Merge branch 'main' into test@bslib@main

.pre-commit-config.yaml

@@ -17,14 +17,13 @@ repos:
         additional_dependencies:
           - davidgohel/flextable # Error: package 'flextable' is not available
           - davidgohel/gdtools # for flextable
+          - mirai
           - checkmate
-          - future
           - jsonlite
           - lifecycle
           - logger
           - magrittr
           - methods
-          - promises
           - renv
           - rlang
           - shiny

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: teal
 Title: Exploratory Web Apps for Analyzing Clinical Trials Data
-Version: 0.15.2.9063
-Date: 2024-09-17
+Version: 0.15.2.9064
+Date: 2024-09-23
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-9533-457X")),
@@ -42,13 +42,10 @@ Depends:
 Imports:
     bslib (>= 0.8.0),
     checkmate (>= 2.1.0),
-    future (>= 1.33.2),
     jsonlite,
     lifecycle (>= 0.2.0),
     logger (>= 0.2.0),
     methods,
-    promises (>= 1.3.0),
-    renv (>= 1.0.7),
     rlang (>= 1.0.0),
     shinyjs,
     stats,
@@ -59,8 +56,10 @@ Imports:
     utils
 Suggests:
     knitr (>= 1.42),
+    mirai (>= 1.1.1),
     MultiAssayExperiment,
     R6,
+    renv (>= 1.0.7),
     rmarkdown (>= 2.23),
     rvest,
     shinytest2,
@@ -73,15 +72,15 @@ VignetteBuilder:
 RdMacros:
     lifecycle
 Config/Needs/verdepcheck: rstudio/shiny, insightsengineering/teal.data,
-    insightsengineering/teal.slice, mllg/checkmate,
-    HenrikBengtsson/future, jeroen/jsonlite, r-lib/lifecycle,
-    daroczig/logger, rstudio/promises, rstudio/renv, r-lib/rlang,
-    daattali/shinyjs, insightsengineering/teal.code,
-    insightsengineering/teal.logger, insightsengineering/teal.reporter,
-    insightsengineering/teal.widgets, rstudio/bslib, yihui/knitr,
-    bioc::MultiAssayExperiment, r-lib/R6, rstudio/rmarkdown,
-    tidyverse/rvest, rstudio/shinytest2, rstudio/shinyvalidate,
-    r-lib/testthat, r-lib/withr, yaml=vubiostat/r-yaml
+    insightsengineering/teal.slice, mllg/checkmate, jeroen/jsonlite,
+    r-lib/lifecycle, daroczig/logger, shikokuchuo/mirai,
+    shikokuchuo/nanonext, rstudio/renv, r-lib/rlang, daattali/shinyjs,
+    insightsengineering/teal.code, insightsengineering/teal.logger,
+    insightsengineering/teal.reporter, insightsengineering/teal.widgets,
+    rstudio/bslib, yihui/knitr, bioc::MultiAssayExperiment, r-lib/R6,
+    rstudio/rmarkdown, tidyverse/rvest, rstudio/shinytest2,
+    rstudio/shinyvalidate, r-lib/testthat, r-lib/withr,
+    yaml=vubiostat/r-yaml
 Config/Needs/website: insightsengineering/nesttemplate
 Encoding: UTF-8
 Language: en-US
@@ -106,6 +105,7 @@ Collate:
     'module_snapshot_manager.R'
     'module_teal.R'
     'module_teal_data.R'
+    'module_teal_lockfile.R'
     'module_teal_with_splash.R'
     'module_transform_data.R'
     'reporter_previewer_module.R'
@@ -116,7 +116,6 @@ Collate:
     'teal_data_module-eval_code.R'
     'teal_data_module-within.R'
     'teal_data_utils.R'
-    'teal_lockfile.R'
     'teal_reporter.R'
     'teal_slices-store.R'
     'teal_slices.R'

NEWS.md

@@ -1,4 +1,4 @@
-# teal 0.15.2.9063
+# teal 0.15.2.9064
 
 ### New features
 

R/init.R

@@ -153,9 +153,6 @@ init <- function(data,
   # log
   teal.logger::log_system_info()
 
-  # invoke lockfile creation
-  teal_lockfile()
-
   # argument transformations
   ## `modules` - landing module
   landing <- extract_module(modules, "teal_module_landing")

R/module_teal.R

@@ -133,7 +133,7 @@ ui_teal <- function(id,
         footer,
         teal.widgets::verbatim_popup_ui(ns("sessionInfo"), "Session Info", type = "link"),
         br(),
-        downloadLink(ns("lockFile"), "Download .lock file"),
+        ui_teal_lockfile(ns("lockfile")),
         textOutput(ns("identifier"))
       )
     )
@@ -151,6 +151,8 @@ srv_teal <- function(id, data, modules, filter = teal_slices()) {
   moduleServer(id, function(input, output, session) {
     logger::log_debug("srv_teal initializing.")
 
+    srv_teal_lockfile("lockfile")
+
     output$identifier <- renderText(
       paste0("Pid:", Sys.getpid(), " Token:", substr(session$token, 25, 32))
     )
@@ -161,8 +163,6 @@ srv_teal <- function(id, data, modules, filter = teal_slices()) {
       title = "SessionInfo"
     )
 
-    output$lockFile <- teal_lockfile_downloadhandler()
-
     # `JavaScript` code
     run_js_files(files = "init.js")
 

R/module_teal_lockfile.R

@@ -0,0 +1,201 @@
+#' 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$invoke()
+  })
+
+  logger::log_debug("Lockfile creation started based on { getwd() }.")
+
+  process
+}
+
+#' @rdname module_teal_lockfile
+.renv_snapshot <- function(lockfile_path) {
+  out <- utils::capture.output(
+    res <- renv::snapshot(
+      lockfile = lockfile_path,
+      prompt = FALSE,
+      force = TRUE,
+      type = renv::settings$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
+}