Cleanup PyKS docs
@@ -117,30 +117,30 @@ Kilosort3
pykilosort
----------
-* python, requires cuda
+* Python, requires cuda
* Url: https://github.com/MouseLand/pykilosort
-* Authors: Marius Pachitariu, Shashwat Sridhar, Alexander Morley, Cyril Rossant
+* Authors: Marius Pachitariu, Shashwat Sridhar, Alexander Morley, Cyrille Rossant
* Install the python cuda toolkit. In principle, this should work::
pip install cupy (or pip install cupy-cudaXXX)
-* However, I had to use conda to complete this installation successfully::
+* However, conda installation could be less painful::
conda install cupy
-* Next, install pykilosort::
+* Next, clone and install pykilosort. Note that we support the newer version on the `develop` branch::
pip install phylib, pypandoc
git clone https://github.com/MouseLand/pykilosort
+ git checkout develop
cd pykilosort
+ pip install -r requirements.txt
python setup.py install
-* Finally, a few package dependencies may be missing. I fixed this with::
+* Alternatively, you can use the `pyks2.yml` environment file in the pykilosort repo and update your favorite environment with::
- pip install numba, pydantic
-
-* Finally the pykilosort install may not copy the cuda files to the installed location. I had to copy these manually to my install location, e.g. ~/.conda/MY-ENV/lib/site-packages/pykilosort/pykilosort-ibl_1.3.0-py3.8.egg/pykilosort/cuda.
+ conda env update --name my-fav-env --file pyks2.yml --prune
* See also https://github.com/MouseLand/pykilosort#installation
