From aa611608611a2141630f793f6b7617bcf77da670 Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Tue, 23 Jan 2024 09:31:57 +1100
Subject: [PATCH 1/5] fix arguments

---
 DESCRIPTION           | 2 +-
 NAMESPACE             | 2 +-
 R/functions_OLD.R     | 1 -
 R/functions_chr_int.R | 3 +--
 4 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 22bc172..9c4036c 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -20,7 +20,7 @@ Depends:
     R (>= 3.6.0)
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.3.0
 Imports: 
     utils,
     graphics,
diff --git a/NAMESPACE b/NAMESPACE
index fc5eadd..8fc5da7 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -21,7 +21,7 @@ importFrom(graphics,par)
 importFrom(graphics,plot)
 importFrom(graphics,points)
 importFrom(lifecycle,deprecate_warn)
-importFrom(magrittr,"%>%")
+importFrom(magrittr,)
 importFrom(magrittr,equals)
 importFrom(magrittr,set_rownames)
 importFrom(purrr,imap)
diff --git a/R/functions_OLD.R b/R/functions_OLD.R
index b3970c6..52b4d72 100644
--- a/R/functions_OLD.R
+++ b/R/functions_OLD.R
@@ -346,7 +346,6 @@ gate_interactive <-
 #' @param .dim2 A column symbol. The y dimension
 #' @param gate_list A list of gates. Each element of the list is a data frame with x and y columns. Each row is a coordinate. The order matter.
 #' @param name A character string. The name of the new column
-#' @param ... Further parameters passed to the function gatepoints::fhs
 #'
 #' @return A tibble with additional columns
 #'
diff --git a/R/functions_chr_int.R b/R/functions_chr_int.R
index 302cbe0..6e735af 100644
--- a/R/functions_chr_int.R
+++ b/R/functions_chr_int.R
@@ -265,7 +265,7 @@ pretty_plot_chr_int = function(.data,
 #' @param .size A column symbol. Size of points
 #' @param opacity A number between 0 and 1. The opacity level of the data points
 #' @param how_many_gates An integer. The number of gates to label
-#' @param gate_list A list of gates. It is returned by gate function as attribute \"gate\". If you want to create this list yourself, each element of the list is a data frame with x and y columns. Each row is a coordinate. The order matter.
+#' @param is_size_fixed A logical value indicating if the size of points is fixed, or it is a column name.
 #' @param ... Further parameters passed to the function gatepoints::fhs
 #'
 #' @return A tibble with additional columns
@@ -371,7 +371,6 @@ gate_interactive_chr_int <-
 #' @param .dim1 A column symbol. The x dimension
 #' @param .dim2 A column symbol. The y dimension
 #' @param gate_list A list of gates. Each element of the list is a data frame with x and y columns. Each row is a coordinate. The order matter.
-#' @param ... Further parameters passed to the function gatepoints::fhs
 #'
 #' @return A tibble with additional columns
 #'

From 867f657298ab18dee5c0a47e1dce3681b3b8ff57 Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Tue, 23 Jan 2024 10:52:37 +1100
Subject: [PATCH 2/5] drop when and %>%

---
 NAMESPACE                        |   1 -
 R/functions_OLD.R                |   2 +-
 R/functions_chr_int.R            | 404 ++++++++++++++++---------------
 R/methods.R                      |   1 -
 R/methods_OLD.R                  |   1 -
 R/nanny.R                        | 104 ++++----
 R/utilities.R                    |  99 ++++----
 man/gate_interactive_chr_int.Rd  |   4 +-
 man/gate_programmatic.Rd         |   2 -
 man/gate_programmatic_chr_int.Rd |   2 -
 10 files changed, 319 insertions(+), 301 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 8fc5da7..12078c1 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -21,7 +21,6 @@ importFrom(graphics,par)
 importFrom(graphics,plot)
 importFrom(graphics,points)
 importFrom(lifecycle,deprecate_warn)
-importFrom(magrittr,)
 importFrom(magrittr,equals)
 importFrom(magrittr,set_rownames)
 importFrom(purrr,imap)
diff --git a/R/functions_OLD.R b/R/functions_OLD.R
index 52b4d72..656c09f 100644
--- a/R/functions_OLD.R
+++ b/R/functions_OLD.R
@@ -12,7 +12,7 @@
 #' @importFrom utils head
 #' @importFrom stringr str_pad
 #' @importFrom scales alpha
-
+#' @importFrom purrr when
 pretty_plot = function(.data,
                        .dim1,
                        .dim2,
diff --git a/R/functions_chr_int.R b/R/functions_chr_int.R
index 6e735af..2b16f13 100644
--- a/R/functions_chr_int.R
+++ b/R/functions_chr_int.R
@@ -3,22 +3,22 @@ parse_gate_list = function(.data, my_df){
   # Comply with CRAN NOTES
   point = NULL
   
-  .data %>%
-    imap( ~ tibble(gate = .y, point = .x)) %>%
-    reduce(.f = full_join, by = "point") %>%
+  .data |>
+    imap( ~ tibble(gate = .y, point = .x)) |>
+    reduce(.f = full_join, by = "point") |>
     
     # Add all points
-    full_join(tibble(point = as.character(1:nrow(my_df))), by = "point") %>%
-    arrange(as.numeric(point)) %>%
+    full_join(tibble(point = as.character(1:nrow(my_df))), by = "point") |>
+    arrange(as.numeric(point)) |>
     
     # Unite in case of a point belonging to multiple gates
     tidyr::unite(contains("gate"),
                  col = "gate",
                  sep = ",",
-                 na.rm = TRUE) %>%
+                 na.rm = TRUE) |>
     
     # Replace NAs
-    mutate(gate := if_else(gate == "", "0", gate)) %>%
+    mutate(gate := if_else(gate == "", "0", gate)) |>
     
     # Pull
     pull(gate)
@@ -60,100 +60,79 @@ pretty_plot_chr_int = function(.data,
   my_size_range = c(1, 3)
   
   
+  .data_formatted <- .data
+  
+  # Define COLOR
+  # If not defined
+  if (pull(.data_formatted, !!.color) |> unique() |> is.na() |> all()) {
+    .data_formatted <- .data_formatted |> mutate(.color = "grey25", color_hexadecimal = "#3B3B3B")
+  }
+  # If continuous
+  else if (quo_is_symbol(.color) && select(.data_formatted, !!.color) |> sapply(class) |> `%in%`(c("numeric", "integer", "double")) |> any()) {
+    order_ <- .data_formatted |> pull(!!.color) |> sort() |> findInterval(pull(.data_formatted, !!.color))
+    .data_formatted <- .data_formatted |> mutate(color_hexadecimal = grDevices::colorRampPalette(viridis(n = 5))(max(order_))[order_])
+  }
+  # If discrete
+  else if (quo_is_symbol(.color)) {
+    how_many_colors <- .data_formatted |> distinct(!!.color) |> nrow()
+    .data_formatted <- .data_formatted |> mutate(color_hexadecimal =
+                                                   grDevices::colorRampPalette(RColorBrewer::brewer.pal(min(9, how_many_colors), "Set1"))(how_many_colors)[factor(pull(.data_formatted, !!.color))])
+  }
+  
+  # Define SIZE
+  # If not defined
+  if (pull(.data_formatted, !!.size) |> unique() |> is.na() |> all()) {
+    .data_formatted <- .data_formatted |> mutate(.size = 2)
+  }
+  # If it is a number and not a column name
+  else if (exists("is_size_fixed") && is_size_fixed) {
+    .data_formatted <- .data_formatted |> mutate(.size = !!.size)
+  }
+  # If continuous
+  else if (quo_is_symbol(enquo(.size)) && select(.data_formatted, !!enquo(.size)) |> sapply(class) |> `%in%`(c("numeric", "integer", "double")) |> any()) {
+    .data_formatted <- .data_formatted |> mutate(.size = pull(., !!enquo(.size)) |> rescale(to = my_size_range))
+  }
+  # If discrete
+  else if (quo_is_symbol(enquo(.size))) {
+    warning("tidygate says: .size has to be a continuous variable. .size has been ignored")
+    .data_formatted <- .data_formatted |> mutate(.size = 2)
+  }
+  else {
+    stop("tidygate says: the parameter .size must be NULL, numeric or a symbolic column name")
+  }
+  
+  # Define SHAPE
+  # If not defined
+  if (pull(.data_formatted, !!.shape) |> unique() |> is.na() |> all()) {
+    .data_formatted <- .data_formatted |> mutate(.shape = 19)
+  }
+  # If continuous
+  else if (quo_is_symbol(.shape) && select(.data_formatted, !!.shape) |> sapply(class) |> `%in%`(c("numeric", "integer", "double")) |> any()) {
+    warning("tidygate says: .shape has to be a discrete variable. .shape has been ignored")
+    .data_formatted <- .data_formatted |> mutate(.shape = 19)
+  }
+  # If discrete
+  else if (quo_is_symbol(.shape)) {
+    .data_formatted <- .data_formatted |> mutate(.shape = c(19, 17, 15, 18, 3, 4, 8, 10, 5)[factor(pull(., !!.shape))])
+  }
   
-  .data_formatted =
-    .data %>%
-    
-    # Define COLOR
-    when(
-      
-      # If not defined
-      pull(., !!.color) %>% unique %>% is.na() %>% all() ~ (.) %>% mutate(.color = "grey25", color_hexadecimal = "#3B3B3B"),
-      
-      # If continuous
-      quo_is_symbol(.color) &&
-        (.) %>%
-        select(!!.color) %>%
-        sapply(class) %in% c("numeric", "integer", "double") ~ {
-          order_ = findInterval(pull(., !!.color), sort(pull(., !!.color)))
-          (.) %>% mutate(color_hexadecimal = grDevices::colorRampPalette(viridis(n = 5))(n())[order_])
-        },
-      
-      # If discrete
-      quo_is_symbol(.color) ~ {
-        how_many_colors = .data %>% distinct(!!.color) %>% nrow
-        (.) %>%
-          mutate(color_hexadecimal =
-                   grDevices::colorRampPalette(RColorBrewer::brewer.pal(min(
-                     9, how_many_colors
-                   ), "Set1"))(how_many_colors)[factor(!!.color)])
-      }
-    ) %>%
-    
-    # Define SIZE
-    when(
-      # If not defined
-      pull(., !!.size) %>% unique %>% is.na() %>% all() ~ (.)  %>% mutate(.size = 2),
-      
-      # If it is a number and not a column name
-      is_size_fixed ~ (.)  %>% mutate(.size := !!.size),
-      
-      # If continuous
-      quo_is_symbol(enquo(.size)) &&
-        (.) %>%
-        select(!!enquo(.size)) %>%
-        sapply(class) %in% c("numeric", "integer", "double") ~ 	(.) %>%	mutate(.size := !!enquo(.size) %>% rescale(to = my_size_range)),
-      
-      # If discrete
-      quo_is_symbol(enquo(.size)) ~ {
-        warning("tidygate says: .size has to be a continuous variable. .size has been ignored")
-        (.) %>% mutate(.size = 2)
-      },
-      
-      ~ stop(
-        "tidygate says: the parameter .size must be NULL, numeric or a symbolic column name"
-      )
-    ) %>%
-    
-    # Define SHAPE
-    when(
-      
-      # If not defined
-      pull(., !!.shape) %>% unique %>% is.na() %>% all() ~ (.)  %>% mutate(.shape = 19),
-      
-      # If continuous
-      quo_is_symbol(.shape) &
-        (.) %>%
-        select(!!.shape) %>%
-        sapply(class) %in% c("numeric", "integer", "double") ~ {
-          warning("tidygate says: .shape has to be a discrete variable. .shape has been ignored")
-          (.) %>% mutate(.shape = 19)
-        }	,
-      
-      # If discrete
-      quo_is_symbol(.shape) ~ (.) %>%	mutate(.shape := c(19, 17, 15, 18, 3, 4, 8, 10, 5)[factor(!!.shape)])
-      
-       
-    )
   
   # Plot
-  .data_formatted %>%
-    {
-      plot(
-        (.) %>% pull(!!.dim1),
-        (.) %>% pull(!!.dim2),
-        xlim = range((.) %>% pull(!!.dim1)),
-        ylim = range((.) %>% pull(!!.dim2)),
+  plot(
+        .data_formatted |> pull(!!.dim1),
+        .data_formatted |> pull(!!.dim2),
+        xlim = range(.data_formatted |> pull(!!.dim1)),
+        ylim = range(.data_formatted |> pull(!!.dim2)),
         bty = 'l',
-        pch = (.) %>% pull(.shape),
-        cex = (.) %>% pull(.size),
-        col = (.) %>% pull(color_hexadecimal) %>% alpha(opacity),
-        xlab = quo_names(.dim1) %>% paste(collapse = " "),
-        ylab = quo_names(.dim2) %>% paste(collapse = " "),
+        pch = .data_formatted |> pull(.shape),
+        cex = .data_formatted |> pull(.size),
+        col = .data_formatted |> pull(color_hexadecimal) |> alpha(opacity),
+        xlab = quo_names(.dim1) |> paste(collapse = " "),
+        ylab = quo_names(.dim2) |> paste(collapse = " "),
         xaxt = 'n',
         yaxt = 'n'
       )
-    }
+
   
   axis(1, tck = 1,  col.ticks = "light gray")
   axis(1,
@@ -186,37 +165,67 @@ pretty_plot_chr_int = function(.data,
   
   # Add legend to top right, outside plot region
   inset_y = 0
-  if (pull(.data, !!.color) %>% unique %>% is.na() %>% not() %>% all()) {
+  
+  # Check if the 'color' column in .data is not all NA (missing values)
+  if (pull(.data, !!.color) |> unique() |> is.na() |> not() |> all()) {
+    
+    # Get the class/type of the 'color' column in .data_formatted
+    color_class <- pull(.data_formatted, !!.color) |> class()
+    
+    # If the 'color' column is of numeric, integer, or double type (continuous data)
+    if (color_class %in% c("numeric", "integer", "double")) {
+      # Create a legend for continuous color data
+      color_legend <- .data_formatted |> 
+        arrange(!!.color) |> 
+        slice(1, n()) |> 
+        pull(!!.color) |> 
+        round(digits = 4)
+      color_col <- .data_formatted |> 
+        arrange(!!.color) |> 
+        slice(1, n()) |> 
+        pull(color_hexadecimal)
+    } else {
+      # Create a legend for non-continuous (discrete) color data
+      color_legend <- .data_formatted |> 
+        arrange(!!.color) |> 
+        distinct(!!.color) |> 
+        pull(!!.color)
+      color_col <- .data_formatted |> 
+        arrange(!!.color) |> 
+        distinct(color_hexadecimal) |> 
+        pull(color_hexadecimal)
+    }
+    
+    # Add the color legend to the plot
     legend(
       "topleft",
       inset = c(1.05, inset_y),
-      legend = .data_formatted %>% 
-        
-        # If continuous
-        when(
-          pull(., !!.color) %>% class %in% c("numeric", "integer", "double") ~ arrange(., !!.color) %>% slice(1, n()) %>% pull(!!.color) %>% round(digits = 4),
-          ~ arrange(., !!.color) %>% distinct(!!.color) %>% pull(!!.color) 
-        ),
+      legend = color_legend,
       pch = 19,
-      col =  .data_formatted %>% 
-        
-        # If continuous
-        when(
-          pull(., !!.color) %>% class %in% c("numeric", "integer", "double") ~ arrange(., !!.color) %>% slice(1, n()) %>% pull(color_hexadecimal),
-          ~ arrange(., !!.color) %>% distinct(color_hexadecimal) %>% pull(color_hexadecimal)
-        ),
+      col = color_col,
       title = color_title,
       box.col = "white",
       xjust = 0
     )
-    inset_y = inset_y + distinct(.data_formatted,!!.color, .color) %>% nrow %>% magrittr::multiply_by(.1)
+    
+    # Adjust the position for the next legend
+    inset_y <- inset_y + (.data_formatted |> distinct(!!.color, .color) |> nrow() * 0.1)
   }
-  if (pull(.data, !!.size) %>% unique %>% is.na() %>% not() %>% all() &&
-      (.data %>% select(!!enquo(.size)) %>% sapply(class) %in% c("numeric", "integer", "double"))) {
+  
+  # Check if the 'size' column in .data is not all NA and is numeric
+  if (pull(.data, !!.size) |> unique() |> is.na() |> not() |> all() &&
+      (.data |> select(!!enquo(.size)) |> sapply(class) |> `%in%`(c("numeric", "integer", "double")) |> any())) {
+    # Create a legend for the size variable
+    size_legend <- .data_formatted |> 
+      distinct(!!enquo(.size)) |> 
+      pull(!!enquo(.size)) |> 
+      range()
+    
+    # Add the size legend to the plot
     legend(
       "topleft",
       inset = c(1.05, inset_y),
-      legend = distinct(.data_formatted,!!enquo(.size)) %>% pull(!!enquo(.size)) %>% range,
+      legend = size_legend,
       pch = 19,
       col = "black",
       pt.cex = my_size_range,
@@ -224,20 +233,31 @@ pretty_plot_chr_int = function(.data,
       box.col = "white",
       xjust = 0
     )
-    inset_y = inset_y + 0.3
+    
+    # Adjust the position for the next legend
+    inset_y <- inset_y + 0.3
   }
-  if (pull(.data, !!.shape) %>% unique %>% is.na() %>% not() %>% all()) {
+  
+  # Check if the 'shape' column in .data is not all NA
+  if (pull(.data, !!.shape) |> unique() |> is.na() |> not() |> all()) {
+    # Create a legend for the shape variable
+    shape_legend <- .data |> distinct(!!.shape) |> pull(!!.shape)
+    shape_pch <- .data_formatted |> distinct(!!.shape, .shape) |> pull(.shape)
+    
+    # Add the shape legend to the plot
     legend(
       "topleft",
       inset = c(1.05, inset_y),
-      legend = distinct(.data,!!.shape) %>% pull(!!.shape),
-      pch = distinct(.data_formatted,!!.shape, .shape) %>% pull(.shape),
+      legend = shape_legend,
+      pch = shape_pch,
       col = "black",
       title = shape_title,
       box.col = "white",
       yjust = 0
     )
-    inset_y = inset_y + distinct(.data_formatted,!!.shape, .shape) %>% nrow %>% magrittr::multiply_by(.1)
+    
+    # Adjust the position for the next legend
+    inset_y <- inset_y + (.data_formatted |> distinct(!!.shape, .shape) |> nrow() * 0.1)
   }
   
   
@@ -294,25 +314,20 @@ gate_interactive_chr_int <-
     
     name = "gate"
     
-    # my df
-    my_df =
-      .data %>%
-      
-      # Check if dimensions are NA
-      check_dimensions(!!.dim1,!!.dim2)
+    # Check if dimensions are NA and create my_df
+    my_df <- .data |>
+      check_dimensions(!!.dim1, !!.dim2)
     
-    my_matrix	=
-      my_df %>%
-      select(!!.dim1,!!.dim2) %>%
-      .as_matrix()
+    # Create my_matrix from my_df
+    my_matrix <- my_df |>
+      select(!!.dim1, !!.dim2) |>
+      as.matrix()
     
     # Add extra space to right of plot area; change clipping to figure
-    if (pull(.data, !!.color) %>% unique %>% is.na() %>% not() %>% all() |
-        pull(.data, !!.shape) %>% unique %>% is.na() %>% not() %>% all()|
-        (pull(.data, !!.size) %>% unique %>% is.na() %>% not() %>% all() &&
-         (
-           .data %>% select(!!.size) %>% sapply(class) %in% c("numeric", "integer", "double")
-         ))) {
+    if ((pull(.data, !!.color) |> unique() |> is.na() |> not() |> all()) |
+        (pull(.data, !!.shape) |> unique() |> is.na() |> not() |> all()) |
+        (pull(.data, !!.size) |> unique() |> is.na() |> not() |> all() &&
+         (.data |> select(!!.size) |> sapply(class) |> `%in%`(c("numeric", "integer", "double")) |> any()))) {
       # Reset par on exit
       opar <- par(no.readonly = TRUE)
       on.exit(par(opar))
@@ -320,42 +335,36 @@ gate_interactive_chr_int <-
       # Set the new par
       par(mar = c(5.1, 4.1, 4.1, 8.1),
           xpd = TRUE,
-          
-          # Reduce tick length
-          tck = -.01 
-      )
+          tck = -.01) # Reduce tick length
     }
     
-    
     # Plot
-    my_df %>% pretty_plot_chr_int(
-      !!.dim1,!!.dim2,
-      .color = !!.color,
-      .shape = !!.shape,
-      
-      # size can be number or column
-      .size = !!.size,
-      
-      opacity = opacity,
-      is_size_fixed = is_size_fixed
-    )
+    my_df |> 
+      pretty_plot_chr_int(
+        !!.dim1, !!.dim2,
+        .color = !!.color,
+        .shape = !!.shape,
+        .size = !!.size,
+        opacity = opacity,
+        is_size_fixed = is_size_fixed
+      )
     
-    # Loop over gates # Variable needed for recalling the attributes later
-    gate_list = map(1:how_many_gates,
-                    ~ my_matrix %>% fhs(mark = TRUE, ...))
+    # Loop over gates and create gate_list
+    gate_list <- map(1:how_many_gates,
+                     ~ my_matrix |> fhs(mark = TRUE, ...))
     
     # Save gate list
-    temp_file = sprintf("%s.rds", tempfile())
+    temp_file <- sprintf("%s.rds", tempfile())
     message(sprintf("tidygate says: the gates have been saved in %s", temp_file))
-    gate_list %>% 
-      map(~ attr(.x, "gate")) %>%
+    gate_list |> 
+      map(~ attr(.x, "gate")) |>
       saveRDS(temp_file)
     
-    # Return
-    gate_list %>% parse_gate_list(my_df)
-    
+    # Return the parsed gate list
+    gate_list |> parse_gate_list(my_df)
   }
 
+
 #' Get points within a user drawn gate
 #'
 #' @keywords internal
@@ -391,29 +400,43 @@ gate_programmatic_chr_int <-
     
     # my df
     my_df =
-      .data %>%
+      .data |>
       
       # Check if dimensions are NA
       check_dimensions(!!.dim1,!!.dim2)
     
     my_matrix	=
-      my_df %>%
-      select(!!.dim1,!!.dim2) %>%
+      my_df |>
+      select(!!.dim1,!!.dim2) |>
       .as_matrix()
     
     # Loop over gates # Variable needed for recalling the attributes later
-    gate_list_result = map(gate_list,
-                           ~ .x %>%
-                             when("data.frame" %in% class(.) ~ .as_matrix(.), ~ (.)) %>%
-                             applyGate(my_matrix, .) %>%
-                             which() %>%
-                             as.character() %>%
-                             
-                             # Avoid error for empty gates
-                             when(!is.null(.) ~ (.) %>% add_attr(.x, "gate")))
+    # Loop over gates
+    gate_list_result <- map(gate_list, function(.x) {
+      # Check the class of the item
+      if ("data.frame" %in% class(.x)) {
+        result <- .as_matrix(.x)
+      } else {
+        result <- .x
+      }
+      
+      # Apply gate and convert to character
+      result <- applyGate(my_matrix, result) |>
+        which() |>
+        as.character()
+      
+      # Avoid error for empty gates
+      if (!is.null(result)) {
+        result <- result |>
+          add_attr(.x, "gate")
+      }
+      
+      return(result)
+    })
+    
     
     # Return
-    gate_list_result %>%
+    gate_list_result |>
       
       parse_gate_list(my_df)
   
@@ -439,15 +462,13 @@ gate_programmatic_chr_int <-
   point = NULL
   
   # If gouping is complex multicolumn
-  .group_by =
-    .group_by %>%
-    when(
-      !is.null(.group_by) ~ matrix(ncol = length(.group_by) / length(.dim1)) %>%
-        as.data.frame() %>%
-        unite(".group_by", everything(), sep = "___") %>%
-        pull(.group_by),
-      ~ (.)
-    )
+  if (!is.null(.group_by)) {
+    .group_by <- .group_by |> 
+      matrix(ncol = length(.group_by) / length(.dim1)) |> 
+      as.data.frame() |> 
+      unite(".group_by", everything(), sep = "___") |> 
+      pull(.group_by)
+  }
   
     
   # Create tibble
@@ -464,14 +485,15 @@ gate_programmatic_chr_int <-
   if(!is.null(.group_by)) input_df = input_df |> mutate(., .group_by = !!.group_by)
   
   
-  unique_df = 
-    input_df  %>%
-    
-    # Nesting is the case
-    when(!is.null(.group_by) ~ nest(., data___ = .group_by),
-         (.)) %>%
-    
-    distinct()
+  if (!is.null(.group_by)) {
+    unique_df <- input_df |> 
+      nest(data___ = .group_by)
+  } else {
+    unique_df <- input_df
+  }
+  
+  # Apply 'distinct()' outside of the if-else block
+  unique_df <- unique_df |> distinct()
   
   # Interactive
   if(is.null(gate_list))
@@ -515,9 +537,9 @@ gate_programmatic_chr_int <-
   else if(output_type == "int") result_vector = result_vector |> as.integer()
 
   # Integrate maintaining order in case of nesting
-  input_df %>%
+  input_df |>
     left_join(
-      unique_df %>%
+      unique_df |>
         mutate(gate = result_vector)
     ) |> 
     suppressMessages() |> 
diff --git a/R/methods.R b/R/methods.R
index 48ad11c..aac5ee8 100755
--- a/R/methods.R
+++ b/R/methods.R
@@ -6,7 +6,6 @@
 #'
 #' @importFrom rlang enquo
 #' @importFrom rlang quo_is_null
-#' @importFrom magrittr "%>%"
 #'
 #' @name gate_chr
 #'
diff --git a/R/methods_OLD.R b/R/methods_OLD.R
index 9a11f8e..565b166 100644
--- a/R/methods_OLD.R
+++ b/R/methods_OLD.R
@@ -7,7 +7,6 @@
 #' @description gate() takes as input a `tbl` formatted as | <DIMENSION 1> | <DIMENSION 2> | <...> | and calculates the rotated dimensional space of the feature value.
 #'
 #' @importFrom rlang enquo
-#' @importFrom magrittr "%>%"
 #' @importFrom lifecycle deprecate_warn
 #'
 #' @name gate
diff --git a/R/nanny.R b/R/nanny.R
index c85d003..1eb5801 100755
--- a/R/nanny.R
+++ b/R/nanny.R
@@ -32,24 +32,27 @@ get_specific_annotation_columns = function(.data, .col){
   n_x = .data %>% distinct_at(vars(!!.col)) %>% nrow
   
   # element wise columns
-  .data %>%
-    select(-!!.col) %>%
-    colnames %>%
+  .data = 
+    .data |>
+    select(-!!.col) |>
+    colnames() |>
     map(
-      ~
-        .x %>%
-        when(
-          .data %>%
-            distinct_at(vars(!!.col, .x)) %>%
-            nrow %>%
-            equals(n_x) ~ .x,
-          ~ NULL
-        )
-    ) %>%
-    
-    # Drop NULL
-    {	(.)[lengths((.)) != 0]	} %>%
-    unlist
+      ~ {
+        current_col <- .x
+        # Check condition
+        if (nrow(.data |> distinct_at(vars(!!.col, current_col))) == n_x) {
+          result <- current_col
+        } else {
+          result <- NULL
+        }
+        result
+      }
+    ) 
+  
+  # Drop null
+  .data[lengths(.data) != 0] |> 
+    unlist()
+  
   
 }
 
@@ -58,54 +61,41 @@ get_specific_annotation_columns = function(.data, .col){
 #' @importFrom magrittr set_rownames
 #' @importFrom rlang quo_is_null
 #' @importFrom rlang quo_is_symbolic
-#' @importFrom purrr when
-.as_matrix = function(.data,
-                      rownames = NULL,
-                      do_check = TRUE,
-                      sep_rownames = "___") {
-  
+.as_matrix = function(.data, rownames = NULL, do_check = TRUE, sep_rownames = "___") {
   # Comply with CRAN NOTES
   variable = NULL
   
   rownames = enquo(rownames)
   
-  
-  .data %>%
-    
-    # Through warning if data frame is not numerical beside the rownames column (if present)
-    when(
-      do_check &&
-        (.) %>%
-        # If rownames defined eliminate it from the data frame
-        when(!quo_is_null(rownames) ~ (.) %>% select(-!!rownames), ~ (.)) %>%
-        dplyr::summarise_all(class) %>%
-        tidyr::gather(variable, class) %>%
-        pull(class) %>%
-        unique() %>%
-        `%in%`(c("numeric", "integer")) %>% `!`() %>% any() ~ {
-          warning("tidygate says: there are NON-numerical columns, the matrix will NOT be numerical")
-          (.)
-        },
-      ~ (.)
-    ) %>%
-    
-    # If rownames multiple enquo (e.g., c(col1, col2)) merge them
-    when(!quo_is_null(rownames) ~ (.) %>% unite(col = "rn", !!rownames, sep = sep_rownames), ~ (.)) %>%
+  # Process data based on conditions
+  if (do_check) {
+    if (!quo_is_null(rownames)) {
+      # If rownames are not null, select columns except rownames
+      .data <- .data |> select(-!!rownames)
+    }
     
-    as.data.frame() %>%
-    
-    # Deal with rownames column if present
-    when(
-      !quo_is_null(rownames) ~ (.) %>%
-        set_rownames((.) %>% pull(rn)) %>%
-        select(-rn), 
-      ~ (.)
-    ) %>%
-    
-    # Convert to matrix
-    as.matrix()
+    # Check for non-numeric columns
+    if (any(!unique(.data |> summarise_all(class) |> gather(variable, class) |> pull(class)) %in% c("numeric", "integer"))) {
+      warning("tidygate says: there are NON-numerical columns, the matrix will NOT be numerical")
+    }
+  }
+  
+  # Merge columns for rownames if rownames are not null
+  if (!quo_is_null(rownames)) {
+    .data <- .data |> unite(col = "rn", !!rownames, sep = sep_rownames)
+  }
+  
+  # Convert to data frame and then to matrix, handling rownames if present
+  if (!quo_is_null(rownames)) {
+    .data <- .data |> 
+      set_rownames(pull(.data, rn)) |> 
+      select(-rn)
+  } 
+  
+  .data |> as.matrix()
 }
 
+
 #' Convert array of quosure (e.g. c(col_a, col_b)) into character vector
 #' 
 #' @keywords internal
diff --git a/R/utilities.R b/R/utilities.R
index af16d5a..16261ed 100755
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -1,35 +1,48 @@
 # Negation
 not = function(is){	!is }
 
-check_data_unique = function(.data,
-                             .element,
-                             .dim1,
-                             .dim2) {
-  # Get column names
+check_data_unique = function(.data, .element, .dim1, .dim2) {
+  # Get column names as quosures
   .element = enquo(.element)
   .dim1 = enquo(.dim1)
   .dim2 = enquo(.dim2)
   
-  if (.data %>%
-      select(!!.element,!!.dim1,!!.dim2) %>%
-      distinct %>%
-      
-      # Count
-      group_by_at(vars(!!.element,!!.dim1,!!.dim2)) %>%
-      tally() %>%
-      ungroup() %>%
-      
-      # Check
-      pull(n) %>%
-      max %>%
-      `>` (1))
-  stop(sprintf(
-    "tidygate says: %s must be unique for each row for the calculation",
-    quo_names(.element)
-  ))
+  # Check if the combination of .element, .dim1, and .dim2 is unique for each row
+  if (
+    # Select the specified columns
+    .data |> 
+    select(!!.element, !!.dim1, !!.dim2) |> 
+    
+    # Remove duplicate rows
+    distinct() |>                         
+    
+    # Group by these columns
+    group_by_at(vars(!!.element, !!.dim1, !!.dim2)) |> 
+    
+    # Count the number of rows in each group
+    tally() |>                            
+    
+    # Remove the grouping
+    ungroup() |>                          
+    
+    # Extract the count column
+    pull(n) |>                            
+    
+    # Check if the maximum count is greater than 1
+    max() > 1
+  ) {
+    
+    # If duplicates are found, stop the function and return an error message
+    stop(sprintf(
+      "tidygate says: %s must be unique for each row for the calculation",
+      quo_names(.element)
+    ))
+  }
 }
 
 
+
+
 reattach_internals = function(.data,
                               .data_internals_from = NULL,
                               .name = "gate") {
@@ -58,29 +71,29 @@ check_dimensions = function(.data, .dim1, .dim2) {
   .dim1 = enquo(.dim1)
   .dim2 = enquo(.dim2)
   
-  .data %>%
-    when(# If NAs in dimensions
-      (.) %>%
-        filter(!!.dim1 %>% is.na | !!.dim2 %>% is.na) %>%
-        nrow() %>%
-        `>` (0) ~ {
-          warning(
-            "tidygate says: you have some elements with non-valid dimensions. Those elements points will be filtered out"
-          )
-          (.) %>%
-            filter(!!.dim1 %>% is.na | !!.dim2 %>% is.na) %>%
-            capture.output() %>%
-            paste0(collapse = "\n") %>%
-            message()
-          
-          # Return
-          (.) %>%	filter(!(!!.dim1 %>% is.na | !!.dim2 %>% is.na))
-        },
-      
-      # Otherwise
-      ~ (.))
+  # Check if there are NAs in dimensions
+  if (
+    .data |>
+    filter( is.na(!!.dim1) | is.na(!!.dim2)) |>
+    nrow() > 0
+  ) {
+    warning("tidygate says: you have some elements with non-valid dimensions. Those elements points will be filtered out")
+    
+    # Capture and message the filtered data
+    filtered_data <- .data |>
+      filter(is.na(!!.dim1) | is.na(!!.dim2))
+    capture_output <- capture.output(print(filtered_data)) |> 
+      paste0(collapse = "\n") |> 
+      message()
+    
+    # Filter out non-valid elements
+    .data <- .data |> filter(!is.na(!!.dim1) & !is.na(!!.dim2))
+  }
+  
+  return(.data)
 }
 
+
 format_gatepoints = function(.data, .element, name, .idx) {
   # Comply CRAN check
   value = NULL
diff --git a/man/gate_interactive_chr_int.Rd b/man/gate_interactive_chr_int.Rd
index 23c828e..965ce7c 100644
--- a/man/gate_interactive_chr_int.Rd
+++ b/man/gate_interactive_chr_int.Rd
@@ -34,9 +34,9 @@ gate_interactive_chr_int(
 
 \item{how_many_gates}{An integer. The number of gates to label}
 
-\item{...}{Further parameters passed to the function gatepoints::fhs}
+\item{is_size_fixed}{A logical value indicating if the size of points is fixed, or it is a column name.}
 
-\item{gate_list}{A list of gates. It is returned by gate function as attribute \"gate\". If you want to create this list yourself, each element of the list is a data frame with x and y columns. Each row is a coordinate. The order matter.}
+\item{...}{Further parameters passed to the function gatepoints::fhs}
 }
 \value{
 A tibble with additional columns
diff --git a/man/gate_programmatic.Rd b/man/gate_programmatic.Rd
index 59999f4..ed228f4 100644
--- a/man/gate_programmatic.Rd
+++ b/man/gate_programmatic.Rd
@@ -18,8 +18,6 @@ gate_programmatic(.data, .element, .dim1, .dim2, gate_list, name = "gate")
 \item{gate_list}{A list of gates. Each element of the list is a data frame with x and y columns. Each row is a coordinate. The order matter.}
 
 \item{name}{A character string. The name of the new column}
-
-\item{...}{Further parameters passed to the function gatepoints::fhs}
 }
 \value{
 A tibble with additional columns
diff --git a/man/gate_programmatic_chr_int.Rd b/man/gate_programmatic_chr_int.Rd
index 91537de..fe3a506 100644
--- a/man/gate_programmatic_chr_int.Rd
+++ b/man/gate_programmatic_chr_int.Rd
@@ -14,8 +14,6 @@ gate_programmatic_chr_int(.data, .dim1, .dim2, gate_list)
 \item{.dim2}{A column symbol. The y dimension}
 
 \item{gate_list}{A list of gates. Each element of the list is a data frame with x and y columns. Each row is a coordinate. The order matter.}
-
-\item{...}{Further parameters passed to the function gatepoints::fhs}
 }
 \value{
 A tibble with additional columns

From 1fd713ce02f8c28793371f02cceb7ddd02b56675 Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Tue, 23 Jan 2024 11:18:36 +1100
Subject: [PATCH 3/5] solving further errors due to conversion

---
 NAMESPACE                     |  2 ++
 R/functions_OLD.R             |  1 +
 R/methods.R                   | 10 +++++-----
 R/nanny.R                     | 24 +++++++++++++++---------
 R/utilities.R                 | 13 +++++++------
 man/gate_chr-methods.Rd       | 10 +++++-----
 tests/testthat/test-methods.R | 24 ++++++++++++------------
 7 files changed, 47 insertions(+), 37 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 12078c1..5c9ab96 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -21,6 +21,7 @@ importFrom(graphics,par)
 importFrom(graphics,plot)
 importFrom(graphics,points)
 importFrom(lifecycle,deprecate_warn)
+importFrom(magrittr,"%>%")
 importFrom(magrittr,equals)
 importFrom(magrittr,set_rownames)
 importFrom(purrr,imap)
@@ -37,5 +38,6 @@ importFrom(rlang,quo_squash)
 importFrom(scales,alpha)
 importFrom(scales,rescale)
 importFrom(stringr,str_pad)
+importFrom(utils,capture.output)
 importFrom(utils,head)
 importFrom(viridis,viridis)
diff --git a/R/functions_OLD.R b/R/functions_OLD.R
index 656c09f..4993331 100644
--- a/R/functions_OLD.R
+++ b/R/functions_OLD.R
@@ -13,6 +13,7 @@
 #' @importFrom stringr str_pad
 #' @importFrom scales alpha
 #' @importFrom purrr when
+#' @importFrom magrittr %>%
 pretty_plot = function(.data,
                        .dim1,
                        .dim2,
diff --git a/R/methods.R b/R/methods.R
index aac5ee8..12b9d67 100755
--- a/R/methods.R
+++ b/R/methods.R
@@ -33,8 +33,8 @@
 #' 
 #'   if(interactive()){
 #'
-#'  tidygate::tidygate_data  %>%
-#'  distinct(`ct 1` , `ct 2`, Dim1, Dim2) %>%
+#'  tidygate::tidygate_data  |>
+#'  distinct(`ct 1` , `ct 2`, Dim1, Dim2) |>
 #'  mutate(gate = gate_chr( Dim1, Dim2)) 
 #'
 #'   }
@@ -46,13 +46,13 @@
 #' 
 #' # Standard use - programmatic
 #' res_distinct =
-#'  tidygate::tidygate_data  %>%
-#'  distinct(`ct 1` , `ct 2`, Dim1, Dim2) %>%
+#'  tidygate::tidygate_data  |>
+#'  distinct(`ct 1` , `ct 2`, Dim1, Dim2) |>
 #'  mutate(gate = gate_chr( Dim1, Dim2,gate_list = tidygate::gate_list)) 
 #'
 #' # Grouping - programmatic
 #' res =
-#'  tidygate::tidygate_data  %>%
+#'  tidygate::tidygate_data  |>
 #'    mutate(gate = gate_chr( 
 #'      Dim1, Dim2,
 #'      .group_by = c(`ct 1` , `ct 2`), 
diff --git a/R/nanny.R b/R/nanny.R
index 1eb5801..a7a425b 100755
--- a/R/nanny.R
+++ b/R/nanny.R
@@ -12,9 +12,9 @@
 quo_names <- function(v) {
   
   v = quo_name(quo_squash(v))
-  gsub('^c\\(|`|\\)$', '', v) %>% 
-    strsplit(', ') %>% 
-    unlist 
+  gsub('^c\\(|`|\\)$', '', v) |> 
+    strsplit(', ') |> 
+    unlist()
 }
 
 #' @importFrom magrittr equals
@@ -29,7 +29,7 @@ get_specific_annotation_columns = function(.data, .col){
   .col = enquo(.col)
   
   # x-annotation df
-  n_x = .data %>% distinct_at(vars(!!.col)) %>% nrow
+  n_x = .data |> distinct_at(vars(!!.col)) |> nrow()
   
   # element wise columns
   .data = 
@@ -62,20 +62,24 @@ get_specific_annotation_columns = function(.data, .col){
 #' @importFrom rlang quo_is_null
 #' @importFrom rlang quo_is_symbolic
 .as_matrix = function(.data, rownames = NULL, do_check = TRUE, sep_rownames = "___") {
+  
   # Comply with CRAN NOTES
   variable = NULL
+  rn = NULL
   
   rownames = enquo(rownames)
   
   # Process data based on conditions
   if (do_check) {
+    .data_check = .data
+    
     if (!quo_is_null(rownames)) {
       # If rownames are not null, select columns except rownames
-      .data <- .data |> select(-!!rownames)
+      .data_check <- .data_check |> select(-!!rownames)
     }
     
     # Check for non-numeric columns
-    if (any(!unique(.data |> summarise_all(class) |> gather(variable, class) |> pull(class)) %in% c("numeric", "integer"))) {
+    if (any(!unique(.data_check |> summarise_all(class) |> gather(variable, class) |> pull(class)) %in% c("numeric", "integer"))) {
       warning("tidygate says: there are NON-numerical columns, the matrix will NOT be numerical")
     }
   }
@@ -85,6 +89,8 @@ get_specific_annotation_columns = function(.data, .col){
     .data <- .data |> unite(col = "rn", !!rownames, sep = sep_rownames)
   }
   
+  .data = .data |>  as.data.frame()
+  
   # Convert to data frame and then to matrix, handling rownames if present
   if (!quo_is_null(rownames)) {
     .data <- .data |> 
@@ -109,7 +115,7 @@ get_specific_annotation_columns = function(.data, .col){
 quo_names <- function(v) {
   
   v = quo_name(quo_squash(v))
-  gsub('^c\\(|`|\\)$', '', v) %>% 
-    strsplit(', ') %>% 
-    unlist 
+  gsub('^c\\(|`|\\)$', '', v) |> 
+    strsplit(', ') |> 
+    unlist()
 }
\ No newline at end of file
diff --git a/R/utilities.R b/R/utilities.R
index 16261ed..feb9158 100755
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -46,10 +46,10 @@ check_data_unique = function(.data, .element, .dim1, .dim2) {
 reattach_internals = function(.data,
                               .data_internals_from = NULL,
                               .name = "gate") {
-  if (.data_internals_from %>% is.null)
+  if (.data_internals_from |> is.null())
     .data_internals_from = .data
   
-  .data %>% add_attr(.data_internals_from %>% attr(.name), .name)
+  .data |> add_attr(.data_internals_from |> attr(.name), .name)
 }
 
 #' Add attribute to abject
@@ -67,6 +67,7 @@ add_attr = function(var, attribute, name) {
   var
 }
 
+#' @importFrom utils capture.output
 check_dimensions = function(.data, .dim1, .dim2) {
   .dim1 = enquo(.dim1)
   .dim2 = enquo(.dim2)
@@ -101,12 +102,12 @@ format_gatepoints = function(.data, .element, name, .idx) {
   # Column name
   .element = enquo(.element)
   
-  .data %>%
-    as.character %>%
-    as_tibble() %>%
+  .data |>
+    as.character() |>
+    as_tibble() |>
     
     # Reconstitute columns
-    separate(value, quo_names(.element), sep = "___") %>%
+    separate(value, quo_names(.element), sep = "___") |>
     
     mutate(!!as.symbol(sprintf("%s%s", name, .idx)) := .idx)
 }
diff --git a/man/gate_chr-methods.Rd b/man/gate_chr-methods.Rd
index a8f71c1..a4b591b 100644
--- a/man/gate_chr-methods.Rd
+++ b/man/gate_chr-methods.Rd
@@ -73,8 +73,8 @@ This function allow the user to label data points in inside one or more 2D gates
 
   if(interactive()){
 
- tidygate::tidygate_data  \%>\%
- distinct(`ct 1` , `ct 2`, Dim1, Dim2) \%>\%
+ tidygate::tidygate_data  |>
+ distinct(`ct 1` , `ct 2`, Dim1, Dim2) |>
  mutate(gate = gate_chr( Dim1, Dim2)) 
 
   }
@@ -86,13 +86,13 @@ library(dplyr)
 
 # Standard use - programmatic
 res_distinct =
- tidygate::tidygate_data  \%>\%
- distinct(`ct 1` , `ct 2`, Dim1, Dim2) \%>\%
+ tidygate::tidygate_data  |>
+ distinct(`ct 1` , `ct 2`, Dim1, Dim2) |>
  mutate(gate = gate_chr( Dim1, Dim2,gate_list = tidygate::gate_list)) 
 
 # Grouping - programmatic
 res =
- tidygate::tidygate_data  \%>\%
+ tidygate::tidygate_data  |>
    mutate(gate = gate_chr( 
      Dim1, Dim2,
      .group_by = c(`ct 1` , `ct 2`), 
diff --git a/tests/testthat/test-methods.R b/tests/testthat/test-methods.R
index 656bcd8..e0b1228 100755
--- a/tests/testthat/test-methods.R
+++ b/tests/testthat/test-methods.R
@@ -3,8 +3,8 @@
 # test_that("gate dimensions", {
 # library(dplyr)
 # res =
-# tidygate::tidygate_data %>%
-#  mutate(sh = factor(hierarchy)) %>%
+# tidygate::tidygate_data |>
+#  mutate(sh = factor(hierarchy)) |>
 #   mutate(
 #     gate =  gate_chr(
 #       Dim1, Dim2,
@@ -17,8 +17,8 @@
 
 #   
 #   res2 =
-#     tidygate::tidygate_data  %>%
-#     mutate(sh = factor(hierarchy)) %>%
+#     tidygate::tidygate_data  |>
+#     mutate(sh = factor(hierarchy)) |>
 #     gate(
 #       .element = c(`ct 1`, `ct 2`),
 #       Dim1, Dim2,
@@ -33,8 +33,8 @@ test_that("gate dimensions", {
   library(dplyr)
 
   res =
-    tidygate::tidygate_data  %>%
-    distinct(`ct 1` , `ct 2`, Dim1, Dim2) %>%
+    tidygate::tidygate_data  |>
+    distinct(`ct 1` , `ct 2`, Dim1, Dim2) |>
     mutate(gate = gate_chr( Dim1, Dim2,gate_list = tidygate::gate_list))
     
   
@@ -42,8 +42,8 @@ test_that("gate dimensions", {
   
   
   res =
-    tidygate::tidygate_data  %>%
-    distinct(`ct 1` , `ct 2`, Dim1, Dim2) %>%
+    tidygate::tidygate_data  |>
+    distinct(`ct 1` , `ct 2`, Dim1, Dim2) |>
     mutate(gate = gate_int(Dim1, Dim2, gate_list = tidygate::gate_list))
   
   expect_equal(ncol(res) , 5)
@@ -54,13 +54,13 @@ test_that("gate grouping", {
   library(dplyr)
   
   res_distinct =
-    tidygate::tidygate_data  %>%
-    distinct(`ct 1` , `ct 2`, Dim1, Dim2) %>%
+    tidygate::tidygate_data  |>
+    distinct(`ct 1` , `ct 2`, Dim1, Dim2) |>
     mutate(gate = gate_chr( Dim1, Dim2,gate_list = tidygate::gate_list)) 
   
   res =
-    tidygate::tidygate_data  %>%
-    mutate(gate = gate_chr( Dim1, Dim2, .group_by = c(`ct 1` , `ct 2`), gate_list = tidygate::gate_list)) %>%
+    tidygate::tidygate_data  |>
+    mutate(gate = gate_chr( Dim1, Dim2, .group_by = c(`ct 1` , `ct 2`), gate_list = tidygate::gate_list)) |>
     distinct(`ct 1` , `ct 2`, Dim1, Dim2, gate)
   
   

From d1e0d2f2cdc6ae24728e5d028129fcbb50ec6a5e Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Tue, 23 Jan 2024 11:18:43 +1100
Subject: [PATCH 4/5] version UP

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 9c4036c..0fc176f 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: tidygate
 Type: Package
 Title: Add Gate Information to Your Tibble
-Version: 0.4.9
+Version: 0.4.10
 Authors@R: 
     c(person(given = "Stefano",
            family = "Mangiola",

From 5f22c170d0fdcbf25af464c0e9d7d3b822aabdbb Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Tue, 23 Jan 2024 11:21:45 +1100
Subject: [PATCH 5/5] use rworkflows

---
 .github/workflows/R-CMD-check.yaml | 103 -----------------------------
 .github/workflows/rworkflows.yml   |  57 ++++++++++++++++
 2 files changed, 57 insertions(+), 103 deletions(-)
 delete mode 100644 .github/workflows/R-CMD-check.yaml
 create mode 100644 .github/workflows/rworkflows.yml

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
deleted file mode 100644
index 2420e65..0000000
--- a/.github/workflows/R-CMD-check.yaml
+++ /dev/null
@@ -1,103 +0,0 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
-on:
-  push:
-    branches:
-      - dev
-      - master
-  pull_request:
-    branches:
-      - dev
-      - master
-
-name: R-CMD-check
-
-jobs:
-  R-CMD-check:
-    runs-on: ${{ matrix.config.os }}
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
-    strategy:
-      fail-fast: false
-      matrix:
-        config:
-          - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-        # - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-
-    env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
-
-    steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@v1
-        with:
-          r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-          _R_CHECK_FORCE_SUGGESTS_ : false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), build_args = "--no-manual", error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-          
-      - name: Install pkgdown
-        if: github.ref == 'refs/heads/master' && runner.os == 'Linux'
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown")
-        shell: Rscript {0}
-        
-      - name: Install package
-        if: github.ref == 'refs/heads/master' && runner.os == 'Linux'
-        run: R CMD INSTALL .
-
-      - name: Deploy package
-        if: github.ref == 'refs/heads/master' && runner.os == 'Linux'
-        run: |
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
-        shell: bash {0}
-          
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml
new file mode 100644
index 0000000..94d43eb
--- /dev/null
+++ b/.github/workflows/rworkflows.yml
@@ -0,0 +1,57 @@
+name: rworkflows
+'on':
+  push:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+  pull_request:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+jobs:
+  rworkflows:
+    permissions: write-all
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          bioc: devel
+          r: auto
+          cont: ghcr.io/bioconductor/bioconductor_docker:devel
+          rspm: ~
+        - os: macOS-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+        - os: windows-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+    steps:
+    - uses: neurogenomics/rworkflows@master
+      with:
+        run_bioccheck: ${{ false }}
+        run_rcmdcheck: ${{ true }}
+        as_cran: ${{ true }}
+        run_vignettes: ${{ true }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ true }}
+        run_pkgdown: ${{ true }}
+        has_runit: ${{ false }}
+        has_latex: ${{ false }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ false }}
+        DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
+        runner_os: ${{ runner.os }}
+        cache_version: cache-v1
+        docker_registry: ghcr.io