Merge branch 'main' into sparsity_method_to_densify

.github/workflows/installation-tips-test.yml

@@ -0,0 +1,33 @@
+name: Creates Conda Install for Installation Tips
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 12 * * 0"  # Weekly at noon UTC on Sundays
+
+jobs:
+  installation-tips-testing:
+    name: Build Conda Env on ${{ matrix.os }} OS
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -el {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            label: linux_dandi
+          - os: macos-latest
+            label: mac
+          - os: windows-latest
+            label: windows
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+    - name: Test Conda Environment Creation
+      uses: conda-incubator/[email protected]
+      with:
+        environment-file: ./installation_tips/full_spikeinterface_environment_${{ matrix.label }}.yml

doc/api.rst

@@ -19,6 +19,8 @@ spikeinterface.core
     .. autofunction:: extract_waveforms
     .. autofunction:: load_waveforms
     .. autofunction:: compute_sparsity
+    .. autoclass:: ChannelSparsity
+        :members:
     .. autoclass:: BinaryRecordingExtractor
     .. autoclass:: ZarrRecordingExtractor
     .. autoclass:: BinaryFolderRecording
@@ -48,17 +50,15 @@ spikeinterface.core
     .. autofunction:: get_template_extremum_channel
     .. autofunction:: get_template_extremum_channel_peak_shift
     .. autofunction:: get_template_extremum_amplitude
-
-..
-    .. autofunction:: read_binary
-    .. autofunction:: read_zarr
     .. autofunction:: append_recordings
     .. autofunction:: concatenate_recordings
     .. autofunction:: split_recording
     .. autofunction:: select_segment_recording
     .. autofunction:: append_sortings
     .. autofunction:: split_sorting
     .. autofunction:: select_segment_sorting
+    .. autofunction:: read_binary
+    .. autofunction:: read_zarr
 
 Low-level
 ~~~~~~~~~
@@ -67,7 +67,6 @@ Low-level
     :noindex:
 
     .. autoclass:: BaseWaveformExtractorExtension
-    .. autoclass:: ChannelSparsity
     .. autoclass:: ChunkRecordingExecutor
 
 spikeinterface.extractors
@@ -83,6 +82,7 @@ NEO-based
     .. autofunction:: read_alphaomega_event
     .. autofunction:: read_axona
     .. autofunction:: read_biocam
+    .. autofunction:: read_binary
     .. autofunction:: read_blackrock
     .. autofunction:: read_ced
     .. autofunction:: read_intan
@@ -98,10 +98,13 @@ NEO-based
     .. autofunction:: read_openephys_event
     .. autofunction:: read_plexon
     .. autofunction:: read_plexon_sorting
+    .. autofunction:: read_plexon2
+    .. autofunction:: read_plexon2_sorting
     .. autofunction:: read_spike2
     .. autofunction:: read_spikegadgets
     .. autofunction:: read_spikeglx
     .. autofunction:: read_tdt
+    .. autofunction:: read_zarr
 
 
 Non-NEO-based
@@ -214,8 +217,10 @@ spikeinterface.sorters
     .. autofunction:: print_sorter_versions
     .. autofunction:: get_sorter_description
     .. autofunction:: run_sorter
+    .. autofunction:: run_sorter_jobs
     .. autofunction:: run_sorters
     .. autofunction:: run_sorter_by_property
+    .. autofunction:: read_sorter_folder
 
 Low level
 ~~~~~~~~~

doc/conf.py

@@ -67,6 +67,8 @@
     'numpydoc',
     "sphinx.ext.intersphinx",
     "sphinx.ext.extlinks",
+    "IPython.sphinxext.ipython_directive",
+    "IPython.sphinxext.ipython_console_highlighting"
 ]
 
 numpydoc_show_class_members = False

doc/development/development.rst

@@ -1,5 +1,5 @@
 Development
-==========
+===========
 
 How to contribute
 -----------------
@@ -14,15 +14,15 @@ There are various ways to contribute to SpikeInterface as a user or developer. S
 * Writing unit tests to expand code coverage and use case scenarios.
 * Reporting bugs and issues.
 
-We use a forking workflow <https://www.atlassian.com/git/tutorials/comparing-workflows/forking-workflow>_ to manage contributions. Here's a summary of the steps involved, with more details available in the provided link:
+We use a forking workflow `<https://www.atlassian.com/git/tutorials/comparing-workflows/forking-workflow>`_ to manage contributions. Here's a summary of the steps involved, with more details available in the provided link:
 
 * Fork the SpikeInterface repository.
 * Create a new branch (e.g., :code:`git switch -c my-contribution`).
 * Modify the code, commit, and push changes to your fork.
 * Open a pull request from the "Pull Requests" tab of your fork to :code:`spikeinterface/main`.
 * By following this process, we can review the code and even make changes as necessary.
 
-While we appreciate all the contributions please be mindful of the cost of reviewing pull requests <https://rgommers.github.io/2019/06/the-cost-of-an-open-source-contribution/>_ .
+While we appreciate all the contributions please be mindful of the cost of reviewing pull requests `<https://rgommers.github.io/2019/06/the-cost-of-an-open-source-contribution/>`_ .
 
 
 How to run tests locally
@@ -201,7 +201,7 @@ Implement a new extractor
 SpikeInterface already supports over 30 file formats, but the acquisition system you use might not be among the
 supported formats list (***ref***). Most of the extractord rely on the `NEO <https://github.com/NeuralEnsemble/python-neo>`_
 package to read information from files.
-Therefore, to implement a new extractor to handle the unsupported format, we recommend make a new `neo.rawio `_ class.
+Therefore, to implement a new extractor to handle the unsupported format, we recommend make a new :code:`neo.rawio.BaseRawIO` class (see `example <https://github.com/NeuralEnsemble/python-neo/blob/master/neo/rawio/examplerawio.py#L44>`_).
 Once that is done, the new class can be easily wrapped into SpikeInterface as an extension of the
 :py:class:`~spikeinterface.extractors.neoextractors.neobaseextractors.NeoBaseRecordingExtractor`
 (for :py:class:`~spikeinterface.core.BaseRecording` objects) or