Getting Python On Your Machine: Mamba!
Overview
Mamba is an open-source, cross-platform, language-agnostic package manager and environment management system that allows you to quickly install, run, and update packages within your work environment(s).
Here we will cover:
What are packages?
Installing Mamba
Creating a Mamba environment
Useful Mamba commands
Conda vs. Mamba
For the Cook-off we’re recommending something a bit different than the installation instructions in Pythia Foundations
You may have already used conda to install Python and other packages on your machine. Maybe you’ve also gotten frustrated by extremely slow installations! mamba is basically a drop-in replacement for conda that is much faster!
Short story: follow these instructions to install mamba and use mamba for your Python package management, and you’ll be happier!
What are Packages?
A Python package is a collection of modules, which, in turn, are essentially Python scripts that contain published functionality. There are Python packages for data input, data analysis, data visualization, etc. Each package offers a unique toolset and may have its own unique syntax rules.
Package management is useful because you may want to update a package for one of your projects, but keep it at the same version in other projects to ensure that they continue to run as expected.
Installing Mamba
We recommend you install mambaforge. You can do that by following the mambaforge documentation.
You will need to download and install packages from their Github repository, selecting the installation suitable for your machine (ex. Macbook Pro with an M1 processor)
Mambaforge only comes with the mamba package management system; it is a pared-down version of the full Anaconda Python distribution.
We recommend mambaforge for three reasons:
It’s much faster than conda.
Takes up much less disk space than a full Anacaonda Python installation.
It encourages you to install only the packages you need in reproducible isolated environments for specific projects. This is generally a more robust way to work with open source tools.
Once you have mamba via the mambaforge installer, the next step is to create an environment and install packages.
Creating and Managing Python Environments with Mamba
A mamba environment is an interoperable collection of specific versions of packages or libraries that you install and use for a specific workflow. Mamba’s package manager takes care of dependencies so everything works together in a predictable way. One huge advantage of using environments is that any changes you make to one environment will not affect your other environments at all, so you are much less likely to “break” something!
Creating a Python Environment
To create a new mamba environment, type mamba create --name and the name of your environment in your terminal, and then specify any packages that you would like to have installed. For example, to install a Jupyter-ready environment called sample_environment, type
mamba create --name sample_environment python jupyterlab
The above invocation will install the python and jupyterlab packages and their dependencies into your sample_environment . Once that environment is created, you will be prompted to activate it in your current terminal session:
mamba activate sample_environment
It is a good idea to create new environments for different projects because since Python is open source, new versions of the tools are released very frequently. Isolated environments help guarantee that your script will use the same versions of packages and libraries and should run the same as you expect it to. Similarly, it is best practice to NOT modify your base environment.
Create a Python environment from an environment file
Many projects have lengthy lists of packages. Rather than listing each package individually in a mamba create command, it’s common practice to list packages in a text file usually called environment.yml. For example, each Cookbook repository contains an environment.yml file at the root of the repository.
We recommend having a separate named environment for each Cookbook you are working on, and managing these through environment files. The name of the environment is usually specified in the environment.yml file as well.
To create and activate environment named my-cookbook-env (for example) from an environment.yml file, do the following:
mamba env create -f environment.yml
mamba activate my-cookbook-env
Modifying Your Environment
When you are working with cookbooks, it is recommended that when you install new packages, you add those packages to your environment.yml file.
Adding New Packages to Your Environment
Here is a sample of what this environment.yml file looks like:
name: cookbook-dev
channels:
- conda-forge
dependencies:
- jupyter-book
- jupyterlab
If you wanted to add another package, for example, xarray, which is useful when working with weather and climate datasets, your new file would look like the following:
name: cookbook-dev
channels:
- conda-forge
dependencies:
- jupyter-book
- jupyterlab
- xarray
You would update your environment using the mamba env update command, specifying the environment.yml file as the place to check to see if there are new packages to install!
mamba env update -f environment.yml
Creating a New Environment
You can also rename your environment using the environment.yml file. This is helpful when creating your own cookbook! For example, let’s create a new environment my-cookbook-dev.
name: my-cookbook-dev
channels:
- conda-forge
dependencies:
- jupyter-book
- jupyterlab
- xarray
Following the steps outlined in the previous section, we would run
mamba env create -f environment.yml
mamba activate my-cookbook-dev
Useful Mamba commands
Here are some commands that you will typically use:
Activating a specific environment
mamba activate sample_environment
Deactivating the current environment
mamba deactivate
Deactivating an environment will switch you back to your original, or base environment.
Checking what packages/versions are installed in the current environment
mamba list
Check if a particular package is available for install:
mamba repoquery search somepackage
Installing a new package into the current environment
mamba install somepackage
Installing a specific version of a package into the current environment
mamba install somepackage=0.17
Updating all packages in the current environment to the latest versions
mamba update --all
Checking what conda environments you have
mamba env list
Deleting an environment
mamba env remove --name sample_environment
Remember, mamba is a variant of conda. While it is not a one-to-one replacement for conda, its usage is very similar, We therefore recommend you refer to Conda’s documentation or this handy Conda cheat sheet.
Summary
Mamba is an optimized package and environment management system, based on conda, that allows you to quickly install, run, and update packages within your work environment(s). This is important for gathering all of the tools necessary for your workflow. Use the command line to manage your Python environments using Mamba.