R/zzz.R

In rformassspectrometry/SpectriPy: Enhancing Cross-Language Mass Spectrometry Data Analysis with R and Python

## based on https://rstudio.github.io/reticulate/articles/package.html#delay-loading-python-modules
matchms <- NULL
matchms_similarity <- NULL
matchms_filtering <- NULL
spectrum_utils <- NULL

.PY_PKGS <- c(matchms = "matchms==0.30.0",
              spectrum_utils = "spectrum_utils==0.3.2",
              numpy = "numpy==2.0.2")

#' @importFrom reticulate import use_virtualenv use_condaenv
#'
#' @importFrom reticulate py_install virtualenv_exists virtualenv_create
#'
#' @importFrom reticulate conda_list conda_create
.onLoad <- function(libname, pkgname) {
    if (!.spectripy_use_system()) {
        if (.spectripy_use_conda()) .initialize_conda()
        else .initialize_virtualenv()
    }
    .initialize_libraries(delay_load = TRUE, convert = FALSE)
}

#' Load all required Python libraries and assign it to global variables
#'
#' @noRd
.initialize_libraries <- function(delay_load = TRUE, convert = FALSE) {
    if (.spectripy_use_system())
        packageStartupMessage("Using system Python")
    matchms <<- import("matchms",
                       delay_load = delay_load,
                       convert = convert)
    matchms_similarity <<- import("matchms.similarity",
                                  delay_load = delay_load,
                                  convert = convert)
    matchms_filtering <<- import("matchms.filtering",
                                 delay_load = delay_load,
                                 convert = convert)
    spectrum_utils <<- import("spectrum_utils",
                              delay_load = delay_load,
                              convert = convert)
}

#' Initialize the conda environment creating it if not already present
#'
#' @noRd
.initialize_conda <- function(envname = .spectripy_env()) {
    if (!(envname %in% conda_list()$name)) {
        packageStartupMessage("Creating conda environment '", envname, "'")
        conda_create(envname)
    }
    packageStartupMessage("Using conda environment '", envname, "'")
    use_condaenv(envname, required = TRUE)
    .py_check_install(pkgs = .PY_PKGS[c("matchms", "spectrum_utils")],
                      envname = envname, use_conda = TRUE)
}

#' Initialize the Python virtualenv if not already present
#'
#' @noRd
.initialize_virtualenv <- function(envname = .spectripy_env()) {
    if (!virtualenv_exists(envname)) {
        packageStartupMessage("Creating virtual environment '", envname, "'")
        virtualenv_create(envname, packages = FALSE)
    }
    packageStartupMessage("Using virtual environment '", envname, "'")
    use_virtualenv(envname, required = TRUE)
    .py_check_install(pkgs = .PY_PKGS[c("matchms", "spectrum_utils")],
                      envname = envname, use_conda = FALSE)
}

.spectripy_env <- function() {
    getOption(
        "spectripy.env", Sys.getenv("SPECTRIPY_ENV", unset = "r-spectripy"))
}

.spectripy_use_conda <- function() {
    as.logical(getOption(
        "spectripy.use_conda",
        Sys.getenv("SPECTRIPY_USE_CONDA", unset = "FALSE")))
}

.spectripy_use_system <- function() {
    as.logical(getOption(
        "spectripy.use_system",
        Sys.getenv("SPECTRIPY_USE_SYSTEM", unset = "FALSE")))
}

#' @importFrom reticulate py_module_available py_install
.py_check_install <- function(pkgs, envname = .spectripy_env(),
                              use_conda = .spectripy_use_conda()) {
    any_install <- FALSE
    for (pkg in pkgs) {
        if (!py_module_available(sub("(>|=).*$", "", pkg))) {
            any_install <- TRUE
            packageStartupMessage("Installing required library '", pkg,"'")
            if (use_conda)
                py_install(pkg, envname = envname, method = "conda",
                           pip = FALSE, channel = c("bioconda", "conda-forge"))
            else py_install(pkg, envname = envname, method = "virtualenv",
                            channel = c("bioconda", "conda-forge"))
        }
    }
    if (any_install)
        packageStartupMessage("\nPlease restart R to load the freshly installed packages.\n")
}