Merge pull request #2015 from zm711/doc-fixes

Fix a few more documentation typos

doc/development/development.rst

@@ -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

doc/install_sorters.rst

@@ -117,7 +117,7 @@ Kilosort2.5
 
       git clone https://github.com/MouseLand/Kilosort
       # provide installation path by setting the KILOSORT2_5_PATH environment variable
-      # or using Kilosort2_5Sorter.set_kilosort2_path()
+      # or using Kilosort2_5Sorter.set_kilosort2_5_path()
 
 * See also for Matlab/CUDA: https://www.mathworks.com/help/parallel-computing/gpu-support-by-release.html
 

doc/modules/sorters.rst

@@ -239,7 +239,7 @@ There are three options:
 1. **released PyPi version**: if you installed :code:`spikeinterface` with :code:`pip install spikeinterface`,
    the latest released version will be installed in the container.
 
-2. **development :code:`main` version**: if you installed :code:`spikeinterface` from source from the cloned repo
+2. **development** :code:`main` **version**: if you installed :code:`spikeinterface` from source from the cloned repo
    (with :code:`pip install .`) or with :code:`pip install git+https://github.com/SpikeInterface/spikeinterface.git`,
    the current development version from the :code:`main` branch will be installed in the container.
 
@@ -458,7 +458,7 @@ Here is the list of external sorters accessible using the run_sorter wrapper:
 * **Kilosort**  :code:`run_sorter('kilosort')`
 * **Kilosort2** :code:`run_sorter('kilosort2')`
 * **Kilosort2.5** :code:`run_sorter('kilosort2_5')`
-* **Kilosort3** :code:`run_sorter('Kilosort3')`
+* **Kilosort3** :code:`run_sorter('kilosort3')`
 * **PyKilosort** :code:`run_sorter('pykilosort')`
 * **Klusta** :code:`run_sorter('klusta')`
 * **Mountainsort4** :code:`run_sorter('mountainsort4')`
@@ -474,7 +474,7 @@ Here is the list of external sorters accessible using the run_sorter wrapper:
 Here a list of internal sorter based on `spikeinterface.sortingcomponents`; they are totally
 experimental for now:
 
-* **Spyking circus2** :code:`run_sorter('spykingcircus2')`
+* **Spyking Circus2** :code:`run_sorter('spykingcircus2')`
 * **Tridesclous2** :code:`run_sorter('tridesclous2')`
 
 In 2023, we expect to add many more sorters to this list.

doc/modules/sortingcomponents.rst

@@ -223,7 +223,7 @@ Here is a short example that depends on the output of "Motion interpolation":
 
 **Notes**:
   * :code:`spatial_interpolation_method` "kriging" or "iwd" do not play a big role.
-  * :code:`border_mode` is a very important parameter. It controls how to deal with the border because motion causes units on the
+  * :code:`border_mode` is a very important parameter. It controls dealing with the border because motion causes units on the
     border to not be present throughout the entire recording. We highly recommend the :code:`border_mode='remove_channels'`
     because this removes channels on the border that will be impacted by drift. Of course the larger the motion is
     the more channels are removed.
@@ -278,7 +278,7 @@ At the moment, there are five methods implemented:
   * 'naive': a very naive implemenation used as a reference for benchmarks
   * 'tridesclous': the algorithm for template matching implemented in Tridesclous
   * 'circus': the algorithm for template matching implemented in SpyKING-Circus
-  * 'circus-omp': a updated algorithm similar to SpyKING-Circus but with OMP (orthogonal macthing
+  * 'circus-omp': a updated algorithm similar to SpyKING-Circus but with OMP (orthogonal matching
     pursuit)
   * 'wobble' : an algorithm loosely based on YASS that scales template amplitudes and shifts them in time
     to match detected spikes