python - Best Practices with Anaconda and Brew

Question

I have just got a new Macbook with OSX Sierra, so want to ensure my development environment is setup properly.

I am looking to follow the 'best practices' mentioned here: https://github.com/nicolashery/mac-dev-setup

I need Python 2.x for work (urllib, Pandas, Numpy, Scikit-learn), and Python 3.x for some online classes (Pandas, Numpy, Django) I am taking. I have installed Python 2 and 3, using brew install python and brew install python3 respectively.

However, on this link, there is no mention of Anaconda, just IPython. Given that I already have Python 2 and 3 installed via Homebrew, is it even advisable to use anaconda, or should I stick to standard IPython as mentioned on the Github link above? I am confused after reading this post: OS X - Deciding between anaconda and homebrew Python environments

If Brew and Anaconda can indeed work together, what specific steps can I take to ensure that there are no conflicts between the two versions?

Answer 1

brew and conda tend not to play nicely together, but I think I have a set up that has worked quite well for me so far. It was inspired by this post.

You can add the following code to your .zshrc:

# Deactivates conda before running brew. 
# Re-activates conda if it was active upon completion.

brew() {
    local conda_env="$CONDA_DEFAULT_ENV"
    while [ "$CONDA_SHLVL" -gt 0  ]; do
        conda deactivate
    done
    command brew $@
    local brew_status=$?
    [ -n "${conda_env:+x}" ] && conda activate "$conda_env"
    return "$brew_status"
}

You want to deactivate conda before running brew so that brew doesn't find conda packages in your PATH whenever it tries to install something. In fact, brew doctor will complain if you have not deactivated conda before running brew, as mentioned in the post I link to above. (See also this question.)

One thing I should mention is that conda environments "stack", but the brew() function I've written above does not keep track of your stack of environments. (See below for a version of this function that keeps track of this.) For example, if you do conda activate newenv while a conda environment oldenv is active, then conda deactivate will return you to oldenv. However, if you run brew using the function I've written above after activating oldenv and then newenv, running conda deactivate will not return you to oldenv but will deactivate your conda environments entirely.

This function also probably creates some unnecessary overhead when running brew, as I believe you only really need to deactivate your conda environment when running brew install. That said, if you're the kind of person to care about that overhead enough, this answer probably doesn't tell you anything you didn't already know.

As a final note, brew cask install anaconda does not strike me as a good idea, since conda was designed to be installed in $HOME, but brew cask will want to install it in /usr/local, so that could lead to unpredictable behaviour.

Edit: Here's is a version of the brew function which leaves your conda environments as it found it:

brew() {
    local -a conda_envs
    while [ "$CONDA_SHLVL" -gt 0  ]; do
        conda_envs=("$CONDA_DEFAULT_ENV" $conda_envs)
        conda deactivate
    done
    command brew $@
    local brew_status=$?
    for env in $conda_envs; do
        conda activate "$env"
    done
    unset env
    return "$brew_status"
}

I've tested this in Zsh. I don't think it will work in Bash. If you want to use it in Bash, you will need to change the for loop declaration to say something like for env in ${conda_envs[@]}. I haven't tested this, however, so please test that it does what you need before use.