I have encountered this problem while trying to activate my virtual environment in a remote machine using SSH. The environment on both sides is Linux. My PC is actually on Windows 10. Thanks to a new Ubuntu container available in Window10, it is highly convenient to run Ubuntu without launching a virtual machine.
Want to know how to resolve Your shell has not been properly configured to use ‘conda activate‘ error? Here is an efficient and clear solution!
Problem:
>>> conda activate
While executing the command above, I got the following error:
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run
$ conda init
Currently supported shells are:
- bash
- fish
- tcsh
- xonsh
- zsh
- powershell
See 'conda init --help' for more information and options.
IMPORTANT: You may need to close and restart your shell after running 'conda init'.
Verification:
Of course, I follow the instruction and run the conda init command. No luck. Then I verify the status of the conda environment:
>>> which conda
==> /home/zkang/.condarc <== ssl_verify: True channels: - defaults
>>> conda info
active environment : None
user config file : /home/zkang/.condarc
populated config files : /home/zkang/.condarc
conda version : 4.7.12
conda-build version : 3.18.9
python version : 3.7.4.final.0
virtual packages : __cuda=10.2
base environment : /anaconda3 (writable)
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /anaconda3/pkgs
/home/zkang/.conda/pkgs
envs directories : /anaconda3/envs
/home/zkang/.conda/envs
platform : linux-64
user-agent : conda/4.7.12 requests/2.22.0 CPython/3.7.4 Linux/4.15.0-76-generic ubuntu/18.04.4 glibc/2.27
So we are sure that conda is installed in the remote machine. Then how to activate my environment?
Solution:
A simpler and cleaner solution is as follows. You
>>> eval "$(conda shell.bash hook)" >>> conda activate
Then the environment can be activated correctly.
Why?
I found this solution in various answers, but they hardly explain why we should do this. Well, I have to say that I am not an expert to the command line nor the conda configuration. I can only dig a little bit deeper and try to reveal some of the truth.
The magic of the command eval can be found here. The basic idea is that the eval command first evaluates the argument and then runs the command stored in the argument. In this case, it means that the script generated by conda shell.bash hook is executed. So what is this script?
Let's have a look:
>>> conda shell.bash hook
export CONDA_EXE='/anaconda3/bin/conda'
export _CE_M=''
export _CE_CONDA=''
export CONDA_PYTHON_EXE='/anaconda3/bin/python'
# Copyright (C) 2012 Anaconda, Inc
# SPDX-License-Identifier: BSD-3-Clause
__add_sys_prefix_to_path() {
# In dev-mode CONDA_EXE is python.exe and on Windows
# it is in a different relative location to condabin.
if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then
SYSP=$(\dirname "${CONDA_EXE}")
else
SYSP=$(\dirname "${CONDA_EXE}")
SYSP=$(\dirname "${SYSP}")
fi
if [ -n "${WINDIR+x}" ]; then
PATH="${SYSP}/bin:${PATH}"
PATH="${SYSP}/Scripts:${PATH}"
PATH="${SYSP}/Library/bin:${PATH}"
PATH="${SYSP}/Library/usr/bin:${PATH}"
PATH="${SYSP}/Library/mingw-w64/bin:${PATH}"
PATH="${SYSP}:${PATH}"
else
PATH="${SYSP}/bin:${PATH}"
fi
\export PATH
}
__conda_hashr() {
if [ -n "${ZSH_VERSION:+x}" ]; then
\rehash
elif [ -n "${POSH_VERSION:+x}" ]; then
: # pass
else
\hash -r
fi
}
__conda_activate() {
if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
# Handle transition from shell activated with conda <= 4.3 to a subsequent activation
# after conda updated to >= 4.4. See issue #6173.
PS1="$CONDA_PS1_BACKUP"
\unset CONDA_PS1_BACKUP
fi
\local cmd="$1"
shift
\local ask_conda
OLDPATH="${PATH}"
__add_sys_prefix_to_path
ask_conda="$(PS1="$PS1" "$CONDA_EXE" $_CE_M $_CE_CONDA shell.posix "$cmd" "$@")" || \return $?
PATH="${OLDPATH}"
\eval "$ask_conda"
__conda_hashr
}
__conda_reactivate() {
\local ask_conda
OLDPATH="${PATH}"
__add_sys_prefix_to_path
ask_conda="$(PS1="$PS1" "$CONDA_EXE" $_CE_M $_CE_CONDA shell.posix reactivate)" || \return $?
PATH="${OLDPATH}"
\eval "$ask_conda"
__conda_hashr
}
conda() {
if [ "$#" -lt 1 ]; then
"$CONDA_EXE" $_CE_M $_CE_CONDA
else
\local cmd="$1"
shift
case "$cmd" in
activate|deactivate)
__conda_activate "$cmd" "$@"
;;
install|update|upgrade|remove|uninstall)
OLDPATH="${PATH}"
__add_sys_prefix_to_path
"$CONDA_EXE" $_CE_M $_CE_CONDA "$cmd" "$@"
\local t1=$?
PATH="${OLDPATH}"
if [ $t1 = 0 ]; then
__conda_reactivate
else
return $t1
fi
;;
*)
OLDPATH="${PATH}"
__add_sys_prefix_to_path
"$CONDA_EXE" $_CE_M $_CE_CONDA "$cmd" "$@"
\local t1=$?
PATH="${OLDPATH}"
return $t1
;;
esac
fi
}
if [ -z "${CONDA_SHLVL+x}" ]; then
\export CONDA_SHLVL=0
# In dev-mode CONDA_EXE is python.exe and on Windows
# it is in a different relative location to condabin.
if [ -n "${_CE_CONDA+x}" ] && [ -n "${WINDIR+x}" ]; then
PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
else
PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
fi
\export PATH
# We're not allowing PS1 to be unbound. It must at least be set.
# However, we're not exporting it, which can cause problems when starting a second shell
# via a first shell (i.e. starting zsh from bash).
if [ -z "${PS1+x}" ]; then
PS1=
fi
fi
If I understand correctly, this script explicitly define some behaviors of the command conda, e.g. activate|deactivate|install|update|upgrade|remove|uninstall. For instance, if we type the command conda activate <env_name>, it would call __conda_activate() function to initialize the environment.
In this way, we don't need to go through the annoying conda init command. As a result, the initialization can be done and the script automatically activates the base environment for use.
That's it! Since I have now the environement ready, I can run my tasks on the remote server freely.
Reference
https://askubuntu.com/questions/849470/how-do-i-activate-a-conda-environment-in-my-bashrc
https://github.com/conda/conda/issues/7980
https://stackoverflow.com/questions/34534513/calling-conda-source-activate-from-bash-script