Issue installing on Windows, due to aux.py?

[hrj21]

Hello!

I tried to install ViScore into a new conda environment with reticulate today using the code below:

library(reticulate)
conda_create('r-phate-vivae', python_version = '3.11.7')
use_condaenv(condaenv = 'r-phate-vivae')

# Install ViVAE
conda_install(
  envname = 'r-phate-vivae',
  packages = c(
    'numpy==1.26.3', 'numba==0.59.0', 'pandas==2.2.0', 'matplotlib==3.8.2',
    'scipy==1.12.0', 'pynndescent==0.5.11', 'scikit-learn==1.4.0', 'pytorch==2.1.0',
    'scanpy==1.9.8'
))

py_install('git+https://github.com/saeyslab/ViVAE.git', pip = TRUE)

## Install ViScore
py_install('pyemd==1.0.0', pip = TRUE)
py_install('git+https://github.com/saeyslab/ViScore.git', pip = TRUE)

All goes fine until the final py_install() call, where I get the error below:

C:\Users\u061745\OneDrive - UCB\Documents\Projects\UCB_cytometry>CALL "C:\Users\u061745\AppData\Local\miniconda3\condabin\activate.bat" "C:\Users\u061745\AppData\Local\miniconda3\envs\r-vivae" 

C:\Users\u061745\OneDrive - UCB\Documents\Projects\UCB_cytometry>conda.bat activate "C:\Users\u061745\AppData\Local\miniconda3\envs\r-vivae" 
Collecting git+https://github.com/saeyslab/ViScore.git
  Cloning https://github.com/saeyslab/ViScore.git to c:\users\u061745\appdata\local\temp\pip-req-build-tfemt3qu
  Running command git clone --filter=blob:none --quiet https://github.com/saeyslab/ViScore.git 'C:\Users\u061745\AppData\Local\Temp\pip-req-build-tfemt3qu'
  error: invalid path 'benchmarking/aux.py'
  fatal: unable to checkout working tree
  warning: Clone succeeded, but checkout failed.
  You can inspect what was checked out with 'git status'
  and retry with 'git restore --source=HEAD :/'

  error: subprocess-exited-with-error
  
  × git clone --filter=blob:none --quiet https://github.com/saeyslab/ViScore.git 'C:\Users\u061745\AppData\Local\Temp\pip-req-build-tfemt3qu' did not run successfully.
  │ exit code: 128
  ╰─> See above for output.
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× git clone --filter=blob:none --quiet https://github.com/saeyslab/ViScore.git 'C:\Users\u061745\AppData\Local\Temp\pip-req-build-tfemt3qu' did not run successfully.
│ exit code: 128
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.
Error: Error installing package(s): "\"git+https://github.com/saeyslab/ViScore.git\""
In addition: Warning message:
In shell(fi, intern = intern) :
  'C:\Users\u061745\AppData\Local\Temp\RtmpcRwFPP\file3c7c53f5296f.bat' execution failed with error code 1

In particular, I'm looking at the line in there: error: invalid path 'benchmarking/aux.py', which it seems might be an illegal file name for Windows:

• https://stackoverflow.com/questions/36225708/cannot-create-a-directory-named-aux-or-starting-by-aux-on-windows-8-1
• https://stackoverflow.com/questions/61614004/cloning-succeded-but-checkout-failed-due-to-invalid-path-what-is-the-path-probl

Apologies if I'm making an incorrect conclusion there, and thanks again for the package.

Hefin