Merge commit '415ae254b9e4a0f74656b03e27dca2c4034d5027'

Author: EmilHvitfeldt

.github/workflows/R-CMD-check.yaml

@@ -9,8 +9,11 @@ on:
     branches: [main, master]
   pull_request:
     branches: [main, master]
+  workflow_dispatch:
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -25,21 +28,25 @@ jobs:
           - {os: macos-latest,   r: 'release'}
 
           - {os: windows-latest, r: 'release'}
-          # use 4.1 to check with rtools40's older compiler
-          - {os: windows-latest, r: '4.1'}
+          # use 4.0 or 4.1 to check with rtools40's older compiler
+          - {os: windows-latest, r: 'oldrel-4'}
 
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
-          - {os: ubuntu-latest,   r: 'oldrel-2'}
-          - {os: ubuntu-latest,   r: 'oldrel-3'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
+          - {os: ubuntu-latest,  r: 'oldrel-2'}
+          - {os: ubuntu-latest,  r: 'oldrel-3'}
+          #- {os: ubuntu-latest,  r: 'oldrel-4'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+      CXX14: g++
+      CXX14STD: -std=c++1y
+      CXX14FLAGS: -Wall -g -02
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -57,3 +64,8 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash

.github/workflows/pkgdown.yaml

@@ -9,7 +9,9 @@ on:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -19,8 +21,10 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -39,7 +43,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/pr-commands.yaml

@@ -4,7 +4,9 @@ on:
   issue_comment:
     types: [created]
 
-name: Commands
+name: pr-commands.yaml
+
+permissions: read-all
 
 jobs:
   document:
@@ -13,8 +15,10 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -50,8 +54,10 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:

.github/workflows/test-coverage.yaml

@@ -6,7 +6,9 @@ on:
   pull_request:
     branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,36 +17,45 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -24,10 +24,10 @@ Imports:
     generics (>= 0.1.2),
     glue (>= 1.6.2),
     hardhat (>= 1.0.0),
-    modelenv (>= 0.1.0),
-    parsnip (>= 1.2.1.9004),
+    modelenv (>= 0.2.0.9000),
+    parsnip (>= 1.0.2),
+    philentropy (>= 0.9.0),
     prettyunits (>= 1.1.0),
-    Rfast (>= 	2.0.6),
     rlang (>= 1.0.6),
     rsample (>= 1.0.0),
     stats,
@@ -49,6 +49,8 @@ Suggests:
     rmarkdown,
     testthat (>= 3.0.0),
     workflows (>= 1.1.2)
+Remotes:
+    tidymodels/modelenv
 Config/Needs/website: pkgdown, tidymodels, tidyverse, palmerpenguins,
     patchwork, ggforce, tidyverse/tidytemplate
 Config/testthat/edition: 3

NEWS.md

@@ -1,5 +1,7 @@
 # tidyclust (development version)
 
+* The philentropy package is now used to calculate distances rather than Rfast. (#199)
+
 # tidyclust 0.2.3
 
 * Update to fix revdep issue for clustMixType. (#190)

R/aaa.R

@@ -3,17 +3,47 @@
 
 utils::globalVariables(
   c(
-    ".", "..object", ".cluster", ".iter_config", ".iter_model",
-    ".iter_preprocessor", ".msg_model", ".submodels", "call_info", "cluster",
-    "component", "component_id", "compute_intercept", "data", "dist", "engine",
-    "engine2", "exposed", "func", "id", "iteration", "lab", "name", "neighbor",
-    "new_data", "object", "orig_label", "original", "predictor_indicators",
-    "remove_intercept", "seed", "sil_width", "splits", "tunable", "type",
-    "value", "x", "y"
+    ".",
+    "..object",
+    ".cluster",
+    ".iter_config",
+    ".iter_model",
+    ".iter_preprocessor",
+    ".msg_model",
+    ".submodels",
+    "call_info",
+    "cluster",
+    "component",
+    "component_id",
+    "compute_intercept",
+    "data",
+    "dist",
+    "engine",
+    "engine2",
+    "exposed",
+    "func",
+    "id",
+    "iteration",
+    "lab",
+    "name",
+    "neighbor",
+    "new_data",
+    "object",
+    "orig_label",
+    "original",
+    "predictor_indicators",
+    "remove_intercept",
+    "seed",
+    "sil_width",
+    "splits",
+    "tunable",
+    "type",
+    "value",
+    "x",
+    "y"
   )
 )
 
-
 release_bullets <- function() {
   c(
     "Run `knit_engine_docs()` and `devtools::document()` to update docs"

R/append.R

@@ -1,9 +1,11 @@
 # https://github.com/tidymodels/tune/blob/main/R/pull.R#L136
-append_predictions <- function(collection,
-                               predictions,
-                               split,
-                               control,
-                               .config = NULL) {
+append_predictions <- function(
+  collection,
+  predictions,
+  split,
+  control,
+  .config = NULL
+) {
   if (!control$save_pred) {
     return(NULL)
   }
@@ -27,14 +29,16 @@ append_predictions <- function(collection,
   dplyr::bind_rows(collection, predictions)
 }
 
-append_metrics <- function(workflow,
-                           collection,
-                           predictions,
-                           metrics,
-                           param_names,
-                           event_level,
-                           split,
-                           .config = NULL) {
+append_metrics <- function(
+  workflow,
+  collection,
+  predictions,
+  metrics,
+  param_names,
+  event_level,
+  split,
+  .config = NULL
+) {
   if (inherits(predictions, "try-error")) {
     return(collection)
   }
@@ -54,20 +58,22 @@ append_metrics <- function(workflow,
   dplyr::bind_rows(collection, tmp_est)
 }
 
-append_extracts <- function(collection,
-                            workflow,
-                            grid,
-                            split,
-                            ctrl,
-                            .config = NULL) {
+append_extracts <- function(
+  collection,
+  workflow,
+  grid,
+  split,
+  ctrl,
+  .config = NULL
+) {
   extracts <-
     grid %>%
-    dplyr::bind_cols(labels(split)) %>%
-    dplyr::mutate(
-      .extracts = list(
-        extract_details(workflow, ctrl$extract)
+      dplyr::bind_cols(labels(split)) %>%
+      dplyr::mutate(
+        .extracts = list(
+          extract_details(workflow, ctrl$extract)
+        )
       )
-    )
 
   if (!rlang::is_null(.config)) {
     extracts <- cbind(extracts, .config)

R/arguments.R

@@ -8,10 +8,12 @@ check_eng_args <- function(args, obj, core_args) {
   if (length(common_args) > 0) {
     args <- args[!(names(args) %in% common_args)]
     common_args <- paste0(common_args, collapse = ", ")
-    rlang::warn(glue::glue(
-      "The following arguments cannot be manually modified ",
-      "and were removed: {common_args}."
-    ))
+    rlang::warn(
+      glue::glue(
+        "The following arguments cannot be manually modified ",
+        "and were removed: {common_args}."
+      )
+    )
   }
   args
 }
@@ -25,7 +27,8 @@ make_x_call <- function(object, target) {
   }
 
   object$method$fit$args[[unname(data_args["x"])]] <-
-    switch(target,
+    switch(
+      target,
       none = rlang::expr(x),
       data.frame = rlang::expr(maybe_data_frame(x)),
       matrix = rlang::expr(maybe_matrix(x)),

R/cluster_spec.R

@@ -10,11 +10,19 @@
 #' @export
 #' @keywords internal
 new_cluster_spec <- function(cls, args, eng_args, mode, method, engine) {
-  modelenv::check_spec_mode_engine_val(model = cls, mode = mode, eng = engine)
+  modelenv::check_spec_mode_engine_val(
+    model = cls,
+    mode = mode,
+    eng = engine,
+    call = rlang::caller_env()
+  )
 
   out <- list(
-    args = args, eng_args = eng_args,
-    mode = mode, method = method, engine = engine
+    args = args,
+    eng_args = eng_args,
+    mode = mode,
+    method = method,
+    engine = engine
   )
   class(out) <- make_classes_tidyclust(cls)
   out <- modelenv::new_unsupervised_spec(out)