Merge branch 'main' of github.com:SpikeInterface/spikeinterface into …

…prepare_release
samuelgarcia · Jul 15, 2024 · d405deb · d405deb
2 parents 922fbf0 + a14ee81
commit d405deb
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diff --git a/.github/workflows/all-tests.yml b/.github/workflows/all-tests.yml
@@ -137,7 +137,7 @@ jobs:
           pip install -e .[extractors,streaming_extractors,test_extractors]
           ./.github/run_tests.sh "extractors and not streaming_extractors" --no-virtual-env
 
-      - name: Test streaming extracotors
+      - name: Test streaming extractors
         shell: bash
         if: env.RUN_STREAMING_EXTRACTORS_TESTS
         run: |

diff --git a/README.md b/README.md
@@ -92,18 +92,18 @@ You can also have a look at the [spikeinterface-gui](https://github.com/SpikeInt
 
 ## How to install spikeinterface
 
-You can install the latest version of `spikeinterface` version with pip:
+You can install the latest version of `spikeinterface` version with pip (using quotes ensures `pip install` works in all terminals/shells):
 
 ```bash
-pip install spikeinterface[full]
+pip install "spikeinterface[full]"
 ```
 
 The `[full]` option installs all the extra dependencies for all the different sub-modules.
 
 To install all interactive widget backends, you can use:
 
 ```bash
- pip install spikeinterface[full,widgets]
+ pip install "spikeinterface[full,widgets]"
 ```
 
 

diff --git a/doc/api.rst b/doc/api.rst
@@ -338,59 +338,58 @@ spikeinterface.curation
 spikeinterface.generation
 -------------------------
 
+.. currentmodule:: spikeinterface.generation
+
 Core
 ~~~~
-.. automodule:: spikeinterface.generation
-
-    .. autofunction:: generate_recording
-    .. autofunction:: generate_sorting
-    .. autofunction:: generate_snippets
-    .. autofunction:: generate_templates
-    .. autofunction:: generate_recording_by_size
-    .. autofunction:: generate_ground_truth_recording
-    .. autofunction:: add_synchrony_to_sorting
-    .. autofunction:: synthesize_random_firings
-    .. autofunction:: inject_some_duplicate_units
-    .. autofunction:: inject_some_split_units
-    .. autofunction:: synthetize_spike_train_bad_isi
-    .. autofunction:: inject_templates
-    .. autofunction:: noise_generator_recording
-    .. autoclass:: InjectTemplatesRecording
-    .. autoclass:: NoiseGeneratorRecording
+
+
+.. autofunction:: generate_recording
+.. autofunction:: generate_sorting
+.. autofunction:: generate_snippets
+.. autofunction:: generate_templates
+.. autofunction:: generate_recording_by_size
+.. autofunction:: generate_ground_truth_recording
+.. autofunction:: add_synchrony_to_sorting
+.. autofunction:: synthesize_random_firings
+.. autofunction:: inject_some_duplicate_units
+.. autofunction:: inject_some_split_units
+.. autofunction:: synthetize_spike_train_bad_isi
+.. autofunction:: inject_templates
+.. autofunction:: noise_generator_recording
+.. autoclass:: InjectTemplatesRecording
+.. autoclass:: NoiseGeneratorRecording
 
 Drift
 ~~~~~
-.. automodule:: spikeinterface.generation
 
-    .. autofunction:: generate_drifting_recording
-    .. autofunction:: generate_displacement_vector
-    .. autofunction:: make_one_displacement_vector
-    .. autofunction:: make_linear_displacement
-    .. autofunction:: move_dense_templates
-    .. autofunction:: interpolate_templates
-    .. autoclass:: DriftingTemplates
-    .. autoclass:: InjectDriftingTemplatesRecording
+.. autofunction:: generate_drifting_recording
+.. autofunction:: generate_displacement_vector
+.. autofunction:: make_one_displacement_vector
+.. autofunction:: make_linear_displacement
+.. autofunction:: move_dense_templates
+.. autofunction:: interpolate_templates
+.. autoclass:: DriftingTemplates
+.. autoclass:: InjectDriftingTemplatesRecording
 
 Hybrid
 ~~~~~~
-.. automodule:: spikeinterface.generation
 
-    .. autofunction:: generate_hybrid_recording
-    .. autofunction:: estimate_templates_from_recording
-    .. autofunction:: select_templates
-    .. autofunction:: scale_template_to_range
-    .. autofunction:: relocate_templates
-    .. autofunction:: fetch_template_object_from_database
-    .. autofunction:: fetch_templates_database_info
-    .. autofunction:: list_available_datasets_in_template_database
-    .. autofunction:: query_templates_from_database
+.. autofunction:: generate_hybrid_recording
+.. autofunction:: estimate_templates_from_recording
+.. autofunction:: select_templates
+.. autofunction:: scale_template_to_range
+.. autofunction:: relocate_templates
+.. autofunction:: fetch_template_object_from_database
+.. autofunction:: fetch_templates_database_info
+.. autofunction:: list_available_datasets_in_template_database
+.. autofunction:: query_templates_from_database
 
 
 Noise
 ~~~~~
-.. automodule:: spikeinterface.generation
 
-    .. autofunction:: generate_noise
+.. autofunction:: generate_noise
 
 
 spikeinterface.sortingcomponents
@@ -408,12 +407,6 @@ Peak Detection
 
     .. autofunction:: detect_peaks
 
-Motion Correction
-~~~~~~~~~~~~~~~~~
-.. automodule:: spikeinterface.sortingcomponents.motion_interpolation
-
-    .. autoclass:: InterpolateMotionRecording
-
 Clustering
 ~~~~~~~~~~
 .. automodule:: spikeinterface.sortingcomponents.clustering
@@ -425,3 +418,15 @@ Template Matching
 .. automodule:: spikeinterface.sortingcomponents.matching
 
     .. autofunction:: find_spikes_from_templates
+
+Motion Correction
+~~~~~~~~~~~~~~~~~
+.. automodule:: spikeinterface.sortingcomponents.motion
+
+    .. autoclass:: Motion
+    .. autofunction:: estimate_motion
+    .. autofunction:: interpolate_motion
+    .. autofunction:: correct_motion_on_peaks
+    .. autofunction:: interpolate_motion_on_traces
+    .. autofunction:: clean_motion_vector
+    .. autoclass:: InterpolateMotionRecording
diff --git a/doc/conf.py b/doc/conf.py
@@ -74,6 +74,8 @@
     "IPython.sphinxext.ipython_console_highlighting"
 ]
 
+autosectionlabel_prefix_document = True
+
 numpydoc_show_class_members = False
 
 
@@ -128,7 +130,7 @@
                                        '../examples/tutorials/widgets',
                                        ]),
     'within_subsection_order': FileNameSortKey,
-    'ignore_pattern': '/generate_',
+    'ignore_pattern': '/generate_*',
     'nested_sections': False,
     'copyfile_regex': r'.*\.rst|.*\.png|.*\.svg'
 }

diff --git a/doc/get_started/install_sorters.rst b/doc/get_started/install_sorters.rst
@@ -27,7 +27,7 @@ sorters to retrieve installation instructions for other operating systems.
 We use **pip** to install packages, but **conda** should also work in many cases.
 
 Some novel spike sorting algorithms are implemented directly in SpikeInterface using the
-:py:mod:`spikeinterface.sortingcomponents` module. Checkout the :ref:`SpikeInterface-based spike sorters` section of this page
+:py:mod:`spikeinterface.sortingcomponents` module. Checkout the :ref:`get_started/install_sorters:SpikeInterface-based spike sorters` section of this page
 for more information!
 
 If you experience installation problems please directly contact the authors of these tools or write on the

diff --git a/doc/get_started/installation.rst b/doc/get_started/installation.rst
@@ -102,4 +102,4 @@ Sub-modules have more dependencies, so you should also install:
 
 
 All external spike sorters can be either run inside containers (Docker or Singularity - see :ref:`containerizedsorters`)
-or must be installed independently (see :ref:`Installing Spike Sorters`).
+or must be installed independently (see :ref:`get_started/install_sorters:Installing Spike Sorters`).
diff --git a/doc/how_to/benchmark_with_hybrid_recordings.rst b/doc/how_to/benchmark_with_hybrid_recordings.rst
@@ -24,7 +24,7 @@ order to smoothly inject spikes into the recording.
     import spikeinterface.generation as sgen
     import spikeinterface.widgets as sw
 
-    from spikeinterface.sortingcomponents.motion_estimation import estimate_motion
+    from spikeinterface.sortingcomponents.motion import estimate_motion
 
     import numpy as np
     import matplotlib.pyplot as plt
@@ -1202,63 +1202,63 @@ drifts when injecting hybrid spikes.
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Original file line number	Diff line number	Diff line change
Expand Up		@@ -102,4 +102,4 @@ Sub-modules have more dependencies, so you should also install:


		All external spike sorters can be either run inside containers (Docker or Singularity - see :ref:`containerizedsorters`)
		or must be installed independently (see :ref:`Installing Spike Sorters`).
		or must be installed independently (see :ref:`get_started/install_sorters:Installing Spike Sorters`).