cotainr.pack module#

cotainr - a user space Apptainer/Singularity container builder.

This module implements packing of software into the container.

Classes#

CondaInstall: A Conda installation in a container sandbox.

API reference#

class cotainr.pack.CondaInstall(*, sandbox, prefix='/opt/conda', license_accepted=False, log_settings=None)#

Bases: object

A Conda installation in a container sandbox.

Bootstraps a Miniforge based Conda installation in a container sandbox. As part of the bootstrapping of Miniforge, the user must accept the Miniforge license terms.

Parameters:

sandboxSingularitySandbox: The sandbox in which Conda should be installed.
prefixstr: The Conda prefix to use for the Conda install.
license_acceptedbool, default=False: The flag to indicate whether or not the user has already accepted the Miniforge license terms.
log_settingsLogSettings, optional: The data used to setup the logging machinery (the default is None which implies that the logging machinery is not used).

Notes

When adding a Conda environment, it is the responsibility of the user of cotainr to make sure they have the necessary rights to use the Conda channels/repositories and packages specified in the Conda environment, e.g. if using the default Anaconda repositories.

Attributes:

sandboxSingularitySandbox: The sandbox in which Conda is installed.
prefixstr: The Conda prefix used for the Conda install.
license_acceptedbool: Whether or not the Miniforge license terms have been accepted.
log_dispatcherLogDispatcher or None.: The log dispatcher used to process stdout/stderr message from Singularity commands that run in sandbox, if the logging machinery is used.

Methods

`add_environment`(*, path, name)	Add an exported Conda environment to the Conda install.
`cleanup_unused_files`()	Remove all unused Conda files.

add_environment(*, path, name)#

Add an exported Conda environment to the Conda install.

Equivalent to calling “conda env create -f path -n name”.

Parameters:

pathos.PathLike: The path to the exported env.yml file describing the Conda environment to install.
namestr: The name to use for the installed Conda environment.

cleanup_unused_files()#

Remove all unused Conda files.

Equivalent to calling “conda clean -a”.