistic
+
+                bins = np.linspace(np.min(all_xs), np.max(all_xs), 20)
+                average, bins, count = binned_statistic(all_xs, all_ys, statistic="mean", bins=bins)
+                ax.plot(bins[:-1] + (bins[1] - bins[0]) / 2.0, average, color=color)
 
         ax.set_ylim(-0.05, 1.05)
 

src/spikeinterface/sorters/tests/test_launcher.py

@@ -193,8 +193,8 @@ def test_run_sorter_jobs_slurm_kwargs(mocker, tmp_path, job_list):
         engine="slurm",
         engine_kwargs=None,
     )
-    tmp_script_folder = "_".join(tempfile.mkdtemp(prefix="spikeinterface_slurm_").split("_")[:-1])
-    assert tmp_script_folder in mock_subprocess_run.call_args_list[-1].args[0][5]
+    tmp_script_folder = Path(tempfile.gettempdir()) / "spikeinterface_slurm_"
+    assert str(tmp_script_folder) in mock_subprocess_run.call_args_list[-1].args[0][5]
 
 
 def test_run_sorter_by_property(create_cache_folder):