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#1276 @pawelru @m7pr This is a `mirai` alternative. Package seems to address the biggest issues reported during a research: - `mirai` has a native support of `ExtendedTask` - `mirai` is not being killed when `runApp` is executed (like `callr` does) - `mirai` by default opens a deamon in parallel R session without a need to handle the `future::plan`. - `mirai` has only one dependency in the whole dependency tree. #### Disadvantages so far: - ~~we need to pass and set `options`, system vars, working directory and `.libPaths` shikokuchuo/mirai#122 #### How does it work: - lockfile creation is invoked in `init` before application starts. This prevents to start the process each time when a new shiny session starts. Process is invoked as a promise and eventually `teal_app.lock` will be created - When shiny session starts `download lockfile` button is hidden by default. If promise is eventually resolved and lockfile is created then download button is shown. - alternatively, app developer can pre-compute lockfile and provide its path in `teal.renv.lockfile` option. In such case `renv::snapshot` will be skipped and user lockfile will be used in an app. #### Logs and notifications Logs are printed for app developer while notifications are presented to the app user: 1. When app uses precomputed file: - log in init: `Lockfile set using option "teal.renv.lockfile" - skipping automatic creation.` - no notification to the app user. 2. When app automatically determines snapshot: - log in init: `Lockfile creation started based on { getwd() }.` - log If lockfile created: `Lockfile {path} containing { n-pkgs } packages created{ with errors or warnings }.` - notification if lockfile created: `Lockfile available to download` - log if lockfile not created: `Lockfile creation failed.` - notification if lockfile not created: `Lockfile creation failed.` --------- Signed-off-by: Marcin <[email protected]> Signed-off-by: Pawel Rucki <[email protected]> Co-authored-by: m7pr <[email protected]> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Marcin <[email protected]> Co-authored-by: Pawel Rucki <[email protected]> Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com> Co-authored-by: Aleksander Chlebowski <[email protected]>
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| Original file line number | Diff line number | Diff line change |
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| #' Generate lockfile for application's environment reproducibility | ||
| #' | ||
| #' @param lockfile_path (`character`) path to the lockfile. | ||
| #' | ||
| #' @section Different ways of creating lockfile: | ||
| #' `teal` leverages [renv::snapshot()], which offers multiple methods for lockfile creation. | ||
| #' | ||
| #' - **Working directory lockfile**: `teal`, by default, will create an `implicit` type lockfile that uses | ||
| #' `renv::dependencies()` to detect all R packages in the current project's working directory. | ||
| #' - **`DESCRIPTION`-based lockfile**: To generate a lockfile based on a `DESCRIPTION` file in your working | ||
| #' directory, set `renv::settings$snapshot.type("explicit")`. The naming convention for `type` follows | ||
| #' `renv::snapshot()`. For the `"explicit"` type, refer to `renv::settings$package.dependency.fields()` for the | ||
| #' `DESCRIPTION` fields included in the lockfile. | ||
| #' - **Custom files-based lockfile**: To specify custom files as the basis for the lockfile, set | ||
| #' `renv::settings$snapshot.type("custom")` and configure the `renv.snapshot.filter` option. | ||
| #' | ||
| #' @section lockfile usage: | ||
| #' After creating the lockfile, you can restore the application's environment using `renv::restore()`. | ||
| #' | ||
| #' @seealso [renv::snapshot()], [renv::restore()]. | ||
| #' | ||
| #' @return `NULL` | ||
| #' | ||
| #' @name module_teal_lockfile | ||
| #' @rdname module_teal_lockfile | ||
| #' | ||
| #' @keywords internal | ||
| NULL | ||
|
|
||
| #' @rdname module_teal_lockfile | ||
| ui_teal_lockfile <- function(id) { | ||
| ns <- NS(id) | ||
| shiny::tagList( | ||
| tags$span("", id = ns("lockFileStatus")), | ||
| shinyjs::disabled(downloadLink(ns("lockFileLink"), "Download lockfile")) | ||
| ) | ||
| } | ||
|
|
||
| #' @rdname module_teal_lockfile | ||
| srv_teal_lockfile <- function(id) { | ||
| moduleServer(id, function(input, output, session) { | ||
| logger::log_debug("Initialize srv_teal_lockfile.") | ||
| enable_lockfile_download <- function() { | ||
| shinyjs::html("lockFileStatus", "Application lockfile ready.") | ||
| shinyjs::hide("lockFileStatus", anim = TRUE) | ||
| shinyjs::enable("lockFileLink") | ||
| output$lockFileLink <- shiny::downloadHandler( | ||
| filename = function() { | ||
| "renv.lock" | ||
| }, | ||
| content = function(file) { | ||
| file.copy(lockfile_path, file) | ||
| file | ||
| }, | ||
| contentType = "application/json" | ||
| ) | ||
| } | ||
| disable_lockfile_download <- function() { | ||
| warning("Lockfile creation failed.", call. = FALSE) | ||
| shinyjs::html("lockFileStatus", "Lockfile creation failed.") | ||
| shinyjs::hide("lockFileLink") | ||
| } | ||
|
|
||
| shiny::onStop(function() { | ||
| if (file.exists(lockfile_path) && !shiny::isRunning()) { | ||
| logger::log_debug("Removing lockfile after shutting down the app") | ||
| file.remove(lockfile_path) | ||
| } | ||
| }) | ||
|
|
||
| lockfile_path <- "teal_app.lock" | ||
| mode <- getOption("teal.lockfile.mode", default = "") | ||
|
|
||
| if (!(mode %in% c("auto", "enabled", "disabled"))) { | ||
| stop("'teal.lockfile.mode' option can only be one of \"auto\", \"disabled\" or \"disabled\". ") | ||
| } | ||
|
|
||
| if (mode == "disabled") { | ||
| logger::log_debug("'teal.lockfile.mode' option is set to 'disabled'. Hiding lockfile download button.") | ||
| shinyjs::hide("lockFileLink") | ||
| return(NULL) | ||
| } | ||
|
|
||
| if (file.exists(lockfile_path)) { | ||
| logger::log_debug("Lockfile has already been created for this app - skipping automatic creation.") | ||
| enable_lockfile_download() | ||
| return(NULL) | ||
| } | ||
|
|
||
| if (mode == "auto" && .is_disabled_lockfile_scenario()) { | ||
| logger::log_debug( | ||
| "Automatic lockfile creation disabled. Execution scenario satisfies teal:::.is_disabled_lockfile_scenario()." | ||
| ) | ||
| shinyjs::hide("lockFileLink") | ||
| return(NULL) | ||
| } | ||
|
|
||
| if (!.is_lockfile_deps_installed()) { | ||
| warning("Automatic lockfile creation disabled. `mirai` and `renv` packages must be installed.") | ||
| shinyjs::hide("lockFileLink") | ||
| return(NULL) | ||
| } | ||
|
|
||
| # - Will be run only if the lockfile doesn't exist (see the if-s above) | ||
| # - We render to the tempfile because the process might last after session is closed and we don't | ||
| # want to make a "teal_app.renv" then. This is why we copy only during active session. | ||
| process <- .teal_lockfile_process_invoke(lockfile_path) | ||
| observeEvent(process$status(), { | ||
| if (process$status() %in% c("initial", "running")) { | ||
| shinyjs::html("lockFileStatus", "Creating lockfile...") | ||
| } else if (process$status() == "success") { | ||
| result <- process$result() | ||
| if (any(grepl("Lockfile written to", result$out))) { | ||
| logger::log_debug("Lockfile containing { length(result$res$Packages) } packages created.") | ||
| if (any(grepl("(WARNING|ERROR):", result$out))) { | ||
| warning("Lockfile created with warning(s) or error(s):", call. = FALSE) | ||
| for (i in result$out) { | ||
| warning(i, call. = FALSE) | ||
| } | ||
| } | ||
| enable_lockfile_download() | ||
| } else { | ||
| disable_lockfile_download() | ||
| } | ||
| } else if (process$status() == "error") { | ||
| disable_lockfile_download() | ||
| } | ||
| }) | ||
|
|
||
| NULL | ||
| }) | ||
| } | ||
|
|
||
| utils::globalVariables(c("opts", "sysenv", "libpaths", "wd", "lockfilepath", "run")) # needed for mirai call | ||
| #' @rdname module_teal_lockfile | ||
| .teal_lockfile_process_invoke <- function(lockfile_path) { | ||
| mirai_obj <- NULL | ||
| process <- shiny::ExtendedTask$new(function() { | ||
| m <- mirai::mirai( | ||
| { | ||
| options(opts) | ||
| do.call(Sys.setenv, sysenv) | ||
| .libPaths(libpaths) | ||
| setwd(wd) | ||
| run(lockfile_path = lockfile_path) | ||
| }, | ||
| run = .renv_snapshot, | ||
| lockfile_path = lockfile_path, | ||
| opts = options(), | ||
| libpaths = .libPaths(), | ||
| sysenv = as.list(Sys.getenv()), | ||
| wd = getwd() | ||
| ) | ||
| mirai_obj <<- m | ||
| m | ||
| }) | ||
|
|
||
| shiny::onStop(function() { | ||
| if (mirai::unresolved(mirai_obj)) { | ||
| logger::log_debug("Terminating a running lockfile process...") | ||
| mirai::stop_mirai(mirai_obj) # this doesn't stop running - renv will be created even if session is closed | ||
| } | ||
| }) | ||
|
|
||
| suppressWarnings({ # 'package:stats' may not be available when loading | ||
| process$invoke() | ||
| }) | ||
|
|
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| logger::log_debug("Lockfile creation started based on { getwd() }.") | ||
|
|
||
| process | ||
| } | ||
|
|
||
| #' @rdname module_teal_lockfile | ||
| .renv_snapshot <- function(lockfile_path) { | ||
| out <- utils::capture.output( | ||
| res <- renv::snapshot( | ||
| lockfile = lockfile_path, | ||
| prompt = FALSE, | ||
| force = TRUE, | ||
| type = renv::settings$snapshot.type() # see the section "Different ways of creating lockfile" above here | ||
| ) | ||
| ) | ||
|
|
||
| list(out = out, res = res) | ||
| } | ||
|
|
||
| #' @rdname module_teal_lockfile | ||
| .is_lockfile_deps_installed <- function() { | ||
| requireNamespace("mirai", quietly = TRUE) && requireNamespace("renv", quietly = TRUE) | ||
| } | ||
|
|
||
| #' @rdname module_teal_lockfile | ||
| .is_disabled_lockfile_scenario <- function() { | ||
| identical(Sys.getenv("CALLR_IS_RUNNING"), "true") || # inside callr process | ||
| identical(Sys.getenv("TESTTHAT"), "true") || # inside devtools::test | ||
| !identical(Sys.getenv("QUARTO_PROJECT_ROOT"), "") || # inside Quarto process | ||
| ( | ||
| ("CheckExEnv" %in% search()) || any(c("_R_CHECK_TIMINGS_", "_R_CHECK_LICENSE_") %in% names(Sys.getenv())) | ||
| ) # inside R CMD CHECK | ||
| } |
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