From 3caffedf2dfbcad18e289181e1ff6408a8d16cf5 Mon Sep 17 00:00:00 2001 From: be-marc Date: Fri, 21 Jun 2024 11:38:53 +0200 Subject: [PATCH 1/6] release: 0.2.3 --- NEWS.md | 2 ++ man/AcqFunction.Rd | 1 + man/mlr_acqfunctions_aei.Rd | 3 ++- man/mlr_acqfunctions_cb.Rd | 1 + man/mlr_acqfunctions_ehvi.Rd | 3 ++- man/mlr_acqfunctions_ehvigh.Rd | 3 ++- man/mlr_acqfunctions_ei.Rd | 3 ++- man/mlr_acqfunctions_eips.Rd | 3 ++- man/mlr_acqfunctions_mean.Rd | 1 + man/mlr_acqfunctions_pi.Rd | 3 ++- man/mlr_acqfunctions_sd.Rd | 1 + man/mlr_acqfunctions_smsego.Rd | 3 ++- 12 files changed, 20 insertions(+), 7 deletions(-) diff --git a/NEWS.md b/NEWS.md index b3afb9e2..8833b518 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # mlr3mbo 0.2.2.9000 +* compatibility: Work with new bbotk and mlr3tuning version 1.0.0. + # mlr3mbo 0.2.2 * refactor: compatibility with upcoming paradox upgrade. diff --git a/man/AcqFunction.Rd b/man/AcqFunction.Rd index ba807720..48fd7926 100644 --- a/man/AcqFunction.Rd +++ b/man/AcqFunction.Rd @@ -76,6 +76,7 @@ Set of required packages.} diff --git a/man/mlr_acqfunctions_aei.Rd b/man/mlr_acqfunctions_aei.Rd index 7e733f3f..6d8554eb 100644 --- a/man/mlr_acqfunctions_aei.Rd +++ b/man/mlr_acqfunctions_aei.Rd @@ -116,10 +116,11 @@ This corresponds to the \code{nugget} estimate when using a \link[mlr3learners:m } } \if{html}{\out{ -
Inherited methods +
Inherited methods
  • bbotk::Objective$eval()
  • bbotk::Objective$format()
    • +
  • bbotk::Objective$help()
  • bbotk::Objective$print()
  • mlr3mbo::AcqFunction$eval_dt()
  • mlr3mbo::AcqFunction$eval_many()
    • diff --git a/man/mlr_acqfunctions_cb.Rd b/man/mlr_acqfunctions_cb.Rd index 501ebece..77a6010a 100644 --- a/man/mlr_acqfunctions_cb.Rd +++ b/man/mlr_acqfunctions_cb.Rd @@ -95,6 +95,7 @@ Other Acquisition Function:
    • bbotk::Objective$eval()
    • bbotk::Objective$format()
      • +
    • bbotk::Objective$help()
    • bbotk::Objective$print()
    • mlr3mbo::AcqFunction$eval_dt()
    • mlr3mbo::AcqFunction$eval_many()
      • diff --git a/man/mlr_acqfunctions_ehvi.Rd b/man/mlr_acqfunctions_ehvi.Rd index 4301ec08..b8df7c87 100644 --- a/man/mlr_acqfunctions_ehvi.Rd +++ b/man/mlr_acqfunctions_ehvi.Rd @@ -95,10 +95,11 @@ Signs are corrected with respect to assuming minimization of objectives.} } } \if{html}{\out{ -
      Inherited methods +
      Inherited methods
      • bbotk::Objective$eval()
      • bbotk::Objective$format()
        • +
      • bbotk::Objective$help()
      • bbotk::Objective$print()
      • mlr3mbo::AcqFunction$eval_dt()
      • mlr3mbo::AcqFunction$eval_many()
        • diff --git a/man/mlr_acqfunctions_ehvigh.Rd b/man/mlr_acqfunctions_ehvigh.Rd index 976ffb61..4b1d4fe9 100644 --- a/man/mlr_acqfunctions_ehvigh.Rd +++ b/man/mlr_acqfunctions_ehvigh.Rd @@ -114,10 +114,11 @@ Nodes are scaled by a factor of \code{sqrt(2)} and weights are normalized under } } \if{html}{\out{ -
        Inherited methods +
        Inherited methods
        • bbotk::Objective$eval()
        • bbotk::Objective$format()
          • +
        • bbotk::Objective$help()
        • bbotk::Objective$print()
        • mlr3mbo::AcqFunction$eval_dt()
        • mlr3mbo::AcqFunction$eval_many()
          • diff --git a/man/mlr_acqfunctions_ei.Rd b/man/mlr_acqfunctions_ei.Rd index 4a12dbda..700e72ab 100644 --- a/man/mlr_acqfunctions_ei.Rd +++ b/man/mlr_acqfunctions_ei.Rd @@ -93,10 +93,11 @@ In the case of maximization, this already includes the necessary change of sign. } } \if{html}{\out{ -
          Inherited methods +
          Inherited methods
          • bbotk::Objective$eval()
          • bbotk::Objective$format()
            • +
          • bbotk::Objective$help()
          • bbotk::Objective$print()
          • mlr3mbo::AcqFunction$eval_dt()
          • mlr3mbo::AcqFunction$eval_many()
            • diff --git a/man/mlr_acqfunctions_eips.Rd b/man/mlr_acqfunctions_eips.Rd index 4c885b74..ae328bd0 100644 --- a/man/mlr_acqfunctions_eips.Rd +++ b/man/mlr_acqfunctions_eips.Rd @@ -110,10 +110,11 @@ In the case of maximization, this already includes the necessary change of sign. } } \if{html}{\out{ -
            Inherited methods +
            Inherited methods
            • bbotk::Objective$eval()
            • bbotk::Objective$format()
              • +
            • bbotk::Objective$help()
            • bbotk::Objective$print()
            • mlr3mbo::AcqFunction$eval_dt()
            • mlr3mbo::AcqFunction$eval_many()
              • diff --git a/man/mlr_acqfunctions_mean.Rd b/man/mlr_acqfunctions_mean.Rd index b09456ba..71b57081 100644 --- a/man/mlr_acqfunctions_mean.Rd +++ b/man/mlr_acqfunctions_mean.Rd @@ -80,6 +80,7 @@ Other Acquisition Function:
              • bbotk::Objective$eval()
              • bbotk::Objective$format()
                • +
              • bbotk::Objective$help()
              • bbotk::Objective$print()
              • mlr3mbo::AcqFunction$eval_dt()
              • mlr3mbo::AcqFunction$eval_many()
                • diff --git a/man/mlr_acqfunctions_pi.Rd b/man/mlr_acqfunctions_pi.Rd index 8f82a67c..99d548bb 100644 --- a/man/mlr_acqfunctions_pi.Rd +++ b/man/mlr_acqfunctions_pi.Rd @@ -93,10 +93,11 @@ In the case of maximization, this already includes the necessary change of sign. } } \if{html}{\out{ -
                Inherited methods +
                Inherited methods
                • bbotk::Objective$eval()
                • bbotk::Objective$format()
                  • +
                • bbotk::Objective$help()
                • bbotk::Objective$print()
                • mlr3mbo::AcqFunction$eval_dt()
                • mlr3mbo::AcqFunction$eval_many()
                  • diff --git a/man/mlr_acqfunctions_sd.Rd b/man/mlr_acqfunctions_sd.Rd index 9fdd0a57..8ff5b526 100644 --- a/man/mlr_acqfunctions_sd.Rd +++ b/man/mlr_acqfunctions_sd.Rd @@ -80,6 +80,7 @@ Other Acquisition Function:
                  • bbotk::Objective$eval()
                  • bbotk::Objective$format()
                    • +
                  • bbotk::Objective$help()
                  • bbotk::Objective$print()
                  • mlr3mbo::AcqFunction$eval_dt()
                  • mlr3mbo::AcqFunction$eval_many()
                    • diff --git a/man/mlr_acqfunctions_smsego.Rd b/man/mlr_acqfunctions_smsego.Rd index 78f23dd6..ddafa56c 100644 --- a/man/mlr_acqfunctions_smsego.Rd +++ b/man/mlr_acqfunctions_smsego.Rd @@ -114,10 +114,11 @@ Note that this requires the \link[bbotk:OptimInstance]{bbotk::OptimInstance} to } } \if{html}{\out{ -
                    Inherited methods +
                    Inherited methods
                    • bbotk::Objective$eval()
                    • bbotk::Objective$format()
                      • +
                    • bbotk::Objective$help()
                    • bbotk::Objective$print()
                    • mlr3mbo::AcqFunction$eval_dt()
                    • mlr3mbo::AcqFunction$eval_many()
                      • From b36b828d98ffdd41ccc7bd6fc19fd7a4ea1d84e3 Mon Sep 17 00:00:00 2001 From: be-marc Date: Fri, 21 Jun 2024 11:39:25 +0200 Subject: [PATCH 2/6] chore: bump version --- DESCRIPTION | 2 +- NEWS.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 07461684..efbcfc5d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: mlr3mbo Title: Flexible Bayesian Optimization -Version: 0.2.2.9000 +Version: 0.2.3 Authors@R: c( person("Lennart", "Schneider", , "lennart.sch@web.de", role = c("cre", "aut"), comment = c(ORCID = "0000-0003-4152-5308")), diff --git a/NEWS.md b/NEWS.md index 8833b518..7a23477e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# mlr3mbo 0.2.2.9000 +# mlr3mbo 0.2.3 * compatibility: Work with new bbotk and mlr3tuning version 1.0.0. From 7fec19f5a2823d7c06c7d126eda7679aafd2525d Mon Sep 17 00:00:00 2001 From: be-marc Date: Fri, 21 Jun 2024 12:11:51 +0200 Subject: [PATCH 3/6] fix: AcqFunction label and man --- R/AcqFunction.R | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/R/AcqFunction.R b/R/AcqFunction.R index 158bb97c..31242b34 100644 --- a/R/AcqFunction.R +++ b/R/AcqFunction.R @@ -47,8 +47,6 @@ AcqFunction = R6Class("AcqFunction", check_packages_installed(packages, msg = sprintf("Package '%%s' required but not installed for acquisition function '%s'", sprintf("<%s:%s>", "AcqFunction", id))) } private$.requires_predict_type_se = assert_flag(requires_predict_type_se) - private$.label = assert_string(label, na.ok = TRUE) - private$.man = assert_string(man, na.ok = TRUE) private$.packages = packages self$direction = assert_choice(direction, c("same", "minimize", "maximize")) if (is.null(surrogate)) { @@ -64,7 +62,7 @@ AcqFunction = R6Class("AcqFunction", self$surrogate_max_to_min = surrogate_mult_max_to_min(surrogate) domain = generate_acq_domain(surrogate) } - super$initialize(id = id, domain = domain, codomain = codomain, constants = constants) + super$initialize(id = id, domain = domain, codomain = codomain, constants = constants, label = label, man = man) }, #' @description From 2952476cdde2c8df8fabff496fc30b2fb0f7f362 Mon Sep 17 00:00:00 2001 From: be-marc Date: Tue, 25 Jun 2024 15:56:53 +0200 Subject: [PATCH 4/6] chore: remove remotes --- DESCRIPTION | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index efbcfc5d..928779c9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -41,14 +41,14 @@ BugReports: https://github.com/mlr-org/mlr3mbo/issues Depends: R (>= 3.1.0) Imports: - bbotk (>= 0.8.0.9000), + bbotk (>= 1.0.0), checkmate (>= 2.0.0), data.table, lgr (>= 0.3.4), mlr3 (>= 0.14.0), mlr3misc (>= 0.11.0), - mlr3tuning (>= 0.20.0.9000), - paradox (>= 0.10.0), + mlr3tuning (>= 1.0.0), + paradox (>= 1.0.0), spacefillr, R6 (>= 2.4.1) Suggests: @@ -66,9 +66,6 @@ Suggests: rpart, stringi, testthat (>= 3.0.0) -Remotes: - mlr-org/bbotk, - mlr-org/mlr3tuning, ByteCompile: no Encoding: UTF-8 Config/testthat/edition: 3 From 82e6b1e1210a9963326d1ecee7e03cdb01a1439f Mon Sep 17 00:00:00 2001 From: be-marc Date: Wed, 26 Jun 2024 21:22:17 +0200 Subject: [PATCH 5/6] docs: remove links --- vignettes/mlr3mbo.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/mlr3mbo.Rmd b/vignettes/mlr3mbo.Rmd index 46576cc4..6ee0e42e 100644 --- a/vignettes/mlr3mbo.Rmd +++ b/vignettes/mlr3mbo.Rmd @@ -454,7 +454,7 @@ Note that important fields of an `OptimizerMbo` such as `$param_classes`, `$pack If arguments such as the `surrogate`, `acq_function`, `acq_optimizer` and `result_assigner` were not fully initialized during construction, e.g., the `surrogate` missing the `archive`, or the `acq_function` missing the `surrogate`, lazy initialization is completed prior to the optimizer being used for optimization. -An object of class `OptimizerMbo` can be used to optimize an object of class `r ref("bbotk::OptimInstanceBatchSingleCrit", "OptimInstanceBatchSingleCrit")` or `r ref("bbotk::OptimInstanceBatchMultiCrit", "OptimInstanceBatchMultiCrit")`. +An object of class `OptimizerMbo` can be used to optimize an object of class `OptimInstanceBatchSingleCrit` or `OptimInstanceBatchMultiCrit`. For hyperparameter optimization, `r ref("mlr3mbo::mlr_tuners_mbo", "TunerMbo")` should be used (which simply relies on an `OptimizerMbo` that is constructed internally): From 02f512e0576f97ee5b375cacd62de28d44c57fda Mon Sep 17 00:00:00 2001 From: be-marc Date: Sun, 30 Jun 2024 21:24:05 +0200 Subject: [PATCH 6/6] fix: links --- man-roxygen/field_feature_types_surrogate.R | 2 +- man-roxygen/field_properties.R | 2 +- man-roxygen/field_properties_surrogate.R | 2 +- man/Surrogate.Rd | 4 ++-- man/SurrogateLearner.Rd | 4 ++-- man/SurrogateLearnerCollection.Rd | 4 ++-- man/mlr_optimizers_mbo.Rd | 2 +- man/mlr_tuners_mbo.Rd | 2 +- 8 files changed, 11 insertions(+), 11 deletions(-) diff --git a/man-roxygen/field_feature_types_surrogate.R b/man-roxygen/field_feature_types_surrogate.R index d47c24da..eabf2581 100644 --- a/man-roxygen/field_feature_types_surrogate.R +++ b/man-roxygen/field_feature_types_surrogate.R @@ -1,3 +1,3 @@ #' @field feature_types (`character()`)\cr #' Stores the feature types the surrogate can handle, e.g. `"logical"`, `"numeric"`, or `"factor"`. -#' A complete list of candidate feature types, grouped by task type, is stored in [`mlr_reflections$task_feature_types`][mlr_reflections]. +#' A complete list of candidate feature types, grouped by task type, is stored in [`mlr_reflections$task_feature_types`][mlr3::mlr_reflections]. diff --git a/man-roxygen/field_properties.R b/man-roxygen/field_properties.R index a05f9890..c9fc652b 100644 --- a/man-roxygen/field_properties.R +++ b/man-roxygen/field_properties.R @@ -1,5 +1,5 @@ #' @field properties (`character()`)\cr #' Set of properties of the optimizer. -#' Must be a subset of [`bbotk_reflections$optimizer_properties`][bbotk_reflections]. +#' Must be a subset of [`bbotk_reflections$optimizer_properties`][bbotk::bbotk_reflections]. #' MBO in principle is very flexible and by default we assume that the optimizer has all properties. #' When fully initialized, properties are determined based on the `loop_function` and `surrogate`. diff --git a/man-roxygen/field_properties_surrogate.R b/man-roxygen/field_properties_surrogate.R index d83718f9..dce10a62 100644 --- a/man-roxygen/field_properties_surrogate.R +++ b/man-roxygen/field_properties_surrogate.R @@ -1,3 +1,3 @@ #' @field properties (`character()`)\cr #' Stores a set of properties/capabilities the surrogate has. -#' A complete list of candidate properties, grouped by task type, is stored in [`mlr_reflections$learner_properties`][mlr_reflections]. +#' A complete list of candidate properties, grouped by task type, is stored in [`mlr_reflections$learner_properties`][mlr3::mlr_reflections]. diff --git a/man/Surrogate.Rd b/man/Surrogate.Rd index 79e3f4d5..73ed916a 100644 --- a/man/Surrogate.Rd +++ b/man/Surrogate.Rd @@ -51,11 +51,11 @@ A warning is signaled if at least one of the packages is not installed, but load \item{\code{feature_types}}{(\code{character()})\cr Stores the feature types the surrogate can handle, e.g. \code{"logical"}, \code{"numeric"}, or \code{"factor"}. -A complete list of candidate feature types, grouped by task type, is stored in \code{\link[=mlr_reflections]{mlr_reflections$task_feature_types}}.} +A complete list of candidate feature types, grouped by task type, is stored in \code{\link[mlr3:mlr_reflections]{mlr_reflections$task_feature_types}}.} \item{\code{properties}}{(\code{character()})\cr Stores a set of properties/capabilities the surrogate has. -A complete list of candidate properties, grouped by task type, is stored in \code{\link[=mlr_reflections]{mlr_reflections$learner_properties}}.} +A complete list of candidate properties, grouped by task type, is stored in \code{\link[mlr3:mlr_reflections]{mlr_reflections$learner_properties}}.} \item{\code{predict_type}}{(\code{character(1)})\cr Retrieves the currently active predict type, e.g. \code{"response"}.} diff --git a/man/SurrogateLearner.Rd b/man/SurrogateLearner.Rd index 038f9487..27f6f69d 100644 --- a/man/SurrogateLearner.Rd +++ b/man/SurrogateLearner.Rd @@ -86,11 +86,11 @@ A warning is signaled if at least one of the packages is not installed, but load \item{\code{feature_types}}{(\code{character()})\cr Stores the feature types the surrogate can handle, e.g. \code{"logical"}, \code{"numeric"}, or \code{"factor"}. -A complete list of candidate feature types, grouped by task type, is stored in \code{\link[=mlr_reflections]{mlr_reflections$task_feature_types}}.} +A complete list of candidate feature types, grouped by task type, is stored in \code{\link[mlr3:mlr_reflections]{mlr_reflections$task_feature_types}}.} \item{\code{properties}}{(\code{character()})\cr Stores a set of properties/capabilities the surrogate has. -A complete list of candidate properties, grouped by task type, is stored in \code{\link[=mlr_reflections]{mlr_reflections$learner_properties}}.} +A complete list of candidate properties, grouped by task type, is stored in \code{\link[mlr3:mlr_reflections]{mlr_reflections$learner_properties}}.} \item{\code{predict_type}}{(\code{character(1)})\cr Retrieves the currently active predict type, e.g. \code{"response"}.} diff --git a/man/SurrogateLearnerCollection.Rd b/man/SurrogateLearnerCollection.Rd index 954b8ea9..83783625 100644 --- a/man/SurrogateLearnerCollection.Rd +++ b/man/SurrogateLearnerCollection.Rd @@ -92,11 +92,11 @@ A warning is signaled if at least one of the packages is not installed, but load \item{\code{feature_types}}{(\code{character()})\cr Stores the feature types the surrogate can handle, e.g. \code{"logical"}, \code{"numeric"}, or \code{"factor"}. -A complete list of candidate feature types, grouped by task type, is stored in \code{\link[=mlr_reflections]{mlr_reflections$task_feature_types}}.} +A complete list of candidate feature types, grouped by task type, is stored in \code{\link[mlr3:mlr_reflections]{mlr_reflections$task_feature_types}}.} \item{\code{properties}}{(\code{character()})\cr Stores a set of properties/capabilities the surrogate has. -A complete list of candidate properties, grouped by task type, is stored in \code{\link[=mlr_reflections]{mlr_reflections$learner_properties}}.} +A complete list of candidate properties, grouped by task type, is stored in \code{\link[mlr3:mlr_reflections]{mlr_reflections$learner_properties}}.} \item{\code{predict_type}}{(\code{character(1)})\cr Retrieves the currently active predict type, e.g. \code{"response"}.} diff --git a/man/mlr_optimizers_mbo.Rd b/man/mlr_optimizers_mbo.Rd index 6a57a9ca..680bc3f7 100644 --- a/man/mlr_optimizers_mbo.Rd +++ b/man/mlr_optimizers_mbo.Rd @@ -128,7 +128,7 @@ This corresponds to the values given by a \link[paradox:ParamSet]{paradox::Param \item{\code{properties}}{(\code{character()})\cr Set of properties of the optimizer. -Must be a subset of \code{\link[=bbotk_reflections]{bbotk_reflections$optimizer_properties}}. +Must be a subset of \code{\link[bbotk:bbotk_reflections]{bbotk_reflections$optimizer_properties}}. MBO in principle is very flexible and by default we assume that the optimizer has all properties. When fully initialized, properties are determined based on the \code{loop_function} and \code{surrogate}.} diff --git a/man/mlr_tuners_mbo.Rd b/man/mlr_tuners_mbo.Rd index 1e625721..6e5261f8 100644 --- a/man/mlr_tuners_mbo.Rd +++ b/man/mlr_tuners_mbo.Rd @@ -84,7 +84,7 @@ This corresponds to the values given by a \link[paradox:ParamSet]{paradox::Param \item{\code{properties}}{(\code{character()})\cr Set of properties of the optimizer. -Must be a subset of \code{\link[=bbotk_reflections]{bbotk_reflections$optimizer_properties}}. +Must be a subset of \code{\link[bbotk:bbotk_reflections]{bbotk_reflections$optimizer_properties}}. MBO in principle is very flexible and by default we assume that the optimizer has all properties. When fully initialized, properties are determined based on the \code{loop_function} and \code{surrogate}.}