Install a managed Python environment for R — simple

Sets up (and optionally populates) a dedicated miniconda Python environment for use from R via reticulate. This is the ecosystem's shared provisioning entry point: packages such as fafbseg, bancr and seatabler all route their Python installation through it, so users have one command to run and one environment to manage.

Usage

simple_python(
  pyinstall = c("basic", "full", "extra", "minimal", "cleanenv", "blast", "none"),
  pkgs = NULL,
  miniconda = TRUE
)

Arguments

pyinstall: Which package bundle to install. One of "basic", "full", "extra", "minimal", "cleanenv", "blast" or "none".
pkgs: Optional character vector of additional Python packages (pip specifications) to install into the environment.
miniconda: Whether to use the managed miniconda environment (strongly recommended). When FALSE your current Python is used as-is.

Value

Invisibly NULL. Called for its side effect of provisioning Python.

Details

With miniconda = TRUE (the default and recommendation) a private miniconda install and r-reticulate conda environment are created/updated, independent of any system Python. The pyinstall bundles install a curated set of packages used across the FlyWire/connectomics ecosystem: "minimal" installs just pandas – nat.python's own baseline, needed by pandas2df(), with numpy coming in as its dependency; "basic" adds cloud-volume, seatable_api and CAVEclient on top; "full" adds navis + fafbseg; "extra" additionally installs skeletonisation tooling (skeletor, meshparty and friends). "none" provisions the environment but installs no bundle, which is what you want when passing your own pkgs. "cleanenv" and "blast" only print the (destructive) commands needed to remove an environment; they never delete anything themselves.

After any installation the cached module versions (forget_module_version()) and the check_module() memoise cache are cleared so that subsequent checks reflect the new environment.

Examples

if (FALSE) { # \dontrun{
simple_python("basic")                          # the common case
simple_python("minimal")                        # just pandas (+ numpy)
simple_python("minimal", pkgs = "seatable_api") # pandas baseline + one pkg
simple_python("none", pkgs = "seatable_api")    # just one package
} # }