ifcb_py_install: Install iRfcb Python Environment

In iRfcb: Tools for Managing Imaging FlowCytobot (IFCB) Data

Install iRfcb Python Environment

Description

This function sets up the Python environment for iRfcb. By default, it creates and activates a Python virtual environment (venv) named "iRfcb" and installs the required Python packages from the "requirements.txt" file. Alternatively, users can opt to use the system Python instead of creating a virtual environment by setting use_venv = FALSE (not recommended).

Usage

ifcb_py_install(
  envname = "~/.virtualenvs/iRfcb",
  use_venv = TRUE,
  packages = NULL
)

Arguments

envname	A character string specifying the name of the virtual environment to create. Default is "~/.virtualenvs/iRfcb".
use_venv	Logical. If TRUE (default), a virtual environment is created. If FALSE, the system Python is used instead, and missing packages are installed globally for the user.
packages	A character vector of additional Python packages to install. If NULL (default), only the packages from "requirements.txt" are installed.

Details

This function requires Python to be available on the system. It uses the reticulate package to manage Python environments and packages.

The USE_IRFCB_PYTHON environment variable can be set to automatically activate an installed Python venv named iRfcb when the iRfcb package is loaded. Ensure that the iRfcb venv is installed in reticulate::virtualenv_root() and available via reticulate::virtualenv_list() (see examples). You can set USE_IRFCB_PYTHON to "TRUE" in your .Renviron file to enable automatic setup. For more details, see the package README at https://europeanifcbgroup.github.io/iRfcb/#python-dependency.

Value

No return value. This function is called for its side effect of configuring the Python environment.

Examples

## Not run: 
# Define the name of the virtual environment in your virtual_root directory
envpath <- file.path(reticulate::virtualenv_root(), "iRfcb")

# Install the iRfcb Python venv in your virtual_root directory
ifcb_py_install(envname = envpath)

# Install the iRfcb Python environment with additional packages
ifcb_py_install(envname = envpath, packages = c("numpy", "plotly"))

# Use system Python instead of a virtual environment
ifcb_py_install(envname = envpath, use_venv = FALSE)

## End(Not run)

iRfcb documentation built on April 16, 2025, 1:09 a.m.