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pythonbashpathanacondaconda
Brad Allen
Brad Allen

Reputation: 145

Conda activate/deactivate environment breaking PATH

I am finding that when I create a Conda environment source activate environment and then deactivate that environment source deactivate environment, my native bash commands no longer work.

I've attached an image of ls working before enabling an environment and then not afterwards. I assume that this is something because of my PATH - but I am a novice and am not sure specifically what to fix. I am doing this in Git Bash on Windows. Anaconda 3 and Python 3.5.

Please work ls, come on

Upvotes: 3

Views: 11220

Answers (4)

joaopcoelho
joaopcoelho

Reputation: 61

The correct way to deactivate a conda environment is to run conda deactivate, rather than source deactivate environment

Source: https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html?highlight=activate#deactivating-an-environment

Upvotes: 2

Richard Plevin
Richard Plevin

Reputation: 21

There are a few bugs in the activate/deactivate scripts, which I've fixed in versions I call activate.cygwin and deactivate.cygwin.

  • activate.cygwin: fixes 2 places where the conda command returns a string with a return "\r" at the end that confounds processing.

  • deactivate.cygwin: fixes conversion of /cygdrive/... to avoid error CondaValueError: Could not find environment: /cygdrivec:\Users\rjp\Anaconda2\envs...

I've posted the modified scripts to https://bitbucket.org/snippets/plevin/. See instructions at the top of activate.cygwin.

Upvotes: 2

chenxin
chenxin

Reputation: 423

I use Git Bash in Windows 10 and encountered the same problem too. The previous answer does not work for me, probably because I don't have any path set in ~/.bash_profile and ~/.bashrc.

I checked my path variable in a fresh git bash, it looks like:

/c/Users/chen_x/bin:/mingw64/bin:/usr/local/bin:/usr/bin:/bin:/mingw64/bin:/usr/bin:/c/Users/chen_x/bin....(more)

After . C:/Users/chen_x/Miniconda3/Scripts/activate C:/Users/chen_x/Miniconda3 and . activate snowflakes, the path becomes:

/C/Users/chen_x/Miniconda3/envs/snowflakes:(blalbla..):C:\Users\chen_x\Miniconda3\Library\bin;C:\Users\chen_x\Miniconda3;....(more)

I assume that git bash does not recognize pathes like C:\program files..., then added the following line to C:/Users/chen_x/Miniconda3/Scripts/activate right after the last EXPORT PATH= command (about line 78):

export PATH="$($_CONDA_PYTHON -c "import re; p=re.sub(r'\\\', r'/', r'$PATH'); p=re.sub('(;|:)([A-Z]):', lambda m: ':/'+m.group(2).lower(), p); print(p)")"

It works.

By the way, I create a ~/condaenv script to start conda environment:

#!/bin/bash
. C:/Users/chen_x/Miniconda3/Scripts/activate C:/Users/chen_x/Miniconda3

It would be convinent to :

. ~/condaenv
. activate snowflakes

Upvotes: 0

Lohit Gupta
Lohit Gupta

Reputation: 1081

Most probably your conda environment is replacing the parameters and environment variables defined in your local bash profile. I am sure if you open a new environment(bash session), you will find everything is working fine.

I would suggest you add a command to reload bash profile after deactivating the environment, so that the profile variable values will again be applied. It should solve the problem.

Upvotes: 2

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