Conda Environments

What is Conda? How it works?

Environment management with Conda Image from: https://angus.readthedocs.io/en/2019/conda_tutorial.html

Conda virtual environments provide a way to install packages without worrying about package conflicts (eg. diferences on package version).

It is posible to create a web-development environment where we install Flask, Gunicorn and Requests libraries and a separate environment where we install pandas, biopython and other packages used to analyze data. Without virtual environments, a package installation may cause your operating system to break due to version conflicts. In the virtual environment, only programs run inside the enviroment will be affected by any of your installations.

What is a package?

A Package is a program that perform specific tasks. Like for example, tidyverse is a package for the R language,pandas is a package for Python language. Each package can include information related to its creation, versions and maintainers.

Base environment

A ‘base’ conda environment, is like the home base inside conda. In this place we do not want to install programs and/or packages because they may have conflicts with whatever you may end up doing in the future.

To avoid any potential issues in between projects it is recomended to create a conda enviroment, and after activating the conda environment, install the packages that your research may need.

Your terminal display should look something similar to the following:

(base) student@hostname~ %

The (base) symbolizes that you are in the conda base environment.

Making a new environment

To create a new conda environment write the following command:

conda create -n name-of-the-new-environment

The base command is conda create, then we are specifying the name of our new environment with -n name-of-the-new-environment. After hitting enter, the terminal is going to start some procesess and is going to ask you if you want to proceed with the creation of the conda environment. Select y (yes) and it will finish the process of creating the environment.

You will be seeing in your terminal something similar to the following:

Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan 

  environment location: /Users/username/anaconda3/envs/name-of-the-new-environment

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate name-of-the-new-environment
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Activate an environment

After creating the new environment, you need to activate so you can use it. To activate that environment, we need to execute:

conda activate name-of-the-new-environment

When you activate the environment, your terminal prompt will change to display the name of your new environment. That will letyou know that we have moved from the base environment to the new one.

(name-of-the-new-environment) student@hostname~ %

You can also see a list of all the environments created by using the following command:

conda env list

conda env list will display all the available conda environments and will place an asterist to the ones that you are using at the moment.

It will display something similar to the following:

(name-of-the-new-environment) student@hostname ~ % conda env list
# conda environments:
#
name-of-the-new-environme    *  /Users/ifraticelli/anaconda3
python-intro                  /Users/ifraticelli/anaconda3/envs/python-intro
test                         /Users/ifraticelli/anaconda3/envs/test

To verify what are the packages that your virtual environment has you can also use conda list.

It will display something similar to the following:

(name-of-the-new-environment) student@hostname % conda list
# packages in environment at /Users/ifraticelli/anaconda3/envs/python-intro:
#
# Name                    Version                   Build  Channel
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pygments                  2.16.1             pyhd8ed1ab_0    conda-forge
python                    3.11.5               hf27a42d_0  
python-dateutil           2.8.2              pyhd3eb1b0_0  
python-tzdata             2023.3             pyhd3eb1b0_0  
python_abi                3.11                    2_cp311    conda-forge
...                       ...                     ...           ...

Exiting an environment

You can deactivate a conda eniroment at any time by running the following code.

conda deactivate

In class exercise:

Move to the conda environment called ‘python-intro’.
Then name two the conda packages that the python-intro environment has.

Solution

conda activate python-intro
Pandas, BioPython, Python…

Want to learn more about Conda Packages?

If you want to learn more about Conda Packages you can visit their repository at the Anaconda Website.