Merge branch 'main' into fix-export-to-phy-unitrefine

Author: chrishalcrow

doc/development/development.rst

@@ -433,12 +433,13 @@ Where the start date is the date of the last release and the end date is the cur
 
 The date of the last release can be found on `PyPI <https://pypi.org/project/spikeinterface/>`_.
 
-
 As a specific example:
+
 .. code-block:: bash
 
     bash auto-release-notes.sh 2025-02-19 2025-03-24
 
+* Add the release to `doc/whatisnew.rst`, by adding it to the list of releases and providing a short description of the release.
 * Finish the release notes and merge
 * Locally tag the main branch with the newly merged release notes with the new version
 * Push the tag to the remote repository which will trigger the release action (.github/workflows/publish-to-pypi.yml)

doc/releases/0.103.1.rst

@@ -0,0 +1,97 @@
+.. _release0.103.1:
+
+SpikeInterface 0.103.1 release notes
+------------------------------------
+
+November 3rd 2025
+
+Minor release with bug fixes
+
+
+core:
+
+* faster write_binary_recording() (#4171)
+* Add RMS method to `get_noise_levels` (#4130)
+
+extractors:
+
+* Update `get_neuropixels_sample_shifts_from_probe` to use `adc_sample_order` (#4184)
+* Add `experiment_name`  argument to  `OpenEphysBinaryRecordingExtractor` (#4177)
+* Updates for probeinterface 0.3.0 (#4092)
+
+sorters:
+
+* Add gpu requirements to rtsort (#4143)
+
+postprocessing:
+
+* Patch for memory usage in `template_similarity` (#4152)
+
+qualitymetrics:
+
+* Alter how quality metrics check extension dependencies (#4080)
+
+curation:
+
+* Future-proof hyperparameter search space for auto-curation (#4174)
+
+widgets:
+
+* Metric list in plot (#4137)
+* Fix `plot_traces` with `t_start` and no times (#4135)
+* Fix `plot_amplitudes` for sortingview (#4097)
+
+generators:
+
+* Fix bug in waveform generation + adapt parameters (#4167)
+
+sortingcomponents:
+
+* Reducing memory footprint for Overlaps during matching (#4157)
+* Big clean in components and reoraginze in folder (#4140)
+* Improve tdc-clustering with a merging step (#4122)
+* Implement isosplit6 into spikeinterface in pure numpy/numba (#4113)
+* Improvement of TDC2, SC2 and ISOSPLIT (#4182)
+
+motion correction:
+
+* dredge: Do more things in place with the larger matrices (#4119)
+
+documentation:
+
+* Improve docs for curation module and model (#4138)
+* Fix typos and buggy code in modules docs (#4105)
+* Improve assertion error message of SortingAnalyzer job kwargs (#4178)
+
+continuous integration:
+
+* Check install ci - use uv (#4123)
+
+packaging:
+
+* Update deprecated cuda import (#4111)
+
+testing:
+
+* Fix size comparison in sorting tools test case (#4112)
+* Fix ks4 tests (#4187)
+
+deprecations:
+
+* Update deprecated cuda import (#4111)
+* Deprecated `spikeinterface.compraison.hybrid` module (#4093)
+* More return_scaled > return_in_uV (#4090)
+
+Contributors:
+
+* @alejoe91
+* @chrishalcrow
+* @cwindolf
+* @emmanuel-ferdman
+* @h-mayorquin
+* @lochhh
+* @nwatters01
+* @samuelgarcia
+* @yger
+* @zm711
+* @MGAMZ

doc/whatisnew.rst

@@ -8,6 +8,7 @@ Release notes
 .. toctree::
   :maxdepth: 1
 
+  releases/0.103.1.rst
   releases/0.103.0.rst
   releases/0.102.3.rst
   releases/0.102.2.rst
@@ -50,6 +51,11 @@ Release notes
   releases/0.9.1.rst
 
 
+Version 0.103.1
+===============
+
+* Minor release with bug fixes
+
 Version 0.103.0
 ===============
 

pyproject.toml

@@ -25,8 +25,8 @@ dependencies = [
     "threadpoolctl>=3.0.0",
     "tqdm",
     "zarr>=2.18,<3",
-    "neo>=0.14.1",
-    "probeinterface>=0.3.0",
+    "neo>=0.14.3",
+    "probeinterface>=0.3.1",
     "packaging",
     "pydantic",
     "numcodecs<0.16.0", # For supporting zarr < 3
@@ -127,8 +127,8 @@ test_core = [
 
     # for github test : probeinterface and neo from master
     # for release we need pypi, so this need to be commented
-    "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",
-    "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",
+    # "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",
+    # "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",
 
     # for slurm jobs,
     "pytest-mock"
@@ -139,8 +139,8 @@ test_extractors = [
     "pooch>=1.8.2",
     "datalad>=1.0.2",
     # Commenting out for release
-    "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",
-    "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",
+    # "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",
+    # "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",
 ]
 
 test_preprocessing = [
@@ -185,8 +185,8 @@ test = [
 
     # for github test : probeinterface and neo from master
     # for release we need pypi, so this need to be commented
-    "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",
-    "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",
+    # "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",
+    # "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",
 
     # for slurm jobs
     "pytest-mock",
@@ -213,8 +213,8 @@ docs = [
     "huggingface_hub", # For automated curation
 
     # for release we need pypi, so this needs to be commented
-    "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",  # We always build from the latest version
-    "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",  # We always build from the latest version
+    # "probeinterface @ git+https://github.com/SpikeInterface/probeinterface.git",  # We always build from the latest version
+    # "neo @ git+https://github.com/NeuralEnsemble/python-neo.git",  # We always build from the latest version
 ]
 
 dev = [

src/spikeinterface/__init__.py

@@ -27,5 +27,5 @@
 # This flag must be set to False for release
 # This avoids using versioning that contains ".dev0" (and this is a better choice)
 # This is mainly useful when using run_sorter in a container and spikeinterface install
-DEV_MODE = True
-# DEV_MODE = False
+# DEV_MODE = True
+DEV_MODE = False

src/spikeinterface/benchmark/benchmark_plot_tools.py

@@ -478,8 +478,9 @@ def _plot_performances_vs_metric(
                     .get_performance()[performance_name]
                     .to_numpy(dtype="float64")
                 )
-                all_xs.append(x)
-                all_ys.append(y)
+                mask = ~np.isnan(x) & ~np.isnan(y)
+                all_xs.append(x[mask])
+                all_ys.append(y[mask])
 
             if with_sigmoid_fit:
                 max_snr = max(np.max(x) for x in all_xs)

src/spikeinterface/postprocessing/template_similarity.py

@@ -94,7 +94,7 @@ def _merge_extension_data(
                 new_sorting_analyzer.sparsity.mask[keep, :], new_unit_ids, new_sorting_analyzer.channel_ids
             )
 
-        new_similarity = compute_similarity_with_templates_array(
+        new_similarity, _ = compute_similarity_with_templates_array(
             new_templates_array,
             all_templates_array,
             method=self.params["method"],
@@ -146,7 +146,7 @@ def _split_extension_data(self, split_units, new_unit_ids, new_sorting_analyzer,
                 new_sorting_analyzer.sparsity.mask[keep, :], new_unit_ids_f, new_sorting_analyzer.channel_ids
             )
 
-        new_similarity = compute_similarity_with_templates_array(
+        new_similarity, _ = compute_similarity_with_templates_array(
             new_templates_array,
             all_templates_array,
             method=self.params["method"],
@@ -188,7 +188,7 @@ def _run(self, verbose=False):
             self.sorting_analyzer, return_in_uV=self.sorting_analyzer.return_in_uV
         )
         sparsity = self.sorting_analyzer.sparsity
-        similarity = compute_similarity_with_templates_array(
+        similarity, _ = compute_similarity_with_templates_array(
             templates_array,
             templates_array,
             method=self.params["method"],
@@ -393,7 +393,13 @@ def get_overlapping_mask_for_one_template(template_index, sparsity, other_sparsi
 
 
 def compute_similarity_with_templates_array(
-    templates_array, other_templates_array, method, support="union", num_shifts=0, sparsity=None, other_sparsity=None
+    templates_array,
+    other_templates_array,
+    method,
+    support="union",
+    num_shifts=0,
+    sparsity=None,
+    other_sparsity=None,
 ):
 
     if method == "cosine_similarity":
@@ -432,10 +438,11 @@ def compute_similarity_with_templates_array(
         templates_array, other_templates_array, num_shifts, method, sparsity_mask, other_sparsity_mask, support=support
     )
 
+    lags = np.argmin(distances, axis=0) - num_shifts
     distances = np.min(distances, axis=0)
     similarity = 1 - distances
 
-    return similarity
+    return similarity, lags
 
 
 def compute_template_similarity_by_pair(
@@ -445,7 +452,7 @@ def compute_template_similarity_by_pair(
     templates_array_2 = get_dense_templates_array(sorting_analyzer_2, return_in_uV=True)
     sparsity_1 = sorting_analyzer_1.sparsity
     sparsity_2 = sorting_analyzer_2.sparsity
-    similarity = compute_similarity_with_templates_array(
+    similarity, _ = compute_similarity_with_templates_array(
         templates_array_1,
         templates_array_2,
         method=method,

src/spikeinterface/postprocessing/tests/test_template_similarity.py

@@ -82,8 +82,9 @@ def test_compute_similarity_with_templates_array(params):
     templates_array = rng.random(size=(2, 20, 5))
     other_templates_array = rng.random(size=(4, 20, 5))
 
-    similarity = compute_similarity_with_templates_array(templates_array, other_templates_array, **params)
+    similarity, lags = compute_similarity_with_templates_array(templates_array, other_templates_array, **params)
     print(similarity.shape)
+    print(lags)
 
 
 pytest.mark.skipif(not HAVE_NUMBA, reason="Numba not available")
@@ -141,5 +142,5 @@ def test_equal_results_numba(params):
     test.cache_folder = Path("./cache_folder")
     test.test_extension(params=dict(method="l2"))
 
-    # params = dict(method="cosine", num_shifts=8)
-    # test_compute_similarity_with_templates_array(params)
+    params = dict(method="cosine", num_shifts=8)
+    test_compute_similarity_with_templates_array(params)