How to solve the issue of the conflict of anaconda and virtualenv

Question

I was using virtualenv all the time and then I had also installed anaconda. Just now I tried to activate a virtual environment using the way of anaconda like source activate helloworld. (Indeed I don't remember if this is exactly the command I typed in). And then the environment had been activated. But when I tried to run the notebook, it was said that some libraries didn't exist even if I had installed them already in that environment. Not until then did I realize I had activated the wrong environment. And then I close the tab and cd to hellowworld and did source bin/activate. But it was too late. I got this as the output prepending /home/lcc/anaconda3/envs/bin to PATH and the environment was not activated expectedly. Do you know how to solve this issue? Thanks!

Here is the full content of the activate file under /hello/world:

#!/bin/bash

# Determine the directory containing this script
if [[ -n $BASH_VERSION ]]; then
    _SCRIPT_LOCATION=${BASH_SOURCE[0]}
    SHELL="bash"
elif [[ -n $ZSH_VERSION ]]; then
    _SCRIPT_LOCATION=${funcstack[1]}
    SHELL="zsh"
else
    echo "Only bash and zsh are supported"
    return 1
fi
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")

if [ $# -gt 1 ]; then
    (>&2 echo "Error: did not expect more than one argument.")
    (>&2 echo "    (Got $@)")
    return 1
fi

case "$(uname -s)" in
    CYGWIN*|MINGW32*|MSYS*)
        EXT=".exe"
        ;;
    *)
        EXT=""
        ;;
esac

# Export whatever PS setting we have, so it is available to Python subprocesses
export PS1

# Ensure that this script is sourced, not executed
# Also note that errors are ignored as `activate foo` doesn't generate a bad
# value for $0 which would cause errors.
if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "activate" ]]; then
    (>&2 echo "Error: activate must be sourced. Run 'source activate envname'
instead of 'activate envname'.
")
    "$_CONDA_DIR/conda" ..activate $SHELL$EXT -h
    exit 1
fi

"$_CONDA_DIR/conda" ..checkenv $SHELL$EXT "$@"
if (( $? != 0 )); then
    return 1
fi

# Ensure we deactivate any scripts from the old env
#   Note: this empties $@.  Preserve a copy.
args=$@
source "$_CONDA_DIR/deactivate"

_NEW_PATH=$("$_CONDA_DIR/conda" ..activate $SHELL$EXT "$args")
if (( $? == 0 )); then
    export CONDA_PATH_BACKUP="$PATH"
    # export this to restore it upon deactivation
    export CONDA_OLD_PS1=$PS1

    export PATH="$_NEW_PATH"
    # Get first path (should be full path prefix of our env)
    # inner string extraction pulls off first path
    # outer string removes /bin if present (on Unix)
    firstpath=${PATH%%:*}
    export CONDA_DEFAULT_ENV="$(echo ${firstpath} | sed "s|/bin$||")" &>/dev/null
    # Legacy support: CONDA_DEFAULT_ENV used to be either env name or full path if given as path.
    #    CONDA_DEFAULT_ENV is now always full path.
    #    Keep CONDA_ENV_PATH around, and have it mirror CONDA_DEFAULT_ENV.
    #    Last date of change: 2016-04-18
    export CONDA_ENV_PATH=$CONDA_DEFAULT_ENV

    export PS1="$( "$_CONDA_DIR/conda" ..setps1 $SHELL$EXT "$args" )"

    # Load any of the scripts found $PREFIX/etc/conda/activate.d AFTER activation
    _CONDA_D="${CONDA_DEFAULT_ENV}/etc/conda/activate.d"
    if [[ -d "$_CONDA_D" ]]; then
        IFS=$(echo -en "\n\b")&>/dev/null  && for f in $(find "$_CONDA_D" -iname "*.sh"); do source "$f"; done
    fi
else
    return $?
fi

if [[ -n $BASH_VERSION ]]; then
    hash -r
elif [[ -n $ZSH_VERSION ]]; then
    rehash
else
    echo "Only bash and zsh are supported"
    return 1
fi

Answer 1

It's not clear from your question what you expect "activate" to do. Is it activating a virtualenv, or is it activating a conda environment.

When you install miniconda or anaconda, you are given an option to add it to PATH. If you do so, then it probably always comes before your virtualenv activate script. You can rename one or the other, or create an alias to the virtualenv one that calls it with an absolute path to the activate script. You can also move Anaconda so that it's appended rather than prepended, but then the virtualenv activate will always be used rather than the conda one (barring absolute paths).

To append conda's path, look in ~/.bashrc or ~/.bash_profile and change

export PATH=<anaconda path>:$PATH

to

export PATH=$PATH:<anaconda path>