More complete pykilosort install instructions
I have submitted a pykilosort issue on the final point, hopefully this can be streamlined.
@@ -121,14 +121,27 @@ pykilosort
* Url: https://github.com/MouseLand/pykilosort
* Authors: Marius Pachitariu, Shashwat Sridhar, Alexander Morley, Cyril Rossant
-* Installation needs Matlab and cudatoolkit::
+* 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::
+
+ conda install cupy
- pip install cupy (or pip install cupy-cudaXXX) >>> can be quite hard
- pip install phylib, pypandic
+* Next, install pykilosort::
+
+ pip install phylib, pypandoc
git clone https://github.com/MouseLand/pykilosort
cd pykilosort
python setup.py install
+* Finally, a few package dependencies may be missing. I fixed this 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.
+
* See also https://github.com/MouseLand/pykilosort#installation
