vip dependancy moved to r-universe

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

@@ -4,11 +4,9 @@ on:
   push:
     branches:
       - main
-      - master
   pull_request:
     branches:
       - main
-      - master
 
 name: R-CMD-check
 
@@ -37,11 +35,12 @@ jobs:
       PYTORCH_MPS_HIGH_WATERMARK_RATIO: 0.0
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          extra-repositories: "https://bgreenwell.r-universe.dev"
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -52,10 +51,11 @@ jobs:
 
       - uses: quarto-dev/quarto-actions/setup@v2
         with:
-          version: 1.7.30
+          version: 1.9.38
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
+          cache-version: 2
           extra-packages: any::rcmdcheck, local::.
           needs: check
 

.github/workflows/pkgdown.yaml

@@ -2,9 +2,11 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches:
+      - main
   pull_request:
-    branches: [main, master]
+    branches:
+      - main
   release:
     types: [published]
   workflow_dispatch:
@@ -22,7 +24,7 @@ jobs:
       TORCH_INSTALL: 1
     steps:
       - name: Checkout
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
 
       - name: Set up Quarto
         uses: quarto-dev/quarto-actions/setup@v2
@@ -38,6 +40,7 @@ jobs:
         uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
+          extra-repositories: "https://bgreenwell.r-universe.dev"
 
       - name: Setup R dependencies
         uses: r-lib/actions/setup-r-dependencies@v2

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tabnet
 Title: Fit 'TabNet' Models for Classification and Regression
-Version: 0.9.0.9000
+Version: 0.9.1
 Authors@R: c(
     person("Daniel", "Falbel", , "daniel@rstudio.com", role = "aut"),
     person(, "RStudio", role = "cph"),
@@ -11,10 +11,11 @@ Authors@R: c(
            comment = c(ORCID = "0000-0002-5573-3952"))
   )
 Description: Implements the 'TabNet' model by Sercan O. Arik et al. (2019)
-    <doi:10.48550/arXiv.1908.07442> with 'Coherent Hierarchical Multi-label
-    Classification Networks' by Giunchiglia et al.  <doi:10.48550/arXiv.2010.10151> and
-    provides a consistent interface for fitting and creating predictions.
-    It's also fully compatible with the 'tidymodels' ecosystem.
+    <doi:10.48550/arXiv.1908.07442> with 'Coherent Hierarchical
+    Multi-label Classification Networks' by Giunchiglia et al.
+    <doi:10.48550/arXiv.2010.10151> and provides a consistent interface
+    for fitting and creating predictions.  It's also fully compatible with
+    the 'tidymodels' ecosystem.
 License: MIT + file LICENSE
 URL: https://mlverse.github.io/tabnet/, https://github.com/mlverse/tabnet
 BugReports: https://github.com/mlverse/tabnet/issues
@@ -62,11 +63,13 @@ Suggests:
     workflows,
     xgboost,
     yardstick
-VignetteBuilder: knitr
+VignetteBuilder: 
+    knitr
+Additional_repositories: https://bgreenwell.r-universe.dev
+Config/roxygen2/version: 8.0.0
 Config/testthat/edition: 3
 Config/testthat/parallel: false
 Config/testthat/start-first: interface, explain, params
 Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
 Language: en-US
-Config/roxygen2/version: 8.0.0
+Roxygen: list(markdown = TRUE)

NEWS.md

@@ -1,4 +1,6 @@
-# tabnet (development version)
+# tabnet 0.9.1
+
+* {vip} is now distributed from r-universe.
 
 # tabnet 0.9.0
 

R/hardhat.R

@@ -471,7 +471,6 @@ predict.tabnet_fit <- function(object, new_data, type = NULL, ..., epoch = NULL)
 }
 
 #' @export
-#' @inheritParams predict.tabnet_fit
 #' @rdname predict.tabnet_fit
 augment.tabnet_fit <- function(x, new_data, ...) {
   res <- predict(x, new_data, ...)

README.md

@@ -106,16 +106,16 @@ augment(fit, test) %>%
 #> # A tibble: 3 × 3
 #>   .metric   .estimator .estimate
 #>   <chr>     <chr>          <dbl>
-#> 1 accuracy  binary         0.847
-#> 2 precision binary         0.853
-#> 3 recall    binary         0.992
+#> 1 accuracy  binary         0.837
+#> 2 precision binary         0.845
+#> 3 recall    binary         0.988
 
 augment(fit, test, type = "prob") %>% 
   roc_auc(Attrition, .pred_No)
 #> # A tibble: 1 × 3
 #>   .metric .estimator .estimate
 #>   <chr>   <chr>          <dbl>
-#> 1 roc_auc binary         0.384
+#> 1 roc_auc binary         0.461
 ```
 
 ## Explain model on test-set with attention map

inst/WORDLIST

@@ -29,6 +29,7 @@ autoassociative
 autograd
 beeing
 callout
+checkpointing
 classif
 cli
 cpu
@@ -42,6 +43,7 @@ et
 explainability
 extensibility
 ggplot
+mps
 mse
 nn
 num
@@ -60,4 +62,5 @@ th
 tibble
 tidymodels
 tunable
+vip
 zeallot

tests/testthat/test-parsnip.R

@@ -109,12 +109,15 @@ test_that("Check we can finalize a workflow from a tune_grid", {
   cv_folds <- small_ames %>%
     rsample::vfold_cv(v = 2, repeats = 1)
 
-  at <- tune::tune_grid(
+  expect_warning(
+    at <- tune::tune_grid(
     object = wf,
     resamples = cv_folds,
     grid = custom_grid,
     metrics = yardstick::metric_set(yardstick::rmse),
     control = tune::control_grid(verbose = F)
+    ),
+  regexp = "No tuning parameters"
   )
 
   best_rmse <- tune::select_best(at, metric = "rmse")

vignettes/Hierarchical_classification.Rmd

@@ -13,6 +13,7 @@ knitr::opts_chunk$set(
   comment = "#>",
   eval = FALSE
 )
+requireNamespace("vip", quietly = TRUE)
 ```
 
 ```{r setup}

vignettes/Missing_data_predictors.Rmd

@@ -15,6 +15,7 @@ knitr::opts_chunk$set(
   comment = "#>",
   eval = FALSE
 )
+requireNamespace("vip", quietly = TRUE)
 ```
 
 # Motivation
@@ -124,7 +125,7 @@ col_with_missings <- ames_missing %>%
   rename(has_missing = "value")
 
 vip_color <- function(object, col_has_missing) {
-  vip_data <- vip::vip(object)$data %>% arrange(Importance)
+  vip_data <- vip::vi(object) %>% arrange(Importance)
   vis_miss_plus <- left_join(vip_data, col_has_missing , by = "Variable") %>%
     mutate(Variable = factor(Variable, levels = vip_data$Variable))
   vis_miss_plus

vignettes/interpretation.Rmd

@@ -19,6 +19,7 @@ knitr::opts_chunk$set(
   out.height = "300px", 
   fig.width = 14
 )
+requireNamespace("vip", quietly = TRUE)
 ```
 
 ```{r setup}