R/install_packages.R

In condathis: Run Any CLI Tool on a 'Conda' Environment

#' Install Packages in a Existing Conda Environment
#' @param packages Character vector with the names of the packages and
#'   version strings if necessary.
#' @param env_name Name of the Conda environment where the packages are
#'   going to be installed. Defaults to 'condathis-env'.
#'
#' @inheritParams create_env
#'
#' @return An object of class `list` representing the result of the command
#'   execution. Contains information about the standard output, standard error,
#'   and exit status of the command.
#'
#' @examples
#' \dontrun{
#' condathis::with_sandbox_dir({
#'   condathis::create_env(
#'     packages = "fastqc",
#'     env_name = "fastqc-env"
#'   )
#'   # Install the package `python` in the `fastqc-env` environment.
#'   # It is not recommended to install multiple packages in the same environment,
#'   #  # as it defeats the purpose of isolation provided by separate environments.
#'   condathis::install_packages(packages = "python", env_name = "fastqc-env")
#' })
#' }
#'
#' @export
install_packages <- function(packages,
                             env_name = "condathis-env",
                             channels = c(
                               "bioconda",
                               "conda-forge"
                             ),
                             additional_channels = NULL,
                             verbose = "silent") {
  if (isFALSE(any(list_envs() %in% env_name))) {
    create_env(
      packages = NULL,
      env_name = env_name,
      verbose = verbose
    )
  }
  quiet_flag <- parse_quiet_flag(verbose = verbose)
  channels_arg <- format_channels_args(
    additional_channels,
    channels
  )
  px_res <- rethrow_error_cmd(
    expr = {
      native_cmd(
        conda_cmd = "install",
        conda_args = c(
          "-n",
          env_name,
          "--yes",
          quiet_flag,
          "--no-channel-priority",
          "--override-channels",
          "--channel-priority=0",
          channels_arg
        ),
        packages,
        verbose = verbose
      )
    }
  )

  if (isTRUE(verbose %in% c("full", "output") && length(packages) > 0L)) {
    cli::cli_inform(
      message = c(
        `!` = "{cli::qty(packages)}Package{?s} {.field {packages}} succesfully installed in environment {.field {env_name}}."
      )
    )
  }
  return(invisible(px_res))
}