Is anyone in the neuroscience field using kilosort 3 through spike interface available to help me with some issues/questions? I am currently trying to set up a pipeline using SpikeInterface but am running through some issues. #spikeinterface #kilosort #spikesorting #mountainsort #neuroscience #Python #programming

Please help #Coding question 🖥️
I am trying to install #Mountainsort (4) on Windows (10) (I know, I know).

It works on one of my Win10 computers, but doesn’t on any other ones that I’m trying to install this on.
When running ‘pip install mountainsort4’ I get this error: “command ‘some_path_on_my_comp\cl.exe’ failed with exit code 2”

I also get this error: " C:\some_path\Local\Temp\pip-install-kykt_efl\isosplit5_3fce77eb41cf47b4a1d4ca22afae35a2\src\isocut5.h(19): fatal error C1083: Cannot open include file: 'stdlib.h': No such file or directory"

I have googled this to death and tried everything and it just won’t fix itself. The cl.exe path exists. I added it to the environment variables (but maybe not properly?). It’s a Visual Studio function.
Seen this before? Any suggestions? 🙏
#Python #Programming

Edit (and thank you for all answers so far!):

  • I have tried running it in the visual studio console, it shows the same error.
  • I have tried running it in as administrator, same error..
  • I have tried replicating the conda environment from the computer that works onto the others, but it comes up with the same errors as when I install manually. The only detectable difference is that the working install has an older version of conda / anaconda.
  • I asked the repo owner and they said to use it on Linux (or using the windows subsystem for Linux), but I’d like to try and keep things as simple as possible (both for me and other users), and this is NOT simple. I know it can work on Win10 so I just want to replicate that.

Edit 2: I reinstalled Visual Studio stuff using these instructions
NOW I do not get the error about the missing stdlib.h anymore, and I can actually install isosplit5 which is a dependency of mountainsort, BUT - when I go back to running pip install mountainsort4 it now has new errors! (progress?) They look like syntax errors as described in this issue and they still end in the cl.exe error. At the end it said that it did build mountainsort4 but not isosplit5 and when I try to actually run mountainsort functions they say it's not installed. so Fail.

Edit 3: I am so desperate that I have created a Question on StackOverflow, yes yes
https://stackoverflow.com/questions/76887010/how-to-fix-missing-stdlib-h-file-and-failed-cl-exe-command-when-installing-m

Edit 4: Am I just using the 'wrong' version of those Visual Studio functions for the code? Like the code has not been adapted to current versions? But how can I know which version the code wants?

Edit 5: if I manage to install isosplit5... why does mountainsort try to 'build the wheels for isosplit5'? Is there a way to tell it to use the one that is already installed?

Edit 6 (Aug 15): I tried my pipeline in the Windows Subsystem for Linux. It had a C++ problem at first, but it worked after I ran sudo apt install build-essential.

Anyone knows about an equivalent to that instruction in Windows?
I think that would fix my problem... if it exists

Configure Visual Studio Code for Microsoft C++

Configure the C++ extension in Visual Studio Code to target Microsoft C++ on Windows.

Hi, is anyone using #Mountainsort with #Neuralynx data? Are you using #SpikeInterface to convert the input data? Would you share your code? 😃​🙏​
#SpikeSorting