Managing Python Environments with Conda

At the end of my article How to install Anaconda on Ubuntu I verified that Anaconda was installed successfully by executing conda list. You've probably noticed (base) that appears in front of command prompt:

(base) $

This happens after we activate conda by executing ~/.bashrc:

$ cat ~/.bashrc

...

# >>> conda initialize >>>

# !! Contents within this block are managed by 'conda init' !!

__conda_setup="$('/home/bojan/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"

if [ $? -eq 0 ]; then

    eval "$__conda_setup"

else

    if [ -f "/home/bojan/anaconda3/etc/profile.d/conda.sh" ]; then

        . "/home/bojan/anaconda3/etc/profile.d/conda.sh"

    else

        export PATH="/home/bojan/anaconda3/bin:$PATH"

    fi

fi

unset __conda_setup

# <<< conda initialize <<<

...

As conda is also an environment manager it is capable of setting a specified or a default environment. 

Each environment has associated:

• name
• collection of packages 
• resources which are stored in a dedicated directory

When conda is activated, it sets a default environment unless some other is specified. Its name appears within parentheses before the prompt in terminal. In our case that was a default environment named base.

To list all available environments with their names and associated directories we can use:

$ conda env list

# conda environments:

#

base                  *  /home/bojan/anaconda3

Asterisk (*) appears next to the currently active environment.

Another way to get the same information is:

$ conda info --envs

# conda environments:

#

base                  *  /home/bojan/anaconda3

Here is the content of the base environment directory:

$ ls -1a /home/bojan/anaconda3

.

..

bin

compiler_compat

condabin

conda-meta

doc

envs

etc

include

lib

libexec

LICENSE.txt

man

mkspecs

phrasebooks

pkgs

plugins

qml

resources

sbin

share

shell

ssl

translations

var

x86_64-conda_cos6-linux-gnu

To deactivate the current environment:

(base) $ conda deactivate

$

To activate default environment again:

$ conda activate

(base) $ 

After installing Conda, base environment is set to be auto activated by default:

(base) $ conda config --show | grep auto_activate_base

auto_activate_base: True

To turn this off we need to set that flag to False (bash - How to remove (base) from terminal prompt after updating conda - Stack Overflow):

(base) $ conda config --set auto_activate_base False

Let's verify it:

(base) $ conda config --show | grep auto_activate_base

auto_activate_base: False

Next time we open a new terminal, we should not see (base) in front of the prompt.

Note that when we have a base environment activated, Terminal shell uses Python from Anaconda installaton:

(base) $ which python

/home/bojan/anaconda3/bin/python

(base) $ which python3

/home/bojan/anaconda3/bin/python3

When no environment is activated, Terminal shell uses Python from a system installation:

$ which python

/usr/bin/python

$ which python3

/usr/bin/python3

Same applies to pip and pip3:

(base) $ which pip

/home/bojan/anaconda3/bin/pip

(base) $ which pip3

/home/bojan/anaconda3/bin/pip3

$ which pip

/home/bojan/.local/bin/pip

$ which pip3

/home/bojan/.local/bin/pip3

Each environment can be specified with its YAML (.yml) file. This file contains all necessary information for conda to recreate the same environment on some other computer:

• name of the environment
• channels
• dependencies

Environment yaml file generic example:

name: my_env

channels:

  - channel1

dependencies:

  - python=3.6

  - some_package=1.2 # it is possible to add comments

  - some_package2

  - jupyter=1.0.0

  - jupyterlab=0.34.9

  - keras=2.2.2=0

  - matplotlib=2.2.3

  - ...

We can create this yaml file manually or can use conda command:

$ conda env export > my_environment.yml

To re-create the environment from a given yaml file:

$ conda env create -f my_environment.yml 

Collecting package metadata (repodata.json): done

Solving environment: done

==> WARNING: A newer version of conda exists. <==

  current version: 4.8.3

  latest version: 4.8.5

Please update conda by running

    $ conda update -n base -c defaults conda

Downloading and Extracting Packages

gmp-6.1.2            | 751 KB    | ##################################### | 100% 

prometheus_client-0. | 44 KB     | ##################################### | 100% 

libstdcxx-ng-9.3.0   | 4.0 MB    | ##################################### | 100% 

defusedxml-0.6.0     | 22 KB     | ##################################### | 100% 

ipython-7.16.1       | 1.1 MB    | ##################################### | 100% 

kiwisolver-1.2.0     | 87 KB     | ##################################### | 100% 

libgcc-ng-9.3.0      | 7.8 MB    | ##################################### | 100% 

...

Preparing transaction: done

Verifying transaction: done

Executing transaction: \ b'Enabling notebook extension jupyter-js-widgets/extension...\n      - Validating: \x1b[32mOK\x1b[0m\n'

done

#

# To activate this environment, use

#

#     $ conda activate my_environment

#

# To deactivate an active environment, use

#

#     $ conda deactivate

We can verify that this environment has now been added to conda:

(base) $ conda env list

# conda environments:

#

base                  *  /home/bojan/anaconda3

my_environment           /home/bojan/anaconda3/envs/my_environment

test-opencv              /home/bojan/anaconda3/envs/test-opencv

To activate this environment:

(base)$ conda activate my_environment

(my_environment)$

To check which packages are installed in the current environment:

(my_environment) $ conda list

# packages in environment at /home/bojan/anaconda3/envs/my_environment:

#

# Name                    Version                   Build  Channel

_libgcc_mutex             0.1                 conda_forge    conda-forge

_openmp_mutex             4.5                       1_gnu    conda-forge

absl-py                   0.10.0           py36h9f0ad1d_0    conda-forge

argon2-cffi               20.1.0           py36h8c4c3a4_1    conda-forge

astor                     0.8.1              pyh9f0ad1d_0    conda-forge

async_generator           1.10                       py_0    conda-forge

atk                       2.25.90           hf2eb9ee_1001    conda-forge

attrs                     20.2.0             pyh9f0ad1d_0    conda-forge

backcall                  0.2.0              pyh9f0ad1d_0    conda-forge

backports                 1.0                        py_2    conda-forge

...

To install additional package to the current environment:

(my_environment) $ conda install pillow

Collecting package metadata (current_repodata.json): done

Solving environment: done

## Package Plan ##

  environment location: /home/bojan/anaconda3/envs/my_environment

  added / updated specs:

    - pillow

The following packages will be downloaded:

    package                    |            build

    ---------------------------|-----------------

    ca-certificates-2020.10.14 |                0         121 KB

    certifi-2020.6.20          |           py36_0         156 KB

    olefile-0.46               |           py36_0          48 KB

    openssl-1.0.2u             |       h7b6447c_0         2.2 MB

    pillow-7.2.0               |   py36hb39fc2d_0         619 KB

    ------------------------------------------------------------

                                           Total:         3.1 MB

The following NEW packages will be INSTALLED:

  lcms2              pkgs/main/linux-64::lcms2-2.11-h396b838_0

  olefile            pkgs/main/linux-64::olefile-0.46-py36_0

  pillow             pkgs/main/linux-64::pillow-7.2.0-py36hb39fc2d_0

The following packages will be UPDATED:

  ca-certificates    conda-forge::ca-certificates-2020.6.2~ --> pkgs/main::ca-certificates-2020.10.14-0

The following packages will be SUPERSEDED by a higher-priority channel:

  certifi            conda-forge::certifi-2020.6.20-py36h9~ --> pkgs/main::certifi-2020.6.20-py36_0

  openssl            conda-forge::openssl-1.0.2u-h516909a_0 --> pkgs/main::openssl-1.0.2u-h7b6447c_0

Proceed ([y]/n)? y

Downloading and Extracting Packages

openssl-1.0.2u       | 2.2 MB    | ################################################################ | 100% 

certifi-2020.6.20    | 156 KB    | ################################################################ | 100% 

pillow-7.2.0         | 619 KB    | ################################################################ | 100% 

ca-certificates-2020 | 121 KB    | ################################################################ | 100% 

olefile-0.46         | 48 KB     | ################################################################ | 100% 

Preparing transaction: done

Verifying transaction: done

Executing transaction: done

We can verify that a new package is indeed installed in new environment:

(my_environment) $ conda list

# packages in environment at /home/bojan/anaconda3/envs/my_environment:

#

# Name                    Version                   Build  Channel

...

pillow                    7.2.0            py36hb39fc2d_0 

...

To install a new package from a specific channel in the current environment:

(my_environment) $ conda install -c channel_name package_name

To install a specific version of a new package from a specific channel in the current environment:

(my_environment) $ conda install -c channel_name package_name=version

To uninstall some package from the current environment:

(my_environment) $ conda remove pillow

To uninstall multiple packages from the current environment:

(my_environment) $ conda remove package1 package2 ...

To update an environment with (new) dependencies in (new) yml file:

(my_environment) $ conda deactivate

$ conda env update --file my_environment.yml

$ conda activate my_environment

To update conda (I've deactivated the current environment):

$ conda update -n base -c defaults conda

Collecting package metadata (current_repodata.json): done

Solving environment: done

## Package Plan ##

  environment location: /home/bojan/anaconda3

  added / updated specs:

    - conda

The following packages will be downloaded:

    package                    |            build

    ---------------------------|-----------------

    conda-4.8.5                |           py38_0         2.9 MB

    ------------------------------------------------------------

                                           Total:         2.9 MB

The following packages will be UPDATED:

  conda                                        4.8.3-py38_0 --> 4.8.5-py38_0

Proceed ([y]/n)? y

Downloading and Extracting Packages

conda-4.8.5          | 2.9 MB    | ################################################################################################################################################################# | 100% 

Preparing transaction: done

Verifying transaction: done

Executing transaction: done

To remove given environment:

$ conda env remove --name test-opencv

Remove all packages in environment /home/bojan/anaconda3/envs/test-opencv:

We can verify that its directory does not exist:

$ ls /home/bojan/anaconda3/envs/test-opencv

ls: cannot access '/home/bojan/anaconda3/envs/test-opencv': No such file or directory

References:

command line - Why does "(base)" appear in front of my terminal prompt? - Ask Ubuntu

Managing environments — conda 4.8.4.post69+3d402ab0 documentation

python - What is the difference between pyenv, virtualenv, anaconda? - Stack Overflow