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-compatible Python environment. If NULL, the environment name will be set to "scop_env". Default is NULL.
conda: The path or command name of a conda-compatible executable (conda, mamba, or micromamba). Use "auto" to allow automatically finding an appropriate environment manager. If "micromamba" is requested and micromamba is not available on PATH, a package-managed micromamba is downloaded automatically.
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", "sccoda", "doubletdetection", "doublet", "palantir", "scvelo", "cellrank", "wot", "phate", "pacmap", "trimap", "multimap", and "scomm". If NULL or omitted in PrepareEnv(), the default environment is installed. The default excludes "sccoda" and "scomm" because their TensorFlow stacks are not compatible with the default JAX/scVI stack in the same environment; request them explicitly for scCODA/scOMM workflows.
pip_options: Additional command line arguments to be passed to uv/pip when installing pip packages.
...: Additional arguments passed to package installation functions.