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Initialize Python Environment for GRNBoost2

Source: R/init_py.R
init_py.Rd

Sets up the Python environment and lazily loads modules required for running GRNBoost2: arboreto, pandas, and numpy. Automatically installs missing Python packages if requested.

Usage

init_py(
  python_path = "/usr/bin/python3",
  required = TRUE,
  install_missing = FALSE,
  install_method = "auto",
  verbose = TRUE
)

Arguments

python_path

Character string. Path to the Python executable, e.g., "/usr/bin/python3". For optimal GRNBoost2 compatibility, Python 3.8.x is strongly recommended.

required

Logical. If TRUE, errors if Python is not available or path is invalid. Default: TRUE.

install_missing

Logical. If TRUE, automatically installs missing Python packages. Default: FALSE.

install_method

Character string. Installation method when install_missing = TRUE. Options: "auto", "conda", "pip". Default: "auto".

verbose

Logical. If TRUE, shows installation progress. Default: TRUE.

Value

A list with three Python module objects:

  • arboreto: GRNBoost2 algorithm module.

  • pandas: Data handling module.

  • numpy: Numerical operations module.

Details

Uses reticulate to bind R to the specified Python interpreter and lazily import modules needed for GRNBoost2. If install_missing = TRUE, automatically installs the 'arboreto' package using the specified method if not found.

Examples

# Initialize Python environment (handles missing modules gracefully)
tryCatch(
    {
        modules <- init_py(required = FALSE)
    },
    error = function(e) {
        message("Python environment not available: ", e$message)
    }
)
#> Using Python version: 3.12
#> Could not check Python version
#> Python modules not available:ModuleNotFoundError: No module named 'arboreto'
#> Run `reticulate::py_last_error()` for details.