2023 spring cleaning

.Rbuildignore

@@ -12,3 +12,4 @@
 ^CODE_OF_CONDUCT\.md$
 ^\.github$
 ^codecov\.yml$
+^README\.Rmd$

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

@@ -33,6 +33,9 @@ jobs:
           - {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 }}

.github/workflows/pkgdown.yaml

@@ -4,12 +4,13 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -19,8 +20,10 @@ 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 +42,7 @@ 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

@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,36 +16,47 @@ 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")
           )
+          print(cov)
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v5
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: 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

.gitignore

@@ -3,3 +3,4 @@
 .Rproj.user
 .DS_Store
 inst/doc
+docs

DESCRIPTION

@@ -4,7 +4,7 @@ Version: 0.0.1.1
 Authors@R: c(
     person("Marly", "Gotti", , "marlygotti@gmail.com", role = c("aut", "cre")),
     person("Max", "Kuhn", , "max@posit.co", role = "aut"),
-    person(given = "Posit Software, PBC", role = c("cph", "fnd"))
+    person("Posit Software, PBC", role = c("cph", "fnd"))
   )
 Description: A modeling package compiling applicability domain methods in
     R.  It combines different methods to measure the amount of
@@ -17,15 +17,15 @@ URL: https://github.com/tidymodels/applicable,
 BugReports: https://github.com/tidymodels/applicable/issues
 Depends: 
     ggplot2,
-    R (>= 3.4)
+    R (>= 3.6)
 Imports: 
     dplyr,
     glue,
-    hardhat (>= 0.1.2),
+    hardhat (>= 1.3.0),
     Matrix,
     proxyC,
     purrr,
-    rlang,
+    rlang (>= 1.1.1),
     stats,
     tibble,
     tidyr,
@@ -35,17 +35,17 @@ Suggests:
     covr,
     knitr,
     modeldata,
-    recipes (>= 0.1.7),
+    recipes (>= 1.0.8),
     rmarkdown,
     spelling,
-    testthat (>= 3.0.0),
+    testthat (>= 3.2.0),
     xml2
 VignetteBuilder: 
     knitr
+Config/Needs/website: tidyverse/tidytemplate
+Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
-Config/Needs/website: tidyverse/tidytemplate
-Config/testthat/edition: 3

NAMESPACE

@@ -31,6 +31,7 @@ export(autoplot.apd_pca)
 export(autoplot.apd_similarity)
 export(score)
 export(score.default)
+import(rlang)
 importFrom(Matrix,Matrix)
 importFrom(Matrix,colSums)
 importFrom(dplyr,"%>%")
@@ -59,9 +60,6 @@ importFrom(hardhat,validate_prediction_size)
 importFrom(proxyC,simil)
 importFrom(purrr,map2_dfc)
 importFrom(purrr,map_dfc)
-importFrom(rlang,abort)
-importFrom(rlang,arg_match)
-importFrom(rlang,enquos)
 importFrom(stats,approx)
 importFrom(stats,ecdf)
 importFrom(stats,prcomp)

R/applicable-package.R

@@ -1,8 +1,50 @@
 #' @keywords internal
 "_PACKAGE"
 
-# The following block is used by usethis to automatically manage
-# roxygen namespace tags. Modify with care!
 ## usethis namespace: start
+
+#' @import rlang
+#' @importFrom dplyr %>%
+#' @importFrom dplyr count
+#' @importFrom dplyr group_by
+#' @importFrom dplyr matches
+#' @importFrom dplyr mutate
+#' @importFrom dplyr mutate_all
+#' @importFrom dplyr rename_all
+#' @importFrom dplyr sample_n
+#' @importFrom dplyr select
+#' @importFrom dplyr slice
+#' @importFrom dplyr starts_with
+#' @importFrom dplyr ungroup
+#' @importFrom ggplot2 ggplot geom_step xlab ylab aes autoplot
+#' @importFrom glue glue
+#' @importFrom hardhat forge
+#' @importFrom hardhat mold
+#' @importFrom hardhat new_model
+#' @importFrom hardhat validate_prediction_size
+#' @importFrom Matrix Matrix colSums
+#' @importFrom proxyC simil
+#' @importFrom purrr map_dfc
+#' @importFrom purrr map2_dfc
+#' @importFrom stats approx
+#' @importFrom stats ecdf
+#' @importFrom stats prcomp
+#' @importFrom stats predict
+#' @importFrom stats quantile
+#' @importFrom stats setNames
+#' @importFrom tibble as_tibble
+#' @importFrom tibble tibble
+#' @importFrom tidyr gather
+#' @importFrom tidyselect vars_select
+#' @importFrom utils globalVariables
 ## usethis namespace: end
+
+# ------------------------------------------------------------------------------
+# global variable" check
+# nocov
+# nocov end
+# Reduce false positives when R CMD check runs its "no visible binding for
+utils::globalVariables(
+  c("cumulative", "n", "sim", "percentile", "component", "value")
+)
 NULL

R/data.R

@@ -30,7 +30,7 @@ NULL
 #' @return \item{okc_binary_train,okc_binary_test}{data frame frames with 61 columns}
 #'
 #' @source
-#' Kim (2015), "OkCupid Data for Introductory Statistics and Data Science Courses", _Journal of Statistics Education_, Volume 23, Number 2. \url{https://www.tandfonline.com/doi/abs/10.1080/10691898.2015.11889737}
+#' Kim (2015), "OkCupid Data for Introductory Statistics and Data Science Courses", _Journal of Statistics Education_, Volume 23, Number 2. \doi{10.1080/10691898.2015.11889737}
 #'
 #' Kuhn and Johnson (2020), _Feature Engineering and Selection_, Chapman and Hall/CRC . \url{https://bookdown.org/max/FES/} and \url{https://github.com/topepo/FES}
 #'
@@ -60,7 +60,7 @@ NULL
 #' Data as an End of Semester Regression Project," \emph{Journal of Statistics
 #' Education},  Volume 19, Number 3.
 #'
-#' \url{https://www.cityofames.org/government/departments-divisions-a-h/city-assessor}
+#' `https://www.cityofames.org/government/departments-divisions-a-h/city-assessor`
 #'
 #' \url{http://jse.amstat.org/v19n3/decock/DataDocumentation.txt}
 #'

R/print.R

@@ -74,7 +74,7 @@ print.apd_hat_values <- function(x, ...) {
 #' tr_x <- matrix(
 #'   sample(0:1, size = 20 * 50, prob = rep(.5, 2), replace = TRUE),
 #'   ncol = 20
-#'  )
+#' )
 #' model <- apd_similarity(tr_x)
 #' print(model)
 #' @export

README.Rmd

@@ -15,16 +15,16 @@ knitr::opts_chunk$set(
 )
 
 options(rlang__backtrace_on_error = "reminder")
-
 ```
 
 # applicable <img src="man/figures/logo.png" align="right"/>
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/tidymodels/applicable/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/tidymodels/applicable/actions/workflows/R-CMD-check.yaml)
-[![Codecov test coverage](https://codecov.io/gh/tidymodels/applicable/branch/main/graph/badge.svg)](https://app.codecov.io/gh/tidymodels/applicable?branch=main)
+[![Codecov test coverage](https://codecov.io/gh/tidymodels/applicable/graph/badge.svg)](https://app.codecov.io/gh/tidymodels/applicable)
 [![Lifecycle:experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html)
 [![CRAN status](https://www.r-pkg.org/badges/version/applicable)](https://cran.r-project.org/package=applicable)
+
 <!-- badges: end -->
 
 ## Introduction
@@ -58,7 +58,7 @@ To learn about how to use applicable, check out the vignettes:
 
 This project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
 
-- For questions and discussions about tidymodels packages, modeling, and machine learning, please [post on RStudio Community](https://community.rstudio.com/new-topic?category_id=15&tags=tidymodels,question).
+- For questions and discussions about tidymodels packages, modeling, and machine learning, please [post on Posit Community](https://community.rstudio.com/new-topic?category_id=15&tags=tidymodels,question).
 
 - If you think you have encountered a bug, please [submit an issue](https://github.com/tidymodels/applicable/issues).