Configuring Conda

Overview

Teaching: 20 min
Exercises: 5 min

Questions

• How can I configure conda ?

• How can I see conda’s configuration values?

• How can I modify conda’s configuration settings?

Objectives

• Use the conda config --show to display all configuration values.

• Modify the .condarc file using the conda config sub command.

• locate and view the contents of the .condarc file.

Configuration

Conda has a number of configuration setting which control how it performs. To display and control these setting we can use the conda config subcommand.

To display all configuration settings run the config --show subcommand :

$ conda config --show

As you can see conda supports a large number of configuration options. To show a single setting add the setting name after the conda config --show command. For example, to show the list of channels conda searches run:

$ conda config --show channels

channels:
  - defaults

By default conda only searches the defaults channel, this is why we had to include conda-forge and bioconda channels via the command line option --channel in the previous episode.

To get more information about an individual conda setting and its’ possible values run conda config --describe <option>. For Example;

conda config --describe channels

# # channels (sequence: primitive)
# #   aliases: channel
# #   env var string delimiter: ','
# #   The list of conda channels to include for relevant operations.
# #
# channels:
#   - defaults

.condarc

A user’s conda setting are store in the runtime configuration configuration file, .condarc. This file allows users to configure various aspects of conda including:

• Where conda looks for packages channels.

• Where conda lists known environments envs_dirs.

• Whether to update the Bash prompt with the currently activated environment name env_prompt.

• What default packages or features to include in new environments create_default_packages.

Like the environment file the .condarc configuration file follows a simple YAML syntax

The .condarc file is not included by default, but it is automatically created in your home directory the first time you run the conda config command.

Creating or modify .condarc

To create or modify a .condarc file, enter the conda config command and use the modifier options --add, --set, --append , --prepend or --remove followed by the configuration key and a value .

conda config <modifier> <KEY> <VALUE>

Adding a configuration value

To add conda-forge to the list of channels we can use the --add, --append or --prepend modifier option:

For example, if we want to add a channel to our list of channels in our configuration file rather than specific it on the command line every time we can can use the conda config --add option modifier.

$ conda config --add channels conda-forge

This would add the conda-forge channel to the top of the channel list.

$ conda config --show channels

We can use the conda config modifier --append to add conda-forge to the end of the channel list, giving it the lowest priority.

$ conda config --append channels conda-forge

Warning: 'conda-forge' already in 'channels' list, moving to the bottom

$ conda config --show channels

To move a channel to the highest priority use the conda config --prepend modifier.

$ conda config --prepend channels conda-forge

Warning: 'conda-forge' already in 'channels' list, moving to the top

$ conda config --show channels

Note: It is generally best to have conda-forge as the highest priority channel as this will usually have the most up-to-date packages.

Adding the channels bioconda and conda-forge to .condarc.

Add the bioconda and conda-forge channels to your .condarc file. Give conda-forge the highest priority.

Solution

To add the bioconda and conda-forge channel to your .condarc file use the command.

$ conda config --add channels bioconda
$ conda config --add channels conda-forge

The above sequence of commands will add the channels to your .condarc . Use the command below to show the channel priority order.

$ conda config --get channels

--add channels 'defaults'   # lowest priority
--add channels 'bioconda'
--add channels 'conda-forge'   # highest priority

Setting configuration settings

If our configuration setting has a single boolean or string value we can use conda config --set to set it.

For example, In a previous episode we set the command line prompt setting for conda using env_prompt.

$ conda config --describe env_prompt

The env_prompt setting takes a value of either '{prefix}', '{name}', and '{default_env}'.

# # env_prompt (str)
# #   Template for prompt modification based on the active environment.
# #   Currently supported template variables are '{prefix}', '{name}', and
# #   '{default_env}'. '{prefix}' is the absolute path to the active
# #   environment. '{name}' is the basename of the active environment
# #   prefix. '{default_env}' holds the value of '{name}' if the active
# #   environment is a conda named environment ('-n' flag), or otherwise
# #   holds the value of '{prefix}'. Templating uses python's str.format()
# #   method.
# #
# env_prompt: '({default_env}) '

To set the env_prompt to the default value '({default_env})' we can run:

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

To change it back to the just the environment name, we can run.

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

Note:: You need to deactivate then reactivate the environment for the changes in env prompt to take effect.

Set conda channel_priority

Use the conda config --describe to investigate the setting channel_priority. Set the channel_priority so that packages in lower priority channels are not considered if a package with the same name appears in a higher priority channel. Why would you want to do change this setting?

Solution

$ conda config --describe channel_priority
$ conda config --set channel_priority strict
$ conda config --show channel_priority

Using Strict channel priority can dramatically speed up conda operations and also reduce package incompatibility problems. This will be the default as of conda 5.0.

Editing the .condarc file manually

You can also use a text editor such as nano to directly edit the .condarc.

To show the location and contents of your .condarc file you can use the conda config --show-sources command.

$ conda config --show-sources

Note: If the .condarc file is in the root environment, it will override any in the home directory

Locate and view the .condarc

Locate your .condarc file. Using your favourite text editor look at the .condarc.

Solution

$ conda config --show-sources

$ nano ~/.condarc

Getting help

As with all conda commands you can use the --help option to get help.

For example, for a complete list of conda config commands run

$ conda config --help

Or see the command reference.

Key Points

• The .condarc is an optional configuration file that stores custom conda setting.

• You can use the conda config subcommand to add, set or remove configuration setting in the .condarc file.

• You can also edit the contents of the .condarc file directly using a text editor.