activateEnvironment: Activate a Conda environment

In LTLA/basilisk.utils: Basilisk Installation Utilities

Activate a Conda environment

Description

Mimic the (de)activation of a Conda environment by modifying environment variables in the current R process.

Usage

activateEnvironment(envpath = NULL, full.activation = NA, loc = getCondaDir())

deactivateEnvironment(listing)

Arguments

envpath	String containing the path to the Conda environment to activate. If NULL, the base Conda instance at getCondaDir() is activated.
full.activation	Logical scalar indicating whether the conda activate command should be run on the environment. Default is NA, which means TRUE on Windows and FALSE anywhere else.
loc	String containing the path to the root of a conda instance.
listing	Named list of strings containing name:value pairs for environment variables, typically the output of activateEnvironment.

Details

Conda environments generally need to be activated with the conda activate command to function properly. This is especially relevant on Windows where the "PATH" variable needs to be modified for the DLL search. When performing full activation, the activateEnvironment function mimics the effect conda activate by modifying environment variables in the current R session. This can be reversed by deactivateEnvironment once the Conda environment is no longer in use.

The activateEnvironment function will also unset a few bothersome environment variables:

• "PYTHONPATH": to avoid compromising the version guarantees if reticulate's import is allowed to search other locations beyond the specified Conda environment.

• "PYTHONNOUSERSITE": similarly, to avoid searching the user's site libraries.

• "RETICULATE_PYTHON": this would otherwise override any choice of Python, even after explicit specification via reticulate's use_Condaenv!

• "RETICULATE_PYTHON_ENV": for similar reasons.

Value

activateEnvironment will modify environment variables to mimic activation of the Conda environment. It returns a named list of the previous values of all variables modified in this manner. (NA values indicate that the corresponding variable was not previously set.)

deactivateEnvironment restores the environment variables to their pre-activation state. It returns NULL invisibly.

Author(s)

Aaron Lun

Examples

# We can't actually run activateEnvironment() here, as it 
# either relies on basilisk already being installed or
# it has a hard-coded path to the basilisk system dir.
print("dummy test to pass BiocCheck")

LTLA/basilisk.utils documentation built on May 3, 2024, 12:51 p.m.