Solve conflicts

doc/api.rst

@@ -239,7 +239,6 @@ spikeinterface.comparison
     .. autofunction:: compare_sorter_to_ground_truth
     .. autofunction:: compare_templates
     .. autofunction:: compare_multiple_templates
-    .. autofunction:: aggregate_performances_table
     .. autofunction:: create_hybrid_units_recording
     .. autofunction:: create_hybrid_spikes_recording
 
@@ -272,12 +271,22 @@ spikeinterface.widgets
     .. autofunction:: set_default_plotter_backend
     .. autofunction:: get_default_plotter_backend
 
+    .. autofunction:: plot_agreement_matrix
     .. autofunction:: plot_all_amplitudes_distributions
     .. autofunction:: plot_amplitudes
     .. autofunction:: plot_autocorrelograms
+    .. autofunction:: plot_confusion_matrix
+    .. autofunction:: plot_comparison_collision_by_similarity
     .. autofunction:: plot_crosscorrelograms
+    .. autofunction:: plot_isi_distribution
     .. autofunction:: plot_motion
+    .. autofunction:: plot_multicomparison_agreement
+    .. autofunction:: plot_multicomparison_agreement_by_sorter
+    .. autofunction:: plot_multicomparison_graph
+    .. autofunction:: plot_peak_activity
+    .. autofunction:: plot_probe_map
     .. autofunction:: plot_quality_metrics
+    .. autofunction:: plot_rasters
     .. autofunction:: plot_sorting_summary
     .. autofunction:: plot_spike_locations
     .. autofunction:: plot_spikes_on_traces
@@ -286,34 +295,18 @@ spikeinterface.widgets
     .. autofunction:: plot_traces
     .. autofunction:: plot_unit_depths
     .. autofunction:: plot_unit_locations
+    .. autofunction:: plot_unit_presence
+    .. autofunction:: plot_unit_probe_map
     .. autofunction:: plot_unit_summary
     .. autofunction:: plot_unit_templates
     .. autofunction:: plot_unit_waveforms_density_map
     .. autofunction:: plot_unit_waveforms
-
-
-Legacy widgets
-~~~~~~~~~~~~~~
-
-These widgets are only available with the "matplotlib" backend
-
-.. automodule:: spikeinterface.widgets
-    :noindex:
-
-    .. autofunction:: plot_rasters
-    .. autofunction:: plot_probe_map
-    .. autofunction:: plot_isi_distribution
-    .. autofunction:: plot_peak_activity_map
-    .. autofunction:: plot_principal_component
-    .. autofunction:: plot_unit_probe_map
-    .. autofunction:: plot_confusion_matrix
-    .. autofunction:: plot_agreement_matrix
-    .. autofunction:: plot_multicomp_graph
-    .. autofunction:: plot_multicomp_agreement
-    .. autofunction:: plot_multicomp_agreement_by_sorter
-    .. autofunction:: plot_comparison_collision_pair_by_pair
-    .. autofunction:: plot_comparison_collision_by_similarity
-    .. autofunction:: plot_sorting_performance
+    .. autofunction:: plot_study_run_times
+    .. autofunction:: plot_study_unit_counts
+    .. autofunction:: plot_study_performances
+    .. autofunction:: plot_study_agreement_matrix
+    .. autofunction:: plot_study_summary
+    .. autofunction:: plot_study_comparison_collision_by_similarity
 
 
 spikeinterface.exporters

doc/import.rst

@@ -0,0 +1,81 @@
+Importing SpikeInterface
+========================
+
+SpikeInterface allows for the generation of powerful and reproducible spike sorting pipelines.
+Flexibility is built into the package starting from import to maximize the productivity of
+the developer and the scientist. Thus there are three ways that SpikeInterface and its components
+can be imported:
+
+
+Importing by Module
+-------------------
+
+Since each spike sorting pipeline involves a series of often repeated steps, many of the developers
+working on SpikeInterface recommend importing in a module by module fashion. This will allow you to
+keep track of your processing steps (preprocessing, postprocessing, quality metrics, etc.). This can
+be accomplished by:
+
+.. code-block:: python
+
+    import spikeinterface.core as si
+
+to import the :code:`core` module followed by:
+
+.. code-block:: python
+
+    import spikeinterface.extractors as se
+    import spikeinterface.preprocessing as spre
+    import spikeinterface.sorters as ss
+    import spikinterface.postprocessing as spost
+    import spikeinterface.qualitymetrics as sqm
+    import spikeinterface.exporters as sexp
+    import spikeinterface.comparsion as scmp
+    import spikeinterface.curation as scur
+    import spikeinterface.sortingcomponents as sc
+    import spikeinterface.widgets as sw
+
+to import any of the other modules you wish to use.
+
+The benefit of this approach is that it is lighter than importing the whole library as a flat module and allows
+you to choose which of the modules you actually want to use. It also reminds you what step of the pipeline each
+submodule is meant to be used for. If you don't plan to export the results out of SpikeInterface then you
+don't have to :code:`import spikeinterface.exporters`. Additionally the documentation of SpikeInterface is set-up
+in a modular fashion, so if you have a problem with the submodule  :code:`spikeinterface.curation`,you will know
+to go to the :code:`curation` section of this documention. The disadvantage of this approach is that you have
+more aliases to keep track of.
+
+
+Flat Import
+-----------
+
+A second option is to import the SpikeInterface package in :code:`full` mode.
+To accomplish this one does:
+
+
+.. code-block:: python
+
+    import spikeinterface.full as si
+
+
+This import statement will import all of the SpikeInterface modules as one flattened module.
+We recommend this approach for advanced (or lazy) users, since it requires a deeper knowledge of the API. The advantage
+being that users can access all functions using one alias without the need of memorizing all aliases.
+
+
+Importing Individual Functions
+------------------------------
+
+Finally, some users may find it useful to have extremely light imports and only import the exact functions
+they plan to use. This can easily be accomplished by importing functions directly into the name space.
+
+For example:
+
+.. code-block:: python
+
+    from spikeinterface.preprocessing import bandpass_filter, common_reference
+    from spikeinterface.core import extract_waveforms
+    from spikeinterface.extractors import read_binary
+
+As mentioned this approach only imports exactly what you plan on using so it is the most minimalist. It does require
+knowledge of the API to know which module to pull a function from. It could also lead to naming clashes if pulling
+functions directly from other scientific libraries. Type :code:`import this` for more information.

doc/index.rst

@@ -40,6 +40,7 @@ SpikeInterface is made of several modules to deal with different aspects of the
 
     overview
     installation
+    import
     modules/index
     how_to/index
     modules_gallery/index

doc/install_sorters.rst

@@ -32,8 +32,8 @@ Some novel spike sorting algorithms are implemented directly in SpikeInterface u
 :py:mod:`spikeinterface.sortingcomponents` module. Checkout the :ref:`si_based` section of this page
 for more information!
 
-If you experience installation problems please directly contact the authors of theses tools or write on the
-related mailing list, google group, etc.
+If you experience installation problems please directly contact the authors of these tools or write on the
+related mailing list, google group, GitHub issue page, etc.
 
 Please feel free to enhance this document with more installation tips.
 
@@ -251,31 +251,6 @@ Combinato
       # or using CombinatoSorter.set_combinato_path()
 
 
-Klusta (LEGACY)
-^^^^^^^^^^^^^^^
-
-* Python
-* Requires SpikeInterface<0.96.0 (and Python 3.7)
-* Url: https://github.com/kwikteam/klusta
-* Authors: Cyrille Rossant, Shabnam Kadir, Dan Goodman, Max Hunter, Kenneth Harris
-* Installation::
-
-       pip install Cython h5py tqdm
-       pip install click klusta klustakwik2
-
-* See also: https://github.com/kwikteam/phy
-
-
-Yass (LEGACY)
-^^^^^^^^^^^^^
-
-* Python, CUDA, torch
-* Requires SpikeInterface<0.96.0 (and Python 3.7)
-* Url: https://github.com/paninski-lab/yass
-* Authors: JinHyung Lee, Catalin Mitelut, Liam Paninski
-* Installation::
-
-      https://github.com/paninski-lab/yass/wiki/Installation-Local
 
 
 .. _si_based:
@@ -302,3 +277,50 @@ working not only at peak times but at all times, recovering more spikes close to
         pip install hdbscan
         pip install spikeinterface
         pip install numba  (or conda install numba as recommended by conda authors)
+
+
+Tridesclous2
+^^^^^^^^^^^^
+
+This is an upgraded version of Tridesclous, natively written in SpikeInterface.
+#Same add his notes.
+
+* Python
+* Requires: HDBSCAN and Numba
+* Authors: Samuel Garcia
+* Installation::
+
+      pip install hdbscan
+      pip install spikeinterface
+      pip install numba
+
+
+
+Legacy Sorters
+--------------
+
+Klusta (LEGACY)
+^^^^^^^^^^^^^^^
+
+* Python
+* Requires SpikeInterface<0.96.0 (and Python 3.7)
+* Url: https://github.com/kwikteam/klusta
+* Authors: Cyrille Rossant, Shabnam Kadir, Dan Goodman, Max Hunter, Kenneth Harris
+* Installation::
+
+       pip install Cython h5py tqdm
+       pip install click klusta klustakwik2
+
+* See also: https://github.com/kwikteam/phy
+
+
+Yass (LEGACY)
+^^^^^^^^^^^^^
+
+* Python, CUDA, torch
+* Requires SpikeInterface<0.96.0 (and Python 3.7)
+* Url: https://github.com/paninski-lab/yass
+* Authors: JinHyung Lee, Catalin Mitelut, Liam Paninski
+* Installation::
+
+      https://github.com/paninski-lab/yass/wiki/Installation-Local

doc/installation.rst

@@ -14,7 +14,7 @@ To install the current release version, you can use:
 
 The :code:`[full]` option installs all the extra dependencies for all the different sub-modules.
 
-Note that if using Z shell (:code:`zsh` - the default shell on mac), you will need to use quotes (:code:`pip install "spikeinterface[full]"`).
+Note that if using Z shell (:code:`zsh` - the default shell on macOS), you will need to use quotes (:code:`pip install "spikeinterface[full]"`).
 
 
 To install all interactive widget backends, you can use:
@@ -63,14 +63,14 @@ as :code:`spikeinterface` strongly relies on these packages to interface with va
 
 
 It is also sometimes useful to have local copies of :code:`neo` and :code:`probeinterface` to make changes to the code. To achieve this, repeat the first set of commands,
-replacing `https://github.com/SpikeInterface/spikeinterface.git` with the appropriate repository in the first code block of this section.
+replacing :code:`https://github.com/SpikeInterface/spikeinterface.git` with the appropriate repository in the first code block of this section.
 
 For beginners
 -------------
 
 We provide some installation tips for beginners in Python here:
 
-https://github.com/SpikeInterface/spikeinterface/tree/master/installation_tips
+https://github.com/SpikeInterface/spikeinterface/tree/main/installation_tips
 
 
 
@@ -89,12 +89,16 @@ Requirements
 Sub-modules have more dependencies, so you should also install:
 
   * zarr
+  * h5py
   * scipy
   * pandas
   * xarray
-  * sklearn
+  * scikit-learn
   * networkx
   * matplotlib
+  * numba
+  * distinctipy
+  * cuda-python (for non-macOS users)
 
 
 All external spike sorters can be either run inside containers (Docker or Singularity - see :ref:`containerizedsorters`)