R/zzz.R

In slendr: A Simulation Framework for Spatiotemporal Population Genetics

# # global references to required Python packages - inspired by:
# # https://cran.r-project.org/web/packages/reticulate/vignettes/package.html
# # (Python environment initialization is now being done using init_env())
tskit <- NULL
pyslim <- NULL
msp <- NULL
tspop <- NULL
# pylib <- NULL

# define slendr's required Python dependencies and compose an environment name
# that will be used specifically for them
PYTHON_ENV <-
  c("msprime==1.3.1", "tskit==0.5.6", "pyslim==1.0.4", "tspop==0.0.2") %>%
  gsub("==", "-", .) %>%
  paste(collapse = "_") %>%
  paste0("Python-3.12_", .)

.onAttach <- function(libname, pkgname) {
  if (Sys.info()[["sysname"]] == "Windows") {
    slim_binary <- "slim.exe"
    renviron_dir <- "C:\\Users\\<your username>\\Documents\\"
    path_dir <- "C:\\path\\to\\directory\\with\\slim.exe\\"
  } else {
    slim_binary <- "slim"
    renviron_dir <- "~/"
    path_dir <- "path/to/directory/with/slim/binary"
  }

  # check for presence of the slim binary in user's PATH and display
  # a warning if it's not present
  path_check <- all(Sys.which(slim_binary) != "")
  if (!path_check) {
    packageStartupMessage(
      "The '", slim_binary, "' binary could not be found in your $PATH. Most of\n",
      "the functionality of slendr will work without any issues but\n",
      "you will not be able to simulate data with the `slim()` function.\n",
      "\nIf you want to run SLiM simulations, make sure to modify the $PATH\n",
      "variable so that it points to the directory containing the slim\n",
      "command-line program. One easy way to do this is to add this:\n\n",
      "PATH=\"", path_dir, "\"\n\n",
      "to your ", renviron_dir, ".Renviron file.\n\n",
      "Alternatively, use the `slim_path` argument",
      " of the `slim()` function.\n--------------------")
  } else {
    required_version <- "4.0"
    slim_version <- system(paste(slim_binary, "-v"), intern = TRUE) %>%
      gsub("SLiM version (.*),.*$", "\\1", .) %>% .[1]
    if (utils::compareVersion(slim_version, required_version) < 0)
      packageStartupMessage(
        "You are running SLiM version ", slim_version,
        " but at least version ", required_version,
        "\nis required. Please upgrade SLiM to the latest version.\n--------------------"
      )
  }

  check_spatial_pkgs(error = FALSE)

  if (!is_slendr_env_present()) {
    if (!getOption("slendr.custom_env")) {
      version <- strsplit(PYTHON_ENV, "_")[[1]] %>% gsub(".*-", "", .)
      packageStartupMessage(
        sprintf(paste0("A slendr Python (%s) environment with the necessary versions of\n",
          "msprime (%s), tskit (%s), pyslim (%s), and tspop (%s)\nhas not been found.\n"),
          version[1], version[2], version[3], version[4], version[5]),
          "\nYou can setup a pre-configured environment with all of slendr's Python\n",
          "dependencies automatically by running the function `setup_env()`."
      )
    }
  }
}

.onLoad <- function(libname, pkgname) {
  # setup Python module imports (see also slendr's init_env() function)
  tskit <<- reticulate::import("tskit", delay_load = TRUE)
  pyslim <<- reticulate::import("pyslim", delay_load = TRUE)
  msp <<- reticulate::import("msprime", delay_load = TRUE)
  tspop <<- reticulate::import("tspop", delay_load = TRUE)

  # setup slendr options (https://r-pkgs.org/r.html#when-you-do-need-side-effects)
  op <- options()
  op.slendr <- list(slendr.custom_env = FALSE)
  toset <- !(names(op.slendr) %in% names(op))
  if (any(toset)) options(op.slendr[toset])
  invisible()
}