Problems installing phy

I encountered a weird error while trying to reinstall phy. Phy was working well on my machine after initial installation, but stopped working after rebooting my computer. I have reinstalled miniconda, and tried to reinstall phy, but I keep running into the following error when typing conda env create -n phy:

AttributeError: '_NamespacePath' object has no attribute 'sort'
An unexpected error has occurred.
Please consider posting the following information to the
conda GitHub issue tracker at:

    https://github.com/conda/conda/issues



Current conda install:

               platform : win-64
          conda version : 4.2.12
       conda is private : False
      conda-env version : 4.2.12
    conda-build version : not installed
         python version : 3.5.2.final.0
       requests version : 2.11.1
       root environment : C:\Users\jgeerts\AppData\Local\Continuum\Miniconda3  (
writable)
    default environment : C:\Users\jgeerts\AppData\Local\Continuum\Miniconda3
       envs directories : C:\Users\jgeerts\AppData\Local\Continuum\Miniconda3\en
vs
          package cache : C:\Users\jgeerts\AppData\Local\Continuum\Miniconda3\pk
gs
           channel URLs : https://repo.continuum.io/pkgs/free/win-64
                          https://repo.continuum.io/pkgs/free/noarch
                          https://repo.continuum.io/pkgs/pro/win-64
                          https://repo.continuum.io/pkgs/pro/noarch
                          https://repo.continuum.io/pkgs/msys2/win-64
                          https://repo.continuum.io/pkgs/msys2/noarch
            config file : None
           offline mode : False



`$ C:\Users\jgeerts\AppData\Local\Continuum\Miniconda3\Scripts\conda-env-script.
py create -n phy`




    Traceback (most recent call last):
      File "C:\Users\jgeerts\AppData\Local\Continuum\Miniconda3\lib\site-package
s\conda\exceptions.py", line 479, in conda_exception_handler
        return_value = func(*args, **kwargs)
      File "C:\Users\jgeerts\AppData\Local\Continuum\Miniconda3\lib\site-package
s\conda_env\cli\main_create.py", line 111, in execute
        installer.install(prefix, pkg_specs, args, env)
      File "C:\Users\jgeerts\AppData\Local\Continuum\Miniconda3\lib\site-package
s\conda_env\installers\pip.py", line 8, in install
        pip_cmd = pip_args(prefix) + ['install', ] + specs
      File "C:\Users\jgeerts\AppData\Local\Continuum\Miniconda3\lib\site-package
s\conda_env\pip_util.py", line 30, in pip_args
        pip_version = subprocess.check_output(ret + ['-V']).decode('utf-8').spli
t()[1]
      File "C:\Users\jgeerts\AppData\Local\Continuum\Miniconda3\lib\subprocess.p
y", line 626, in check_output
        **kwargs).stdout
      File "C:\Users\jgeerts\AppData\Local\Continuum\Miniconda3\lib\subprocess.p
y", line 708, in run
        output=stdout, stderr=stderr)
    subprocess.CalledProcessError: Command '['C:\\Users\\jgeerts\\AppData\\Local
\\Continuum\\Miniconda3\\envs\\phy\\python.exe', 'C:\\Users\\jgeerts\\AppData\\L
ocal\\Continuum\\Miniconda3\\envs\\phy\\Scripts\\pip-script.py', '-V']' returned
 non-zero exit status 1

[arnal46]

At first, thank you for the answer! I was installed the gcc and part of the issue disappeared… but the phy software didn’t run.

I find the solution: NOT install miniconda from that webpage http://conda.pydata.org/miniconda.html

You have to install the version 4.1.11 (in my particular case Miniconda3-4.1.11-Linux-x86_64.sh) because it have python 3.5.2. The other installs the 3.6 version and it seems is not compatible. Link to find it: https://repo.continuum.io/miniconda/

I commented the next steps for help to install “more easy”:

1. Download the environment.yml file. (and replace the original file in ‘phy-master’ folder and copy requirements-dev.txt and paste it and rename the copy to: requirements.txt)

2. Open a terminal (on Windows, cmd, not Powershell) in the directory where you saved the file (‘phy-master’) and type:

conda env create -n phy
source activate phy  # omit the `source` on Windows
pip install phy phycontrib

1. Done! Now, to use phy, you have to first type source activate phy in a terminal (omit the source on Windows), and then call phy.

[caraslab]

I was able to get Phy to install by removing klustakwik2 from the environment.yml file. The rest of the libraries installed just fine, and I confirmed with Cyrille that if you’re using Phy with data that’s been processed with kilosort (as I am doing), there’s no need for klustakwik2. Not sure what kind of sorting program you’re using though, so double check first that you don’t actually need klustakwik2. If you do… sorry, I still haven’t found a solution to get it to install. If you find a solution, please do let me know!