This lesson is in the early stages of development (Alpha version)

Working with Environments

Overview

Teaching: 60 min
Exercises: 15 min
Questions
  • What is a Conda environment?

  • How do I create (delete) an environment?

  • How do I activate (deactivate) an environment?

  • How do I install packages into existing environments using Conda (+pip)?

  • Where should I create my environments?

  • How do I find out what packages have been installed in an environment?

  • How do I find out what environments that exist on my machine?

  • How do I delete an environment that I no longer need?

Objectives
  • Understand how Conda environments can improve your research workflow.

  • Create a new environment.

  • Activate (deactivate) a particular environment.

  • Install packages into existing environments using Conda (+pip).

  • Specify the installation location of an environment.

  • List all of the existing environments on your machine.

  • List all of the installed packages within a particular environment.

  • Delete an entire environment.

What is a Conda environment

A Conda environment is a directory that contains a specific collection of Conda packages that you have installed. For example, you may be working on a research project that requires NumPy 1.18 and its dependencies, while another environment associated with an finished project has NumPy 1.12 (perhaps because version 1.12 was the most current version of NumPy at the time the project finished). If you change one environment, your other environments are not affected. You can easily activate or deactivate environments, which is how you switch between them.

Avoid installing packages into your base Conda environment

Conda has a default environment called base that include a Python installation and some core system libraries and dependencies of Conda. It is a “best practice” to avoid installing additional packages into your base software environment. Additional packages needed for a new project should always be installed into a newly created Conda environment.

Creating environments

To create a new environment for Python development using conda you can use the conda create command.

$ conda create --name python3-env python pip

Always install pip in your Python environments

Pip, the default Python package manager, is often already installed on most operating systems (where it is used to manage any packages need by the OS Python). Pip is also included in the Miniconda installer. Including pip as an explicit dependency in your Conda environment avoids difficult to debug issues that can arise when installing packages into environments using some other pip installed outside your environment.

It is a good idea to give your environment a meaningful name in order to help yourself remember the purpose of the environment. While naming things can be difficult, $PROJECT_NAME-env is a good convention to follow.

The command above will create a new Conda environment called “python3” and install the most recent version of Python. If you wish, you can specify a particular version of packages for conda to install when creating the environment.

$ conda create --name python36-env python=3.6 pip=20.0

Always specify a version number for each package you wish to install

In order to make your results more reproducible and to make it easier for research colleagues to recreate your Conda environments on their machines it is a “best practice” to always explicitly specify the version number for each package that you install into an environment. If you are not sure exactly which version of a package you want to use, then you can use search to see what versions are available using the conda search command.

$ conda search $PACKAGE_NAME

So, for example, if you wanted to see which versions of Scikit-learn, a popular Python library for machine learning, were available, you would run the following.

$ conda search scikit-learn

As always you can run conda search --help to learn about available options.

You can create a Conda environment and install multiple packages by simply listing the packages that you wish to install.

$ conda create --name basic-scipy-env ipython=7.13 matplotlib=3.1 numpy=1.18 pip=20.0 scipy=1.4

When conda installs a package into an environment it also installs any required dependencies. For example, even though Python is not listed as a packaged to install into the basic-scipy-env environment above, conda will still install Python into the environment because it is a required dependency of at least one of the listed packages.

Creating a new environment

Create a new environment called “machine-learning-env” with Python and the most current versions of IPython, Matplotlib, Pandas, and Scikit-Learn.

Solution

In order to create a new environment you use the conda create command as follows.

$ conda create --name machine-learning-env \
> ipython \
> matplotlib \
> pandas \
> pip \
> python \
> scikit-learn \

Since no version numbers are provided for any of the Python packages, Conda will download the most current, mutually compatible versions of the requested packages. However, since it is best practice to always provide explicit version numbers, you should prefer the following solution.

$ conda create --name machine-learning-env \
> ipython=7.13
> matplotlib=3.1 \
> pandas=1.0 \
> pip=20.0
> python=3.6 \
> scikit-learn=0.22

Activating an existing environment

Activating environments is essential to making the software in environments work well (or sometimes at all!). Activation of an environment does two things.

  1. Adds entries to PATH for the environment.
  2. Runs any activation scripts that the environment may contain.

Step 2 is particularly important as activation scripts are how packages can set arbitrary environment variables that may be necessary for their operation. Aou activate the basic-scipy-env environment by name using the activate command.

$ conda activate basic-scipy-env

You can see that an environment has been activated because the shell prompt will now include the name of the active environment.

(basic-scipy-env) $

Deactivate the current environment

To deactivate the currently active environment use the deactivate command as follows.

(basic-scipy-env) $ conda deactivate

You can see that an environment has been deactivated because the shell prompt will no longer include the name of the previously active environment.

$

Returning to the base environment

To simply return to the base Conda environment, it’s better to call conda activate with no environment specified, rather than to use deactivate. If you run conda deactivate from your base environment, you may lose the ability to run conda commands at all. Don’t worry if you encounter this undesirable state! Just start a new shell.

Activate an existing environment by name

Activate the machine-learning-env environment created in the previous challenge by name.

Solution

In order to activate an existing environment by name you use the conda activate command as follows.

$ conda activate machine-learning-env

Deactivate the active environment

Deactivate the machine-learning-env environment that you activated in the previous challenge.

Solution

In order to deactivate the active environment you use the conda deactivate command.

(active-environment-name) $ conda deactivate

Installing a package into an existing environment

You can install a package into an existing environment using the conda install command. This command accepts a list of package specifications (i.e., numpy=1.18) and installs a set of packages consistent with those specifications and compatible with the underlying environment. If full compatibility cannot be assured, an error is reported and the environment is not changed.

By default the conda install command will install packages into the current, active environment. The following would activate the basic-scipy-env we created above and install Numba, an open source JIT compiler that translates a subset of Python and NumPy code into fast machine code, into the active environment.

$ conda activate basic-scipy-env
$ conda install numba

As was the case when listing packages to install when using the conda create command, if version numbers are not explicitly provided, Conda will attempt to install the newest versions of any requested packages. To accomplish this, Conda may need to update some packages that are already installed or install additional packages. It is always a good idea to explicitly provide version numbers when installing packages with the conda install command. For example, the following would install a particular version of Scikit-Learn, into the current, active environment.

$ conda install scikit-learn=0.22

Freezing installed packages

To prevent existing packages from being updating when using the conda install command, you can use the --freeze-installed option. This may force Conda to install older versions of the requested packages in order to maintain compatibility with previously installed packages. Using the --freeze-installed option does not prevent additional dependency packages from being installed.

Installing a package into a specific environment

Dask provides advanced parallelism for data science workflows enabling performance at scale for the core Python data science tools such as Numpy Pandas, and Scikit-Learn. Have a read through the official documentation for the conda install command and see if you can figure out how to install Dask into the machine-learning-env that you created in the previous challenge.

Solution

You can install Dask into machine-learning-env using the conda install command as follow.

$ conda install --name machine-learning-env dask=2.16

You could also install Dask into machine-learning-env by first activating that environment and then using the conda install command.

$ conda activate machine-learning-env
$ conda install dask=2.16

Installing packages into Conda environments using pip

Combo is a comprehensive Python toolbox for combining machine learning models and scores. Model combination can be considered as a subtask of ensemble learning, and has been widely used in real-world tasks and data science competitions like Kaggle.

Activate the machine-learning-env you created in a previous challenge and use pip to install combo.

Solution

The following commands will activate the machine-learning-env and install combo.

$ conda activate machine-learning-env
$ pip install combo==0.1.*

For more details on using pip see the official documentation.

Where do Conda environments live?

Environments created with conda, by default, live in the envs/ folder of your miniconda3 directory the absolute path to which will look something the following.

$ /Users/$USERNAME/miniconda3/envs

Running ls on your ~/miniconda3/envs/ directory will list out the directories containing the existing Conda environments.

Location of Conda environments on Binder

If you are working through these lessons using a Binder instance, then the default location of the Conda environments is slightly different.

$ /srv/conda/envs

Running ls /srv/conda/envs/ from a terminal will list out the directories containing any previously installed Conda environments.

How do I specify a location for a Conda environment?

You can control where a Conda environment lives by providing a path to a target directory when creating the environment. For example to following command will create a new environment in a sub-directory of the current working directory called env.

$ conda create --prefix ./env ipython=7.13 matplotlib=3.1 pandas=1.0 python=3.6

You activate an environment created with a prefix using the same command used to activate environments created by name.

$ conda activate ./env

It is a good idea to always specify a path to a sub-directory of your project directory when creating an environment. Why?

  1. Makes it easy to tell if your project utilizes an isolated environment by including the environment as a sub-directory.
  2. Makes your project more self-contained as everything including the required software is contained in a single project directory.

An additional benefit of creating your project’s environment inside a sub-directory is that you can then use the same name for all your environments; if you keep all of your environments in your ~/miniconda3/env/ folder, you’ll have to give each of them a different name.

Conda environment sub-directory naming convention

In order to be consistent with the convention used by tools such as venv and Pipenv, I recommend using env as the name of the sub-directory of your project directory that contains your Conda environment. A benefit of maintaining the convention is that your environment sub-directory will be automatically ignored by the default Python .gitignore file used on GitHub.

Whatever naming convention you adopt it is importanat to be consistent! Using the same name for all of your Conda environments allows you to use the same activate command as well.

$ cd my-project/
$ conda activate ./env

Creating a new environment as a sub-directory within a project directory

First create a project directory called project-dir using the following command.

$ mkdir project-dir
$ cd project-dir

Next, create a new environment inside the newly created project-dir in a sub-directory called env an install Python 3.6, version 3.1 of Matplotlib, version 2.1 of TensorFlow and version 20.0 of pip.

Solution

project-dir $ conda create --prefix ./env \
> python=3.6 \
> matplotlib=3.1 \
> tensorflow=2.1 \
> pip=20.0

Placing Conda environments outside of the default ~/miniconda3/envs/ folder comes with a couple of minor drawbacks. First, conda can no longer find your environment with the --name flag; you’ll generally need to pass the --prefix flag along with the environment’s full path to find the environment.

Second, an annoying side-effect of specifying an install path when creating your Conda environments is that your command prompt is now prefixed with the active environment’s absolute path rather than the environment’s name. After activating an environment using its prefix your prompt will look similar to the following.

(/absolute/path/to/env) $

As you can imagine, this can quickly get out of hand.

(/Users/USER_NAME/research/data-science/PROJECT_NAME/env) $

If (like me!) you find this long prefix to your shell prompt annoying, then there is a quick fix: modify the env_prompt setting in your .condarc file, which you can do with the following command.

$ conda config --set env_prompt '({name})'

This will either edit your ~/.condarc file if you already have one or create a ~/.condarc file if you do not. Now your command prompt will display the active environment’s generic name.

$ cd project-directory
$ conda activate ./env
(env) project-directory $

For more on modifying your .condarc file, see the official Conda docs.

Activate an existing environment by path

Activate the environment created in a previous challenge using the path to the environment directory.

Solution

You can activate an existing environment by providing the path the the environment directory instead of the environment name when using the conda activate command as follows.

$ conda activate ./env

Note that the provided path can either be absolute or relative. If the path is a relative path then it must start with ./ on Unix systems and .\ on Windows.

Conda can create environments for R projects too!

First create a project directory called r-project-dir using the following command.

$ mkdir r-project-dir
$ cd r-project-dir

Next, take a look through the list of R packages available by default for installation using conda. Create a new environment inside the newly created r-project-dir in a sub-directory called env and install r-base (and any other R packages that you think look interesting).

Solution

project-dir $ conda create --prefix ./env \
> r-base \
> r-tidyverse \
> r-sparklyr \

Listing existing environments

Now that you have created a number of Conda environments on your local machine you have probably forgotten the names of all of the environments and exactly where they live. Fortunately, there is a conda command to list all of your existing environments together with their locations.

$ conda env list

Listing the contents of an environment

In addition to forgetting names and locations of Conda environments, at some point you will probably forget exactly what has been installed in a particular Conda environment. Again, there is a conda command for listing the contents on an environment. To list the contents of the basic-scipy-env that you created above, run the following command.

$ conda list --name basic-conda-env

If you created your Conda environment using the --prefix option to install packages into a particular directory, then you will need to use that prefix in order for conda to locate the environment on your machine.

$ conda list --prefix /path/to/conda-env

Listing the contents of a particular environment.

List the packages installed in the machine-learning-env environment that you created in a previous challenge.

Solution

You can list the packages and their versions installed in machine-learning-env using the conda list command as follows.

$ conda list --name machine-learning-env

To list the packages and their versions installed in the active environment simply leave off the --name or --prefix option.

$ conda list

Deleting entire environments

Occasionally, you will want to delete an entire environment. Perhaps you were experimenting with conda commands and you created an environment you have no intention of using; perhaps you no longer need an existing environment and just want to get rid of cruft on your machine. Whatever the reason the command to delete an environment is the following.

$ conda remove --name my-first-conda-env --all

If you wish to delete and environment that you created with a --prefix option, then you will need to provide the prefix again when removing the environment.

$ conda remove --prefix /path/to/conda-env/ --all

Delete an entire environment

Delete the entire “basic-scipy-env” environment.

Solution

In order to delete an entire environment you use the conda remove command as follows.

$ conda remove --name basic-scipy-env --all --yes

This command will remove all packages from the named environment before removing the environment itself. The use of the --yes flag short-circuits the confirmation prompt (and should be used with caution).

Key Points

  • A Conda environment is a directory that contains a specific collection of Conda packages that you have installed.

  • You create (remove) a new environment using the conda create (conda remove) commands.

  • You activate (deactivate) an environment using the conda activate (conda deactivate) commands.

  • You install packages into environments using conda install; you install packages into an active environment using pip install.

  • You should install each environment as a sub-directory inside its corresponding project directory

  • Use the conda env list command to list existing environments and their respective locations.

  • Use the conda list command to list all of the packages installed in an environment.