Merge branch 'main' into focussearch

.Rbuildignore

@@ -22,3 +22,4 @@
 ^Meta$
 ^cran-comments\.md$
 ^CRAN-RELEASE$
+^README\.Rmd$

.github/workflows/tic.yml

@@ -1,5 +1,5 @@
 ## tic GitHub Actions template: linux-macos-windows-deploy
-## revision date: 2020-12-11
+## revision date: 2021-06-27
 # [Custom header]
 on:
   workflow_dispatch:
@@ -45,7 +45,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2.3.4
+      - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-r@master
         with:
@@ -71,22 +71,22 @@ jobs:
 
       - name: "[Cache] Cache R packages"
         if: runner.os != 'Windows'
-        uses: pat-s/always-upload-cache@v2.1.3
+        uses: pat-s/always-upload-cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{steps.date.outputs.date}}
           restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-${{steps.date.outputs.date}}
 
+      - name: "[Stage] [Linux] Install required system libs"
+        if: runner.os == 'Linux'
+        run: sudo apt install libcurl4-openssl-dev libgit2-dev
+
       # for some strange Windows reason this step and the next one need to be decoupled
       - name: "[Stage] Prepare"
         run: |
           Rscript -e "if (!requireNamespace('remotes')) install.packages('remotes', type = 'source')"
           Rscript -e "if (getRversion() < '3.2' && !requireNamespace('curl')) install.packages('curl', type = 'source')"
 
-      - name: "[Stage] [Linux] Install curl and libgit2"
-        if: runner.os == 'Linux'
-        run: sudo apt install libcurl4-openssl-dev libgit2-dev
-
       - name: "[Stage] [macOS] Install libgit2"
         if: runner.os == 'macOS'
         run: brew install libgit2
@@ -99,6 +99,16 @@ jobs:
         if: runner.os == 'Linux' && matrix.config.pkgdown != ''
         run: sudo apt install libharfbuzz-dev libfribidi-dev
 
+      # Try to automatically check for system dependencies and install them
+      # Note: this might not catch all required system libs and manual action might be needed
+      - name: "[Stage] [Linux] Install linux system dependencies"
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
       - name: "[Stage] Install"
         if: matrix.config.os != 'macOS-latest' || matrix.config.r != 'devel'
         run: Rscript -e "remotes::install_github('ropensci/tic')" -e "print(tic::dsl_load())" -e "tic::prepare_all_stages()" -e "tic::before_install()" -e "tic::install()"
@@ -119,7 +129,7 @@ jobs:
 
       - name: "[Stage] Upload R CMD check artifacts"
         if: failure()
-        uses: actions/upload-artifact@v2.2.1
+        uses: actions/upload-artifact@v2
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check

.github/workflows/update-tic.yml

@@ -23,7 +23,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@master
+      - uses: actions/checkout@v2
         with:
           persist-credentials: false
 
@@ -43,7 +43,7 @@ jobs:
             Rscript -e "tic::update_yml()"
 
       - name: "[Stage] Create Pull Request"
-        uses: peter-evans/create-pull-request@master
+        uses: peter-evans/create-pull-request@v3
         with:
           author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
           token: ${{ secrets.TIC_UPDATE }}

DESCRIPTION

@@ -38,14 +38,14 @@ License: LGPL-3
 URL: https://bbotk.mlr-org.com, https://github.com/mlr-org/bbotk
 BugReports: https://github.com/mlr-org/bbotk/issues
 Depends:
+    paradox (>= 0.7.0),
     R (>= 3.1.0)
 Imports:
     checkmate (>= 2.0.0),
     data.table,
     lgr,
     methods,
     mlr3misc (>= 0.7.0),
-    paradox (>= 0.7.0),
     R6
 Suggests:
     adagio,
@@ -94,6 +94,7 @@ Collate:
     'TerminatorStagnation.R'
     'TerminatorStagnationBatch.R'
     'assertions.R'
+    'bb_optimize.R'
     'bbotk_reflections.R'
     'bibentries.R'
     'helper.R'

NAMESPACE

@@ -1,6 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(as.data.table,Archive)
+S3method(bb_optimize,"function")
+S3method(bb_optimize,Objective)
 export(Archive)
 export(ArchiveBest)
 export(Objective)
@@ -33,6 +35,7 @@ export(assert_set)
 export(assert_terminable)
 export(assert_terminator)
 export(assign_result_default)
+export(bb_optimize)
 export(bbotk_reflections)
 export(is_dominated)
 export(mlr_optimizers)

NEWS.md

@@ -1,7 +1,6 @@
 # bbotk 0.3.2.9000
 
-- Same as previous version.
-
+- Adds `bb_optimize()` function for quick optimization.
 
 # bbotk 0.3.2
 
@@ -43,4 +42,3 @@
 # bbotk 0.2
 
 * First version of the Black-Box Optimization Toolkit
-

R/Archive.R

@@ -104,8 +104,7 @@ Archive = R6Class("Archive",
       } else {
         assert_integerish(batch, lower = 1L, upper = self$n_batch, coerce = TRUE)
       }
-      batch_nr = NULL # CRAN check
-      tab = self$data[batch_nr %in% batch]
+      tab = self$data[get("batch_nr") %in% batch, ]
 
       max_to_min = mult_max_to_min(self$codomain)
       if (self$codomain$length == 1L) {

R/Objective.R

@@ -33,7 +33,9 @@ Objective = R6Class("Objective",
     codomain = NULL,
 
     #' @field constants ([paradox::ParamSet]).\cr
-    #' Changeable constants or parameters that are not subject to tuning can be stored and accessed here.
+    #' Changeable constants or parameters that are not subject to tuning can be
+    #' stored and accessed here. Set constant values are passed to `$.eval()`
+    #' and `$.eval_many()` as named arguments.
     constants = NULL,
 
     #' @field check_values (`logical(1)`)\cr
@@ -45,8 +47,8 @@ Objective = R6Class("Objective",
     #' @param id (`character(1)`).
     #' @param properties (`character()`).
     initialize = function(id = "f", properties = character(), domain,
-      codomain = ParamSet$new(list(ParamDbl$new("y", tags = "minimize"))),
-      constants = ParamSet$new(), check_values = TRUE) {
+      codomain = ps(y = p_dbl(tags = "minimize")),
+      constants = ps(), check_values = TRUE) {
       self$id = assert_string(id)
       self$domain = assert_param_set(domain)
       self$codomain = assert_codomain(codomain)
@@ -94,7 +96,7 @@ Objective = R6Class("Objective",
     #' These extra entries are referred to as *extras*.
     eval = function(xs) {
       if (self$check_values) self$domain$assert(xs)
-      res = private$.eval(xs)
+      res = invoke(private$.eval, xs, .args = self$constants$values)
       if (self$check_values) self$codomain$assert(res[self$codomain$ids()])
       return(res)
     },
@@ -119,7 +121,7 @@ Objective = R6Class("Objective",
     #' These extra columns are referred to as *extras*.
     eval_many = function(xss) {
       if (self$check_values) lapply(xss, self$domain$assert)
-      res = private$.eval_many(xss)
+      res = invoke(private$.eval_many, xss, .args = self$constants$values)
       if (self$check_values) {
         self$codomain$assert_dt(res[, self$codomain$ids(), with = FALSE])
       }
@@ -148,11 +150,11 @@ Objective = R6Class("Objective",
   ),
 
   private = list(
-    .eval = function(xs) {
+    .eval = function(xs, ...) { # ... allows constants
       as.list(self$eval_many(list(xs)))
     },
 
-    .eval_many = function(xss) {
+    .eval_many = function(xss, ...) {
       res = map_dtr(xss, function(xs) {
         ys = self$eval(xs)
         as.data.table(lapply(ys, function(y) if (is.list(y)) list(y) else y))

R/ObjectiveRFun.R

@@ -2,38 +2,35 @@
 #'
 #' @description
 #' Objective interface where the user can pass a custom R function that expects a list as input.
+#' 
+#' @template param_domain
+#' @template param_codomain
+#' @template param_check_values
+#' @template param_constants
 #'
+#' @export
 #' @examples
-#' library(paradox)
-#' # Define objective function
+#' # define objective function
 #' fun = function(xs) {
 #'   - (xs[[1]] - 2)^2 - (xs[[2]] + 3)^2 + 10
 #' }
-#'
-#' # Set domain
-#' domain = ParamSet$new(list(
-#'   ParamDbl$new("x1", -10, 10),
-#'   ParamDbl$new("x2", -5, 5)
-#' ))
-#'
-#' # Set codomain
-#' codomain = ParamSet$new(list(
-#'   ParamDbl$new("y", tags = "maximize")
-#' ))
-#'
-#' # Create Objective object
+#' 
+#' # set domain
+#' domain = ps(
+#'   x1 = p_dbl(-10, 10),
+#'   x2 = p_dbl(-5, 5)
+#' )
+#' 
+#' # set codomain
+#' codomain = ps(y = p_dbl(tags = "maximize"))
+#' 
+#' # create Objective object
 #' obfun = ObjectiveRFun$new(
 #'   fun = fun,
 #'   domain = domain,
 #'   codomain = codomain,
 #'   properties = "deterministic"
 #' )
-#'
-#' @template param_domain
-#' @template param_codomain
-#' @template param_check_values
-#' @template param_constants
-#' @export
 ObjectiveRFun = R6Class("ObjectiveRFun",
   inherit = Objective,
   public = list(
@@ -48,9 +45,9 @@ ObjectiveRFun = R6Class("ObjectiveRFun",
     #' @param id (`character(1)`).
     #' @param properties (`character()`).
     initialize = function(fun, domain, codomain = NULL, id = "function",
-      properties = character(), constants = ParamSet$new(), check_values = TRUE) {
+      properties = character(), constants = ps(), check_values = TRUE) {
       if (is.null(codomain)) {
-        codomain = ParamSet$new(list(ParamDbl$new("y", tags = "minimize")))
+        codomain = ps(y = p_dbl(tags = "minimize"))
       }
       private$.fun = assert_function(fun, "xs")
       # asserts id, domain, codomain, properties
@@ -64,7 +61,7 @@ ObjectiveRFun = R6Class("ObjectiveRFun",
     #' @param xs Input values.
     eval = function(xs) {
       if (self$check_values) self$domain$assert(xs)
-      res = private$.fun(xs)
+      res = invoke(private$.fun, xs, .args = self$constants$values)
       if (self$check_values) self$codomain$assert(as.list(res)[self$codomain$ids()])
       return(res)
     }

R/ObjectiveRFunDt.R

@@ -22,9 +22,9 @@ ObjectiveRFunDt = R6Class("ObjectiveRFunDt",
     #' @param id (`character(1)`).
     #' @param properties (`character()`).
     initialize = function(fun, domain, codomain = NULL, id = "function",
-      properties = character(), constants = ParamSet$new(), check_values = TRUE) {
+      properties = character(), constants = ps(), check_values = TRUE) {
       if (is.null(codomain)) {
-        codomain = ParamSet$new(list(ParamDbl$new("y", tags = "minimize")))
+        codomain = ps(y = p_dbl(tags = "minimize"))
       }
       private$.fun = assert_function(fun, "xdt")
       # asserts id, domain, codomain, properties
@@ -45,7 +45,7 @@ ObjectiveRFunDt = R6Class("ObjectiveRFunDt",
     #' `data.table(y = 1:2)` or `data.table(y1 = 1:2, y2 = 3:4)`.
     eval_many = function(xss) {
       if (self$check_values) lapply(xss, self$domain$assert)
-      res = private$.fun(rbindlist(xss, use.names = TRUE, fill = TRUE))
+      res = invoke(private$.fun, rbindlist(xss, use.names = TRUE, fill = TRUE), .args = self$constants$values)
       if (self$check_values) self$codomain$assert_dt(res[, self$codomain$ids(), with = FALSE])
       return(res)
     },
@@ -58,7 +58,7 @@ ObjectiveRFunDt = R6Class("ObjectiveRFunDt",
     #' `data.table(y = 1:2)` or `data.table(y1 = 1:2, y2 = 3:4)`.
     eval_dt = function(xdt) {
       if (self$check_values) self$domain$assert_dt(xdt)
-      res = private$.fun(xdt)
+      res = invoke(private$.fun, xdt, .args = self$constants$values)
       if (self$check_values) self$codomain$assert_dt(res[, self$codomain$ids(), with = FALSE])
       return(res)
     }