anndataR/R/check_requires.R at 5dd4510f0779ed6c3dc0ed1f751746e4854687ca · Bisaloo/anndataR · GitHub

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#' Check required packages
#'
#' Check that required packages are available and give a nice error message with
#' install instructions if not
#'
#' @param what A message stating what the packages are required for. Used at the
#'   start of the error message e.g. "{what} requires...".
#' @param requires Character vector of required package names
#' @param where Where to install the packages from. Either "CRAN", "Bioc", or "Python"
#'
#' @return `'TRUE` invisibly if all packages are available, otherwise calls
#'   [cli::cli_abort()]
#'
#' @importFrom rlang caller_env
#' @noRd
check_requires <- function(
  what,
  requires,
  where = c("CRAN", "Bioc", "Python")
) {
  where <- match.arg(where)

  if (where == "Python") {
    check_python_packages(what, requires)
  } else {
    check_r_packages(what, requires, where)
  }

  invisible(TRUE)
}

#' Check required Python packages
#'
#' @param what A message stating what the packages are required for
#' @param requires Character vector of required Python package names
#'
#' @importFrom rlang caller_env
#' @noRd
check_python_packages <- function(what, requires) {
  check_requires(what, "reticulate")

  is_available <- map_lgl(requires, reticulate::py_module_available)

  if (!all(is_available)) {
    missing <- requires[!is_available]
    # nolint start object_usage_linter
    missing_str <- format_package_list(missing)
    # nolint end object_usage_linter

    cli_abort(
      c(
        "{what} requires the Python {.pkg {missing}} package{?s}",
        "i" = paste(
          "To continue, require {cli::qty(missing)}{?it/them} using",
          "{.code reticulate::py_require({missing_str})} or install",
          "{cli::qty(missing)}{?it/them} them in your Python environment",
          "using another method"
        )
      ),
      call = caller_env()
    )
  }
}

#' Check required R packages
#'
#' @param what A message stating what the packages are required for
#' @param requires Character vector of required R package names
#' @param where Where to install the packages from. Either "CRAN" or "Bioc"
#'
#' @importFrom rlang caller_env
#' @noRd
check_r_packages <- function(what, requires, where) {
  is_available <- map_lgl(requires, requireNamespace, quietly = TRUE)

  if (!all(is_available)) {
    missing <- requires[!is_available]
    # nolint start object_usage_linter
    missing_str <- format_package_list(missing)
    install_fun <- get_r_install_function(where)
    # nolint end object_usage_linter

    cli_abort(
      c(
        "{what} requires the {.pkg {missing}} package{?s}",
        "i" = paste(
          "To continue, install {cli::qty(missing)}{?it/them} using",
          "{.run {install_fun}({missing_str})}"
        )
      ),
      call = caller_env()
    )
  }
}

#' Format package list for installation command
#'
#' @param packages Character vector of package names
#' @return Formatted string for use in installation functions
#' @noRd
format_package_list <- function(packages) {
  missing_str <- paste0("\"", paste(packages, collapse = "\", \""), "\"")
  if (length(packages) > 1) {
    missing_str <- paste0("c(", missing_str, ")")
  }
  missing_str
}

#' Get R package installation function
#'
#' @param where Where to install from. Either "CRAN" or "Bioc"
#' @return Installation function name as string
#' @noRd
get_r_install_function <- function(where) {
  # nolint start object_usage_linter
  switch(
    where,
    CRAN = "install.packages",
    Bioc = "install.packages(\"BiocManager\"); BiocManager::install"
  )
  # nolint end object_usage_linter
}