R/install_measure.R

In forImage: Foraminiferal Image Analysis and Test Measurement

#' Install python packages dependencies for measure function
#'
#' @description
#' The function is a wrapper to install all python packages dependencies for \code{measure} function at once.
#' It will install the following packages:
#' \code{numpy}, \code{scipy}, \code{imutils}, \code{Pillow}, \code{pandas},
#' and \code{opencv-python}.
#' If the latest versions of these packages are already installed, there is no need to run this function.
#'
#'
#' @param method Installation method. By default, "auto" automatically finds a
#' method that will work in the local environment. Change the default to force
#' a specific installation method. Note that the "virtualenv" method is not
#' available on Windows.
#'
#' @param conda Path to conda executable (or "auto" to find conda using the PATH and other conventional install locations).
#' @param envname Name of environment to install packages into.
#' @param extra_packages Additional packages if needed.
#' @param pip Install from pip, if possible.
#'
#' @return No return value. The function is only called to install the required packages.
#'
#' @details On Linux and OS X the "virtualenv" method will be used by default
#' ("conda" will be used if virtualenv isn't available). On Windows,
#' the "conda" method is always used. For more information check the `reticulate` package documentation:
#' https://rstudio.github.io/reticulate/
#
#' @export

install_measure <- function(method = "auto", conda = "auto", envname = NULL,
                            extra_packages = NULL, pip = F) {


    pack <- c(
        #"openssl",
        "numpy",
        "scipy",
        "imutils",
        "PIL",
        "pandas",
        "cv2")

    #have_numpy <- py_module_available("numpy")
    #have_scipy <- py_module_available("scipy")
    #have_imutils <- py_module_available("imutils")
    #have_pillow <- py_module_available("PIL")
    #have_pandas <- py_module_available("pandas")
    #have_opencv <- py_module_available("cv2")

    for(module in pack) {
        if(reticulate::py_module_available(module) == FALSE) {
            warning('module: ', module, ' was not found in python path. ')
        } else {
            stop("\n All modules are already available in python path. \n\n")
        }
    }


    package <- c(
        #"openssl",
        "numpy",
        "scipy",
        "imutils",
        "Pillow",
        "pandas",
        "opencv")



    packages <- c(package, extra_packages)

    reticulate::conda_list(conda = conda)

    reticulate::py_install(
        packages       = packages,
        envname        = envname,
        method         = method,
        conda          = conda,
        pip            = pip
    )

    cat("\n Installation complete. Please restart R.\n\n")

}