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hully

Member

Registered: 2022-11-14

Posts: 150

miniconda altered /usr/bin/env python

I have installed miniconda3 from the AUR

But now `/usr/bin/env python` opens `/opt/miniconda3/bin/python`.

This breaks a lot of my scripts since that python installation lacks the packages I need.

How can I make it point to `/usr/bin/python` again?

Last edited by hully (2022-12-27 16:53:14)

mpan

Member

Registered: 2012-08-01

Posts: 1,207

Website

Re: miniconda altered /usr/bin/env python

If you only built a package based on this PKGBUILD and installed it, this situation is not expected to happen. Something is missing in the description.

Didn’t you also modify your shell’s rc files by sourcing “/opt/miniconda3/etc/profile.d/conda.sh”? Or otherwise making them point to conda version?

If not, didn’t you run their installation script⁽¹⁾ directly instead of doing this through makepkg+pacman?
____
⁽¹⁾ One listed in the sources array.

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ewaller

Administrator

From: Pasadena, CA

Registered: 2009-07-13

Posts: 19,785

Re: miniconda altered /usr/bin/env python

What are the output of which -a python and of echo $PATH   ?

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hully

Member

Registered: 2022-11-14

Posts: 150

Re: miniconda altered /usr/bin/env python

Didn’t you also modify your shell’s rc files by sourcing “/opt/miniconda3/etc/profile.d/conda.sh”?

Yes I did.

It asked me to run some command which put this in my "~/.config/fish/config.fish":

# >>> mamba initialize >>>
# !! Contents within this block are managed by 'mamba init' !!
set -gx MAMBA_EXE "/usr/bin/micromamba"
set -gx MAMBA_ROOT_PREFIX "/home/raffaele/micromamba"
$MAMBA_EXE shell hook --shell fish --prefix $MAMBA_ROOT_PREFIX | source
# <<< mamba initialize <<<

What are the output of which -a python and of echo $PATH   ?

Here it is:

❯ which -a python
/opt/miniconda3/bin/python
/usr/bin/python

hully

Member

Registered: 2022-11-14

Posts: 150

Re: miniconda altered /usr/bin/env python

So how can I use my system's python while at the same time keeping these lines:

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/opt/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/opt/miniconda3/etc/profile.d/conda.sh" ]; then
        . "/opt/miniconda3/etc/profile.d/conda.sh"
    else
        export PATH="/opt/miniconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

at the end of my .bashrc?

They are needed otherwise conda complains when I activate environments

Trilby

Inspector Parrot

Registered: 2011-11-29

Posts: 29,525

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Re: miniconda altered /usr/bin/env python

This breaks a lot of my scripts

If they are your scripts and you want them to use /bin/python rather than whichever python is indicated by /bin/env, then just fix the shebang.

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"UNIX is simple and coherent..." - Dennis Ritchie, "GNU's Not UNIX" -  Richard Stallman

hully

Member

Registered: 2022-11-14

Posts: 150

Re: miniconda altered /usr/bin/env python

I would like to remove those lines from my .bashrc because (1) it slows down opening of interactive shells significantly (2/3 sec) and (2) I would like to install python libraries with pacman, so that I can replicate the package list on other systems.

But at the same time I prefer not to lose the possibility to manage conda environments, as it seems that they are used by every deep learning frameworks / libraries

WorMzy

Forum Moderator

From: Scotland

Registered: 2010-06-16

Posts: 11,858

Website

Re: miniconda altered /usr/bin/env python

So remove the miniconda init junk from your shell init scripts and manually activate the conda environments when you need it.

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hully

Member

Registered: 2022-11-14

Posts: 150

Re: miniconda altered /usr/bin/env python

So remove the miniconda init junk from your shell init scripts and manually activate the conda environments when you need it.

I think I will do that. Thanks!