Python environment requirements — env

The function returns a list of requirements including the required Python version, package versions, and package name aliases for platform-specific packages. All packages will be installed using uv as the primary tool.

Usage

env_requirements(
  version = "3.10-1",
  include_optional = FALSE,
  modules = NULL,
  verbose = TRUE
)

Arguments

version: The Python version of the environment. Default is "3.10-1".
include_optional: Whether to include optional Python dependencies.
modules: Optional requirement modules to include. Supported values are "scanpy", "scvi", "scanorama", "bbknn", "celltypist", "cellphonedb", "magic", "scrublet", "doubletdetection", "sccoda", "doublet", "palantir", "scvelo", "cellrank", "wot", "phate", "pacmap", "trimap", "multimap", "scomm", "scenic", "seacells", and "tage". If NULL, the default environment is returned. The default excludes "sccoda", "scomm", and "scenic" because these workflows require dependency stacks that should be prepared explicitly. The "scenic" module is standalone and always uses Python "3.10-1".
verbose: Whether to print the message. Default is TRUE.

Value

A list containing:

python: Python version string
packages: Named vector of package version specifications
package_aliases: Named list mapping logical package names to actual installed names

Examples

env_requirements("3.10-1")