Reduce package dependencies (#191)

* update docs, tests * remove assertthat, htmltools, magrittr imports * move renv, testthat, usethis to suggests * replace magrittr %>% with native pipe |> * rename pasteMd to paste_md * add CONTRIBUTING.md to .Rbuildignore * fix cran checks on imports and no visible binding for global variables
Yu-Group · Jan 1, 2025 · bf8b8db · bf8b8db
1 parent 828d338
commit bf8b8db
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -5,8 +5,9 @@
 ^pkgdown$
 ^LICENSE\.md$
 ^\.github$
-^vignettes/results$
-^vignettes/example-docs$
+^vignettes/results/*
+^vignettes/example-docs/*
 ^man-roxygen
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^CONTRIBUTING\.md$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -26,18 +26,12 @@ Imports:
     future.apply,
     knitr,
     lifecycle,
-    magrittr,
-    methods,
     purrr,
     R.utils,
-    assertthat,
-    usethis,
-    renv,
     R6,
     rlang,
     rmarkdown,
     stringr,
-    testthat (>= 3.1.0),
     tibble,
     tidyr,
     tidyselect,
@@ -46,20 +40,21 @@ Imports:
 Suggests:
     broom,
     callr,
-    devtools,
     fontawesome,
     fs,
     future.callr,
     ggplot2,
     glmnet,
     here,
-    htmltools,
     lobstr,
     MASS,
     plotly,
     progressr (>= 0.9.0),
     ranger,
+    renv,
     rstudioapi,
+    testthat (>= 3.1.0),
+    usethis,
     vdiffr,
     withr (>= 2.5.0),
     ymlthis
@@ -70,7 +65,7 @@ Remotes:
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Collate: 
     'dgp.R'
     'docs.R'
@@ -86,7 +81,6 @@ Collate:
     'globals.R'
     'init-dir.R'
     'method.R'
-    'reexport-magrittr.R'
     'run-tests.R'
     'signals.R'
     'use_templates.R'

diff --git a/NAMESPACE b/NAMESPACE
@@ -4,7 +4,6 @@ S3method(fp,data.frame)
 S3method(neg,data.frame)
 S3method(pos,data.frame)
 S3method(tp,data.frame)
-export("%>%")
 export(DGP)
 export(Evaluator)
 export(Experiment)
@@ -98,5 +97,4 @@ export(use_feature_selection_template)
 export(use_inference_template)
 export(use_prediction_template)
 export(visualize_experiment)
-importFrom(magrittr,"%>%")
 importFrom(rlang,.data)
diff --git a/R/docs.R b/R/docs.R
@@ -74,8 +74,8 @@ init_docs <- function(experiment, save_dir) {
   if (!identical(descendants, list())) {
     for (field in fields) {
       obj_names <- purrr::map(descendants,
-                              ~names(.x[[paste0("get_", field, "s")]]())) %>%
-        purrr::reduce(c) %>%
+                              ~names(.x[[paste0("get_", field, "s")]]())) |>
+        purrr::reduce(c) |>
         unique()
       for (obj_name in obj_names) {
         fname <- file.path(save_dir, "docs", paste0(field, "s"),
@@ -223,18 +223,14 @@ render_docs <- function(experiment, save_dir, write_rmd = FALSE,
 
   output_format_type <- rlang::call_name(rlang::enexpr(output_format))
   use_vmodern <- output_format_type == "vmodern"
-  if (use_vmodern) {
-    rlang::check_installed("htmltools",
-                           reason = "to run `render_docs(output_format = vthemes::vmodern(), ...)`")
-  }
 
   if (write_rmd) {
     rlang::check_installed("ymlthis",
                            reason = "to run `render_docs(write_rmd = TRUE, ...)`")
-    yml_header <- ymlthis::yml() %>%
-      ymlthis::yml_title(title) %>%
-      ymlthis::yml_author(author) %>%
-      ymlthis::yml_output({{output_format}}) %>%
+    yml_header <- ymlthis::yml() |>
+      ymlthis::yml_title(title) |>
+      ymlthis::yml_author(author) |>
+      ymlthis::yml_output({{output_format}}) |>
       ymlthis::yml_params(
         sim_path = ymlthis::shiny_text(
           label = "Path to Simulation Experiment Folder:",

diff --git a/R/evaluator-lib-feature-selection.R b/R/evaluator-lib-feature-selection.R
@@ -145,6 +145,9 @@ eval_feature_selection_err <- function(fit_results, vary_params = NULL,
                                        estimate_col = NULL, imp_col,
                                        group_cols = NULL, metrics = NULL,
                                        na_rm = FALSE) {
+  # dummies to fix R CMD check note on no visible binding for global variable
+  .estimator <- NULL
+  .eval_result <- NULL
 
   if (!is.null(metrics) && !inherits(metrics, "metric_set")) {
     abort("Unknown metrics. metrics must be of class 'yardstick::metric_set' or NULL.")
@@ -153,7 +156,7 @@ eval_feature_selection_err <- function(fit_results, vary_params = NULL,
   eval_feature_selection_err_fun <- function(data, truth_col, estimate_col,
                                              imp_col, metrics, na_rm) {
 
-    data <- data %>%
+    data <- data |>
       dplyr::mutate(
         dplyr::across(tidyselect::all_of(c(truth_col, estimate_col)),
                       ~factor(as.integer(as.numeric(.x) != 0), levels = 0:1))
@@ -168,8 +171,8 @@ eval_feature_selection_err <- function(fit_results, vary_params = NULL,
     }
 
     out <- metrics(data = data, truth = !!truth_col, estimate = !!estimate_col,
-                   !!imp_col, na_rm = na_rm, event_level = "second") %>%
-      add_na_counts(data = data, value_col = imp_col, na_rm = na_rm) %>%
+                   !!imp_col, na_rm = na_rm, event_level = "second") |>
+      add_na_counts(data = data, value_col = imp_col, na_rm = na_rm) |>
       dplyr::select(-.estimator)
     return(out)
   }
@@ -179,7 +182,7 @@ eval_feature_selection_err <- function(fit_results, vary_params = NULL,
     fun = eval_feature_selection_err_fun, nested_cols = nested_cols,
     truth_col = truth_col, estimate_col = estimate_col, imp_col = imp_col,
     group_cols = group_cols, fun_options = list(metrics = metrics), na_rm = na_rm
-  ) %>%
+  ) |>
     tidyr::unnest(.eval_result)
   return(eval_tib)
 }
@@ -204,7 +207,7 @@ summarize_feature_selection_err <- function(fit_results, vary_params = NULL,
     nested_cols = nested_cols, truth_col = truth_col,
     estimate_col = estimate_col, imp_col = imp_col, group_cols = group_cols,
     metrics = metrics, na_rm = na_rm
-  ) %>%
+  ) |>
     dplyr::group_by(dplyr::across(tidyselect::any_of(group_vars)))
 
   eval_summary <- eval_summarizer(
@@ -322,8 +325,8 @@ eval_feature_selection_curve <- function(fit_results, vary_params = NULL,
                                          curve = c("ROC", "PR"),
                                          na_rm = FALSE) {
   if (is.null(nested_cols) || (truth_col %in% names(fit_results))) {
-    fit_results <- fit_results %>%
-      dplyr::rowwise() %>%
+    fit_results <- fit_results |>
+      dplyr::rowwise() |>
       dplyr::mutate(
         {{truth_col}} := factor(
           as.integer(as.numeric(.data[[truth_col]]) != 0), levels = 1:0
@@ -332,7 +335,7 @@ eval_feature_selection_curve <- function(fit_results, vary_params = NULL,
   } else {
     fit_results[[nested_cols]] <- purrr::map(
       fit_results[[nested_cols]],
-      ~.x %>%
+      ~.x |>
         dplyr::mutate(
           {{truth_col}} := factor(
             as.integer(as.numeric(.data[[truth_col]]) != 0), levels = 1:0
@@ -366,7 +369,9 @@ summarize_feature_selection_curve <- function(fit_results, vary_params = NULL,
                                               eval_id = ifelse(curve == "PR",
                                                                "precision",
                                                                "TPR")) {
-  curve_estimate <- NULL  # to fix no visible binding for global variable error
+  # dummies to fix R CMD check note on no visible binding for global variable
+  curve_estimate <- NULL
+
   if (curve == "PR") {
     xvar <- "recall"
     yvar <- "precision"
@@ -380,13 +385,13 @@ summarize_feature_selection_curve <- function(fit_results, vary_params = NULL,
     fit_results = fit_results, vary_params = vary_params,
     nested_cols = nested_cols, truth_col = truth_col, imp_col = imp_col,
     group_cols = group_cols, curve = curve, na_rm = na_rm
-  ) %>%
-    dplyr::rowwise() %>%
+  ) |>
+    dplyr::rowwise() |>
     dplyr::mutate(curve_estimate = list(rescale_curve(curve_estimate,
                                                       x_grid = x_grid,
                                                       xvar = xvar,
-                                                      yvar = yvar))) %>%
-    tidyr::unnest(curve_estimate) %>%
+                                                      yvar = yvar))) |>
+    tidyr::unnest(curve_estimate) |>
     dplyr::group_by(dplyr::across(tidyselect::any_of(group_vars)))
 
   eval_summary <- eval_summarizer(
@@ -471,13 +476,13 @@ eval_feature_importance <- function(fit_results, vary_params = NULL,
                                     group_cols = NULL) {
   id_vars <- c(".rep", ".dgp_name", ".method_name", vary_params)
   if (!is.null(nested_cols)) {
-    fit_results <- fit_results %>%
+    fit_results <- fit_results |>
       tidyr::unnest(tidyselect::all_of(nested_cols))
   } else {
-    fit_results <- fit_results %>%
+    fit_results <- fit_results |>
       tidyr::unnest(tidyselect::all_of(c(feature_col, imp_col, group_cols)))
   }
-  eval_tib <- fit_results %>%
+  eval_tib <- fit_results |>
     dplyr::select(
       tidyselect::all_of(c(id_vars, feature_col, imp_col, group_cols))
     )
@@ -502,7 +507,7 @@ summarize_feature_importance <- function(fit_results, vary_params = NULL,
     fit_results = fit_results, vary_params = vary_params,
     nested_cols = nested_cols, feature_col = feature_col, imp_col = imp_col,
     group_cols = group_cols
-  ) %>%
+  ) |>
     dplyr::group_by(dplyr::across(tidyselect::all_of(group_vars)))
 
   eval_summary <- eval_summarizer(