Merge branch 'SpikeInterface:main' into more-sphinx-docstring

SpikeInterface · Aug 13, 2024 · c3f0f75 · c3f0f75
2 parents 2307c9b + 9d6ad5b
commit c3f0f75
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ repos:
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 -   repo: https://github.com/psf/black
-    rev: 24.4.2
+    rev: 24.8.0
     hooks:
     -   id: black
         files: ^src/
diff --git a/doc/modules/postprocessing.rst b/doc/modules/postprocessing.rst
@@ -208,9 +208,11 @@ For dense waveforms, sparsity can also be passed as an argument.
 
 .. code-block:: python
 
-    pc = sorting_analyzer.compute(input="principal_components",
-                             n_components=3,
-                             mode="by_channel_local")
+    pc = sorting_analyzer.compute(
+        input="principal_components",
+        n_components=3,
+        mode="by_channel_local"
+    )
 
 For more information, see :py:func:`~spikeinterface.postprocessing.compute_principal_components`
 
@@ -243,9 +245,7 @@ each spike.
 
 .. code-block:: python
 
-    amplitudes = sorting_analyzer.compute(input="spike_amplitudes",
-                             peak_sign="neg",
-                             outputs="concatenated")
+    amplitudes = sorting_analyzer.compute(input="spike_amplitudes", peak_sign="neg")
 
 For more information, see :py:func:`~spikeinterface.postprocessing.compute_spike_amplitudes`
 
@@ -263,15 +263,17 @@ with center of mass (:code:`method="center_of_mass"` - fast, but less accurate),
 
 .. code-block:: python
 
-    spike_locations = sorting_analyzer.compute(input="spike_locations",
-                             ms_before=0.5,
-                             ms_after=0.5,
-                             spike_retriever_kwargs=dict(
-                                channel_from_template=True,
-                                radius_um=50,
-                                peak_sign="neg"
-                                              ),
-                             method="center_of_mass")
+    spike_locations = sorting_analyzer.compute(
+        input="spike_locations",
+        ms_before=0.5,
+        ms_after=0.5,
+        spike_retriever_kwargs=dict(
+            channel_from_template=True,
+            radius_um=50,
+            peak_sign="neg"
+        ),
+        method="center_of_mass"
+    )
 
 
 For more information, see :py:func:`~spikeinterface.postprocessing.compute_spike_locations`
@@ -329,6 +331,12 @@ Optionally, the following multi-channel metrics can be computed by setting:
     Visualization of template metrics. Image from `ecephys_spike_sorting <https://github.com/AllenInstitute/ecephys_spike_sorting/tree/v0.2/ecephys_spike_sorting/modules/mean_waveforms>`_
     from the Allen Institute.
 
+
+.. code-block:: python
+
+    tm = sorting_analyzer.compute(input="template_metrics", include_multi_channel_metrics=True)
+
+
 For more information, see :py:func:`~spikeinterface.postprocessing.compute_template_metrics`
 
 
@@ -340,10 +348,12 @@ with shape (num_units, num_units, num_bins) with all correlograms for each pair
 
 .. code-block:: python
 
-    ccg = sorting_analyzer.compute(input="correlograms",
-                            window_ms=50.0,
-                            bin_ms=1.0,
-                            method="auto")
+    ccg = sorting_analyzer.compute(
+        input="correlograms",
+        window_ms=50.0,
+        bin_ms=1.0,
+        method="auto"
+    )
 
 For more information, see :py:func:`~spikeinterface.postprocessing.compute_correlograms`
 
@@ -357,10 +367,12 @@ This extension computes the histograms of inter-spike-intervals. The computed ou
 
 .. code-block:: python
 
-   isi =  sorting_analyer.compute(input="isi_histograms"
-                            window_ms=50.0,
-                            bin_ms=1.0,
-                            method="auto")
+    isi =  sorting_analyer.compute(
+        input="isi_histograms"
+        window_ms=50.0,
+        bin_ms=1.0,
+        method="auto"
+    )
 
 For more information, see :py:func:`~spikeinterface.postprocessing.compute_isi_histograms`
 

diff --git a/doc/modules/qualitymetrics.rst b/doc/modules/qualitymetrics.rst
@@ -57,7 +57,7 @@ This code snippet shows how to compute quality metrics (with or without principa
 
     # with PCs (depends on "pca" in addition to the above metrics)
 
-    qm_ext = sorting_analyzer.compute(input={"pca": dict(n_components=5, mode="by_channel_local"),
+    qm_ext = sorting_analyzer.compute(input={"principal_components": dict(n_components=5, mode="by_channel_local"),
                                     "quality_metrics": dict(skip_pc_metrics=False)})
      metrics = qm_ext.get_data()
      assert 'isolation_distance' in metrics.columns

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "spikeinterface"
-version = "0.101.0"
+version = "0.101.1"
 authors = [
   { name="Alessio Buccino", email="[email protected]" },
   { name="Samuel Garcia", email="[email protected]" },
@@ -125,16 +125,16 @@ 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",
 ]
 
 test_extractors = [
     # Functions to download data in neo test suite
     "pooch>=1.8.2",
     "datalad>=1.0.2",
-    # "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 = [
@@ -175,8 +175,8 @@ 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",
 ]
 
 docs = [
@@ -199,8 +199,8 @@ docs = [
     "datalad>=1.0.2",
 
     # 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
 
 ]
 

diff --git a/src/spikeinterface/__init__.py b/src/spikeinterface/__init__.py
@@ -30,5 +30,5 @@
 # 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
diff --git a/src/spikeinterface/comparison/basecomparison.py b/src/spikeinterface/comparison/basecomparison.py
@@ -63,9 +63,9 @@ def compute_subgraphs(self):
         Computes subgraphs of connected components.
         Returns
         -------
-        sg_object_names: list
+        sg_object_names : list
             List of sorter names for each node in the connected component subgraph
-        sg_units: list
+        sg_units : list
             List of unit ids for each node in the connected component subgraph
         """
         if self.clean_graph is not None: