Minimal Conda Setup Instructions

There’s an increasing amount of folks complaining that they need to watch a video for all their setting up tools etc.

In this vein, let me summarize what I consider a minimal list of facts and terminal commands to get up and running with a conda-based scientific Python environment.

Some basic facts to understand

A few facts that help to understand what’s going on below:

  • Overall and very approximately (but sufficiently), conda is exactly 2 things:
    • A package/library getter
    • A path manager enabling easy switching between different Python environments.
  • The command conda activate used below simply creates a temporary PATH variable pointing the system’s search for executables into your currently activated conda environment.
  • The conda command line tool is increasingly being replaced by the faster mamba tool.
    • mamba is a drop-in replacement for conda, so for all commands you just replace conda with mamba.
    • However, mamba is still using conda underneath, so don’t uninstall it, you need both!
    • Only install mamba into your base environment.
      • That’s for people who read this and want to add mamba to their system.
      • New starters should use below’s installer that exactly does that.
    • Also, there’s a few remaining commands that still run smoother using conda, so if mamba is giving you a hard time, just try the same command parameters using conda instead of mamba
  • conda/mamba environments are ALWAYS going into user space, never ever should you require root/superuser access.
    • Unless you are an admin that installs a systemwide environment for many users.
  • conda gets its packages from so called channels, and there’s a community channel called conda-forge that most of us are using successfully for years.
    • The installer linked below will configure to use the conda-forge channel all the time (hence the name mambaforge), but you can always change that later, and, winningly, configure this to be different per environment!
    • It is recommended to not install packages from different channels into the same environment
  • Creating new environments is fast and cheap (hard-links between downloaded packages when used in more than one environment.)
    • So, when in doubt if you should install a potentially dodgy Python package into your main work environment, maybe better and simply just create a new one (see commands below).

Installation instructions

Installing base

So, here we go:

  1. Download the script-based installer for your operating system here:

For a Unix-like platform like macOS and Linux, execute these commands, they will first downlad the right installer and then run in:

wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh
bash Mambaforge-$(uname)-$(uname -m).sh
  1. Restart the shell (exit -> open new one)

  2. Check that you have the conda and mamba command available:

which conda
which mamba

They should both point to your chosen install folder + /condabin.

Installing your main work environment

Now you are good to go to:

  1. Create your main work environment.

I DO NOT recommend to work in the base environment, because that’s used for managing all envs, so if you mess up in there, you loose all other envs as well (potentially). This is actually very similar to the old advice on the Mac to not work with the system Python, because the OS was using it for management tasks.

So, let’s say you want to create a Python 3.8 environment as your standard

3.9 is also fully supported for science analysis I’d say, just some dev tools don’t like it yet.

I usually call my main envs by the python version that’s installed in there, so in this case:

conda create -n py38 python=3.8

After that’s executed successfully you need to activate it:

conda activate py38

and NOW we change to use mamba because the packages we like to install need to be checked for each other’s dependency requirements which is the time consuming task at which mamba excels so much.

Let’s say we want to install some important basic science packages:

mamba install pandas scipy astropy jupyterlab nb_conda_kernels

nb_conda_kernels is an extremely useful package that helps you to easily switch between conda envs inside jupyter notebooks

This install command will now churn and come back with a HUGE list of packages to install because those packages are what your wanted ones are based of.

You should confirm the choices by typing return (or y) and then mamba will download quite fast in parallel the required packages and make them available to your current env.

PIP installs

What if the package of your choice isn’t available on conda-forge? (mamba search <pkg_name>)

Then you could install it from pypi.org using pip.

Unfortunately, pip installs still in 2021 can mess up your conda envs. :(

Having said that, with a bit of care I manage to mix a lot of PIP installs into my conda envs without any issues. Here is my strategy:

NOTE: Activate the conda env where you need the pip things BEFORE you start installing with pip! It’s one of the most frequent problems for Python beginners to have not done that and then have pip installed new packages somewhere where you didn’t expect it to be.

  • Find out what other packages the pip package depends on and install as many of them as possible via mamba/conda.
  • As the last step, if possible, only install your required package via pip, like pip install nbverbose for example.
  • Don’t worry if there’s other packages coming in, that part works just like in conda.

Let me repeat above advice again in other words as it’s really that important:

  • pip is “current path dependent”.
    • That means, you have to activate the conda env where you want things to end up in, because then the PATH points to the right pip.
    • Yes, every conda env has its own pip command.
    • Alternatively, you can use the full path to the pip command you should be using, but I find that to be quite more scary and less user-friendly for new terminal users, which is why I prefer my above advice to simply always activate the env where you want things to install.

Hope this helps someone!

Let me know if you have any questions or suggestions in the linked Twitter thread!

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Michael Aye
Michael Aye
Research Scientist in Planetary Science

My research interests include remote sensing of surfaces, related machine learning studies and open source software.

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