Activate Python Environment for SeuratExtend — activate

This function activates a Python environment (default: "seuratextend") and imports specified packages. It's particularly important for macOS users to call this function at the beginning of their workflow to prevent R session crashes when running Python-dependent functions later.

activate_python(conda_env = "seuratextend", verbose = TRUE, packages = c("os"))

Arguments

conda_env: Character string specifying the conda environment name. Default is "seuratextend".
verbose: Logical indicating whether to print status messages. Default is TRUE.
packages: Character vector of Python packages to import.

Value

Invisible TRUE if successful

Details

This function serves two main purposes:

1. It activates the specified conda environment and imports the specified Python packages.

2. **For macOS users (especially on Apple Silicon M1/M2/M3/M4)**: Running this function at the start of your R session, before loading any R objects, prevents memory management issues between R and Python that can otherwise cause R to crash when running operations like PCA on AnnData objects.

This is a crucial first step for macOS users working with `scVelo` functions.

Examples

if (FALSE) {
# For macOS users, run this at the beginning of your session
activate_python()

# Then load your Seurat objects and continue with your analysis
seu <- readRDS("my_seurat_object.rds")

# Custom environment with verbose output
activate_python(conda_env = "my_custom_env", verbose = TRUE)
}