refactor: clean and fix custom checks and use set_values for param_set (

#49)

* refactor: clean and fix custom checks and use set_values for param_set

* fix: fix positive count check

* refactor: change back to numeric

* fix: replace and with or in check_centers

* fix: fix showplot check for dbscanfpc and fix bracket for dbscan

* fix: encapsulate crate functions inside lambda function and update .lintr w/ minor styling changes

* refactor: add back newline between train and predict methods

* fix: don't wrap check_centers in lambda function

* chore: bump mlr3misc and paradox min version to 0.10 and document

* chore: add missing licence file

* chore: update precommit

.lintr

@@ -1,10 +1,10 @@
-linters: with_defaults(
+linters: linters_with_defaults(
     # lintr defaults: https://github.com/jimhester/lintr#available-linters
     # the following setup changes/removes certain linters
     assignment_linter = NULL, # do not force using <- for assignments
     object_name_linter = object_name_linter(c("snake_case", "CamelCase")), # only allow snake case and camel case object names
     cyclocomp_linter = NULL, # do not check function complexity
     commented_code_linter = NULL, # allow code in comments
-    line_length_linter = line_length_linter(120)
+    line_length_linter = line_length_linter(120),
+    object_length_linter = object_length_linter(40)
     )
-

.pre-commit-config.yaml

@@ -1,22 +1,47 @@
 # All available hooks: https://pre-commit.com/hooks.html
+# R specific hooks: https://github.com/lorenzwalthert/precommit
 repos:
--   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.1.2
+  - repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.4.0
     hooks:
-    # any R project
-    -   id: style-files
-        args: [--style_pkg=styler, --style_fun=mlr_style] # install with remotes::install_github("pat-s/styler@mlr-style")
-    # -   id: lintr
-    -   id: parsable-R
-    -   id: no-browser-statement
-    -   id: readme-rmd-rendered
-    #  R package development
-    -   id: roxygenize
-    -   id: use-tidy-description
-    #-   id: deps-in-desc
-        args: [--allow_private_imports]
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.1.0
+      - id: style-files
+        args: [--style_pkg=styler.mlr, --style_fun=mlr_style]
+        additional_dependencies:
+          - mlr-org/styler.mlr
+      - id: roxygenize
+        additional_dependencies:
+        - backports
+        - checkmate
+        - clue
+        - fpc
+        - cluster
+        - data.table
+        - mlr3misc
+        - paradox
+        - R6
+      # codemeta must be above use-tidy-description when both are used
+      - id: use-tidy-description
+      - id: readme-rmd-rendered
+      - id: parsable-R
+      - id: no-browser-statement
+      - id: deps-in-desc
+        exclude: data-raw|inst
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
     hooks:
-    -   id: check-added-large-files
-        args: ['--maxkb=200']
+      - id: check-added-large-files
+        args: [--maxkb=200]
+      - id: file-contents-sorter
+        files: '^\.Rbuildignore$'
+      - id: end-of-file-fixer
+        exclude: '\.Rd'
+  - repo: local
+    hooks:
+      - id: forbid-to-commit
+        name: Don't commit common R artifacts
+        entry: Cannot commit .Rhistory, .RData, .Rds or .rds.
+        language: fail
+        files: '\.Rhistory|\.RData|\.Rds|\.rds$'
+        # `exclude: <regex>` to allow committing specific files.
+ci:
+  autoupdate_schedule: monthly

DESCRIPTION

@@ -26,8 +26,8 @@ Imports:
     fpc,
     cluster,
     data.table,
-    mlr3misc (>= 0.9.4),
-    paradox,
+    mlr3misc (>= 0.10.0),
+    paradox (>= 0.10.0),
     R6,
     stats
 Suggests:
@@ -43,7 +43,7 @@ Suggests:
     testthat (>= 3.0.0)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE, r6 = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Collate:
     'LearnerClust.R'
     'aaa.R'

LICENSE

@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
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+the following:
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+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version.
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.

R/LearnerClust.R

@@ -45,9 +45,8 @@ LearnerClust = R6Class("LearnerClust",
 
     #' @description
     #' Creates a new instance of this [R6][R6::R6Class] class.
-    initialize = function(id, param_set = ps(), predict_types = "partition",
-      feature_types = character(), properties = character(),
-      packages = character(), label = NA_character_, man = NA_character_) {
+    initialize = function(id, param_set = ps(), predict_types = "partition", feature_types = character(),
+      properties = character(), packages = character(), label = NA_character_, man = NA_character_) {
       super$initialize(
         id = id, task_type = "clust", param_set = param_set,
         predict_types = predict_types,

R/LearnerClustAffinityPropagation.R

@@ -26,14 +26,8 @@ LearnerClustAP = R6Class("LearnerClustAP",
     initialize = function() {
       ps = ps(
         s = p_uty(tags = c("required", "train")),
-        p = p_uty(custom_check = function(x) {
-          if (test_numeric(x)) {
-            return(TRUE)
-          } else {
-            stopf("`p` needs to be a numeric vector")
-          }
-        }, default = NA, tags = "train"),
-        q = p_dbl(lower = 0L, upper = 1, tags = "train"),
+        p = p_uty(default = NA, tags = "train", custom_check = crate(function(x) check_numeric(x))),
+        q = p_dbl(lower = 0, upper = 1, tags = "train"),
         maxits = p_int(lower = 1L, default = 1000L, tags = "train"),
         convits = p_int(lower = 1L, default = 100L, tags = "train"),
         lam = p_dbl(lower = 0.5, upper = 1, default = 0.9, tags = "train"),
@@ -69,14 +63,16 @@ LearnerClustAP = R6Class("LearnerClustAP",
 
       return(m)
     },
+
     .predict = function(task) {
       sim_func = self$param_set$values$s
       exemplar_data = attributes(self$model)$exemplar_data
 
       d = task$data()
-      sim_mat = sim_func(rbind(exemplar_data, d),
-        sel = (1:nrow(d)) +
-          nrow(exemplar_data))[1:nrow(exemplar_data), ]
+      sim_mat = sim_func(
+        rbind(exemplar_data, d),
+        sel = (seq_len(nrow(d))) + nrow(exemplar_data)
+      )[seq_len(nrow(exemplar_data)), ]
       partition = unname(apply(sim_mat, 2, which.max))
       PredictionClust$new(task = task, partition = partition)
     }

R/LearnerClustAgnes.R

@@ -24,25 +24,29 @@ LearnerClustAgnes = R6Class("LearnerClustAgnes",
       ps = ps(
         metric = p_fct(default = "euclidean", levels = c("euclidean", "manhattan"), tags = "train"),
         stand = p_lgl(default = FALSE, tags = "train"),
-        method = p_fct(default = "average", levels = c("average", "single", "complete", "ward", "weighted", "flexible", "gaverage"), tags = "train"),
+        method = p_fct(
+          default = "average",
+          levels = c("average", "single", "complete", "ward", "weighted", "flexible", "gaverage"),
+          tags = "train"
+        ),
         trace.lev = p_int(lower = 0L, default = 0L, tags = "train"),
         k = p_int(lower = 1L, default = 2L, tags = "predict"),
-        par.method = p_uty(tags = "train", custom_check = function(x) {
-            if (test_numeric(x) || test_list(x)) {
-              if (length(x) %in% c(1L, 3L, 4L)) {
-                return(TRUE)
-              }
-              stopf("`par.method` needs be of length 1, 3, or 4")
-            } else {
-              stopf("`par.method` needs to be a numeric vector")
-            }
-          })
+        par.method = p_uty(tags = "train", custom_check = crate(function(x) {
+          if (!(test_numeric(x) || test_list(x))) {
+            return("`par.method` needs to be a numeric vector")
+          }
+          if (length(x) %in% c(1L, 3L, 4L)) {
+            TRUE
+          } else {
+            "`par.method` needs be of length 1, 3, or 4"
+          }
+        }))
       )
 
       # param deps
       ps$add_dep("par.method", "method", CondAnyOf$new(c("flexible", "gaverage")))
 
-      ps$values = list(k = 2L)
+      ps$set_values(k = 2L)
 
       super$initialize(
         id = "clust.agnes",