Prepare the python environment — PrepareEnv • scop

Prepare the python environment by installing the required dependencies and setting up the environment.

Usage

PrepareEnv(
  envname = NULL,
  conda = "auto",
  miniconda_repo = "https://repo.anaconda.com/miniconda",
  version = if (is_windows()) "3.11-1" else "3.10-1",
  force = FALSE,
  modules = NULL,
  pip_options = character(),
  ...
)

Arguments

envname: The name of the conda environment. If NULL, the environment name will be set to "scop_env". Default is NULL.
conda: The path to a conda executable. Use "auto" to allow automatically finding an appropriate conda binary.
miniconda_repo: Repository URL for miniconda. Default is https://repo.anaconda.com/miniconda.
version: The Python version. Default is "3.10-1" on macOS and Unix and "3.11-1" on Windows.
force: Whether to force recreation of the environment. If TRUE, the existing environment will be removed and recreated. Default is FALSE.
modules: Optional Python dependency modules to install in addition to the default scientific stack. Supported values are "scanpy", "scvi", "glue", "scanorama", "bbknn", "celltypist", "cellphonedb", "magic", "scrublet", "doubletdetection", "doublet", "palantir", "scvelo", "cellrank", "wot", "phate", "pacmap", "trimap", "multimap", and "scomm". If NULL or omitted in PrepareEnv(), the complete environment is installed.
pip_options: Additional command line arguments to be passed to uv/pip when installing pip packages.
...: Additional arguments passed to package installation functions.