From 2f4d50a6651d4fc0ba568463df61a350d62ddd33 Mon Sep 17 00:00:00 2001 From: zm711 <92116279+zm711@users.noreply.github.com> Date: Tue, 19 Sep 2023 08:32:16 -0400 Subject: [PATCH 1/2] typo corrections, link corrections --- doc/development/development.rst | 6 +++--- doc/install_sorters.rst | 2 +- doc/modules/sorters.rst | 6 +++--- doc/modules/sortingcomponents.rst | 4 ++-- 4 files changed, 9 insertions(+), 9 deletions(-) diff --git a/doc/development/development.rst b/doc/development/development.rst index f1371639c3..4704b9b1e6 100644 --- a/doc/development/development.rst +++ b/doc/development/development.rst @@ -14,7 +14,7 @@ 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 _ to manage contributions. Here's a summary of the steps involved, with more details available in the provided link: +We use a 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`). @@ -22,7 +22,7 @@ We use a forking workflow _ . +While we appreciate all the contributions please be mindful of the cost of reviewing pull requests ``_ . 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 `_ 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 ` class. 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 diff --git a/doc/install_sorters.rst b/doc/install_sorters.rst index 3fda05848c..10a3185c5c 100644 --- a/doc/install_sorters.rst +++ b/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 diff --git a/doc/modules/sorters.rst b/doc/modules/sorters.rst index 34ab3d1151..1b27ed442c 100644 --- a/doc/modules/sorters.rst +++ b/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. diff --git a/doc/modules/sortingcomponents.rst b/doc/modules/sortingcomponents.rst index aa62ea5b33..422eaea890 100644 --- a/doc/modules/sortingcomponents.rst +++ b/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 From b90e35b9df6bb03bac2a7c3e76e36c79c3f68af3 Mon Sep 17 00:00:00 2001 From: Zach McKenzie <92116279+zm711@users.noreply.github.com> Date: Tue, 19 Sep 2023 08:56:48 -0400 Subject: [PATCH 2/2] Update doc/development/development.rst Co-authored-by: Alessio Buccino --- doc/development/development.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/development/development.rst b/doc/development/development.rst index 4704b9b1e6..7656da11ab 100644 --- a/doc/development/development.rst +++ b/doc/development/development.rst @@ -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 `_ package to read information from files. -Therefore, to implement a new extractor to handle the unsupported format, we recommend make a new :code:``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 `_). 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