In crotman/kludgenudger: support for Bruno Crotman's thesis about kludges in software development

knitr::opts_chunk$set(echo = FALSE, size = "small", warning = FALSE, message = FALSE, cache = FALSE, fig.pos="H")



library(tidyverse)
library(tidymodels)
library(patchwork)
library(ggrepel)

tictoc::tic("compare_versions")
output_function <- compare_versions_read_outside(
  dir_old <- "C:/doutorado/joda-time/joda-time-2.9",
  dir_new <-  "C:/doutorado/joda-time/joda-time-2.10",
  log = "jodatime-2_9-2_10"
)
tictoc::toc()


tictoc::tic("compare_versions")
output_function <- compare_versions_read_outside(
  dir_old <- "C:/doutorado/joda-time/joda-time-2.8",
  dir_new <-  "C:/doutorado/joda-time/joda-time-2.9",
  log = "jodatime-2_8-2_9"
)
tictoc::toc()


tictoc::tic("compare_versions")
output_function <- compare_versions_read_outside(
  dir_old <- "C:/doutorado/joda-time/joda-time-2.7",
  dir_new <-  "C:/doutorado/joda-time/joda-time-2.8",
  log = "jodatime-2_7-2_8"
)
tictoc::toc()



tictoc::tic("compare_versions")
output_function <- compare_versions_read_outside(
  dir_old <- "C:/doutorado/joda-time/joda-time-2.6",
  dir_new <-  "C:/doutorado/joda-time/joda-time-2.7",
  log = "jodatime-2_6-2_7"
)
tictoc::toc()



tictoc::tic("compare_versions")
output_function <- compare_versions_read_outside(
  dir_old <- "C:/doutorado/joda-time/joda-time-2.5",
  dir_new <-  "C:/doutorado/joda-time/joda-time-2.6",
  log = "jodatime-2_5-2_6"
)
tictoc::toc()


tictoc::tic("compare_versions")
output_function <- compare_versions_read_outside(
  dir_old <- "C:/doutorado/joda-time/joda-time-2.4",
  dir_new <-  "C:/doutorado/joda-time/joda-time-2.5",
  log = "jodatime-2_4-2_5"
)
tictoc::toc()


tictoc::tic("compare_versions")
output_function <- compare_versions_read_outside(
  dir_old <- "C:/doutorado/joda-time/joda-time-2.3",
  dir_new <-  "C:/doutorado/joda-time/joda-time-2.4",
  log = "jodatime-2_3-2_4"
)
tictoc::toc()




tictoc::tic("compare_versions")
output_function <- compare_versions_read_outside(
  dir_old <- "C:/doutorado/joda-time/joda-time-2.2",
  dir_new <-  "C:/doutorado/joda-time/joda-time-2.3",
  log = "jodatime-2_2-2_3"
)
tictoc::toc()



tictoc::tic("compare_versions")
output_function <- compare_versions_read_outside(
  dir_old <- "C:/doutorado/joda-time/joda-time-2.1",
  dir_new <-  "C:/doutorado/joda-time/joda-time-2.2",
  log = "jodatime-2_1-2_2"
)
tictoc::toc()




tictoc::tic("compare_versions")
output_function <- compare_versions_read_outside(
  dir_old <- "C:/doutorado/joda-time/joda-time-2.0",
  dir_new <-  "C:/doutorado/joda-time/joda-time-2.1",
  log = "jodatime-2_0-2_1"
)
tictoc::toc()



tictoc::tic("compare_versions")
output_function <- compare_versions_read_outside(
  dir_old <- "C:/doutorado/joda-time/joda-time-1.6",
  dir_new <-  "C:/doutorado/joda-time/joda-time-2.0",
  log = "jodatime-1_6-2_0"
)
tictoc::toc()


tictoc::tic("compare_versions")
output_function <- compare_versions_read_outside(
  dir_old <- "C:/doutorado/joda-time/joda-time-1.5",
  dir_new <-  "C:/doutorado/joda-time/joda-time-1.6",
  log = "jodatime-1_5-1_6"
)
tictoc::toc()


tictoc::tic("compare_versions")
output_function <- compare_versions_read_outside(
  dir_old <- "C:/doutorado/joda-time/joda-time-1.4",
  dir_new <-  "C:/doutorado/joda-time/joda-time-1.5",
  log = "jodatime-1_4-1_5"
)
tictoc::toc()

tictoc::tic("compare_versions")
output_function <- compare_versions_read_outside(
  dir_old <- "C:/doutorado/joda-time/joda-time-1.3",
  dir_new <-  "C:/doutorado/joda-time/joda-time-1.4",
  log = "jodatime-1_3-1_4"
)
tictoc::toc()


tictoc::tic("compare_versions")
output_function <- compare_versions_read_outside(
  dir_old <- "C:/doutorado/joda-time/joda-time-1.2",
  dir_new <-  "C:/doutorado/joda-time/joda-time-1.3",
  log = "jodatime-1_2-1_3"
)
tictoc::toc()





extract_comments_from_directory(
  dir = "C:/doutorado/joda-time/joda-time-2.9",
  dest_file = "comments_jodatime_2_9.rds"
)


extract_comments_from_directory(
  dir = "C:/doutorado/joda-time/joda-time-2.8",
  dest_file = "comments_jodatime_2_8.rds"
)



extract_comments_from_directory(
  dir = "C:/doutorado/joda-time/joda-time-2.7",
  dest_file = "comments_jodatime_2_7.rds"
)



extract_comments_from_directory(
  dir = "C:/doutorado/joda-time/joda-time-2.6",
  dest_file = "comments_jodatime_2_6.rds"
)




extract_comments_from_directory(
  dir = "C:/doutorado/joda-time/joda-time-2.5",
  dest_file = "comments_jodatime_2_5.rds"
)




extract_comments_from_directory(
  dir = "C:/doutorado/joda-time/joda-time-2.4",
  dest_file = "comments_jodatime_2_4.rds"
)




extract_comments_from_directory(
  dir = "C:/doutorado/joda-time/joda-time-2.3",
  dest_file = "comments_jodatime_2_3.rds"
)




extract_comments_from_directory(
  dir = "C:/doutorado/joda-time/joda-time-2.2",
  dest_file = "comments_jodatime_2_2.rds"
)




extract_comments_from_directory(
  dir = "C:/doutorado/joda-time/joda-time-2.1",
  dest_file = "comments_jodatime_2_1.rds"
)




extract_comments_from_directory(
  dir = "C:/doutorado/joda-time/joda-time-2.0",
  dest_file = "comments_jodatime_2_0.rds"
)


extract_comments_from_directory(
  dir = "C:/doutorado/joda-time/joda-time-1.6",
  dest_file = "comments_jodatime_1_6.rds"
)


extract_comments_from_directory(
  dir = "C:/doutorado/joda-time/joda-time-1.5",
  dest_file = "comments_jodatime_1_5.rds"
)


extract_comments_from_directory(
  dir = "C:/doutorado/joda-time/joda-time-1.4",
  dest_file = "comments_jodatime_1_4.rds"
)

extract_comments_from_directory(
  dir = "C:/doutorado/joda-time/joda-time-1.3",
  dest_file = "comments_jodatime_1_3.rds"
)

extract_comments_from_directory(
  dir = "C:/doutorado/joda-time/joda-time-1.2",
  dest_file = "comments_jodatime_1_2.rds"
)



extract_comments_from_directory(
  dir = "C:/doutorado/joda-time/joda-time-1.1",
  dest_file = "comments_jodatime_1_1.rds"
)


extract_comments_from_directory(
  dir = "C:/doutorado/joda-time/joda-time-1.0",   
  dest_file = "comments_jodatime_1.0.rds"
)



extract_comments_from_directory(
  dir = "C:/doutorado/joda-time/joda-time-0.9",
  dest_file = "comments_jodatime_0_9.rds"
)

kludgenudger::save_alerts(
  dir = here::here("joda-time"),
  pattern_versions = "^joda-time-",
  dest_dir = "alerts_jodatime",
  remove_str = "joda-time-",
  string_to_replace = "\\.",
  string_to_replace_with = "_"
)

# rename_file_diff(pattern_diff = "C:/doutorado/joda-time", prefix = "joda-time" )



complement <- tribble(
 ~major_new, ~minor_new ,
 0, 9,
 1, 0,
 1, 1,
 1, 2,
 1, 3,
 1, 4,
 1, 5,
 1, 6,
 2, 0,
 2, 1,
 2, 2,
 2, 3,
 2, 4,
 2, 5,
 2, 6,
 2, 7,
 2, 8,
 2, 9,
 2, 10

) %>% 
  mutate(
    major_old = lag(major_new),
    minor_old = lag(minor_new)
  ) %>%
  filter(
    !is.na(major_old)
  ) %>% 
  mutate(
    file = str_glue("jodatime-{major_old}_{minor_old}-{major_new}_{minor_new}.rds"),
    root_new = str_glue("C:/doutorado/joda-time/joda-time-{major_new}.{minor_new}/"),
    root_old = str_glue("C:/doutorado/joda-time/joda-time-{major_old}.{minor_old}/")
  ) %>% 
  select(
    file, root_new, root_old
  )


generate_diffs_from_versions(
  complement = complement,
  prefix = "jodatime"

)



extract_selected_comments(
  path_to_comments = "comments_joda",
  output = "joda_selected_comments.rds"
)


generate_ast_only_classes(
  dir = "C:/doutorado/joda-time/",
  pattern = "joda-time-.*",
  output_path = "only_classes_jodatime",
  pattern_major_minor_versions = "joda\\-time\\-(.*)\\.(.*)"
)

results_comments <- create_version_comparisons_comment(
  pattern_diff = "jodatime",
  selected_comments_file = "joda_selected_comments.rds",
  dir_only_classes = "only_classes_jodatime",
  pattern_major_minor_versions_only_classes = "([0-9]*)_([0-9]*)"
)

#jodatime
results_alert <- kludgenudger::analyse_alerts_and_categories(
  package_start_outside_read = "\\.*",
  dir_read_all_alerts = here::here("tests/testthat/alerts_jodatime"),
  package_start_read_all_alerts = "\\.*",
  pattern_major_read_all_alerts = "^([0-9]*)[\\._]",
  pattern_minor_read_all_alerts = "^[0-9]*_([0-9]*)",
  prefix = "jodatime"

)


results_comments <- kludgenudger::create_version_comparisons_comment(
  pattern_diff = "jodatime",
  selected_comments_file = "joda_selected_comments.rds",
  dir_only_classes = "only_classes_jodatime",
  pattern_major_minor_versions_only_classes = "([0-9]*)_([0-9]*)"
)

alerts <- results_alert %>% 
  rename_with(
    ~str_glue("{.x}_alerts")
  )


comments <- results_comments %>% 
  rename_with(
    ~str_glue("{.x}_comments")
  ) 


comparison <- alerts %>% 
  inner_join(
    comments,
    by = c(
      "major_version_old_alerts" = "major_version_old_comments" ,
      "minor_version_old_alerts" = "minor_version_old_comments" ,
      "major_version_new_alerts" = "major_version_new_comments" ,
      "minor_version_new_alerts" = "minor_version_new_comments" 
    )
  ) %>% 
  mutate(
    ratio_alerts = new_alerts/(new_alerts + fixed_alerts),
    ratio_comments = new_comments/(new_comments + fixed_comments),
    version = str_glue("{major_version_alerts}.{minor_version_alerts}")
  ) %>% 
  rename_with(
    .cols = matches("_version_"),
    .fn = ~str_remove(.x, pattern = "_alerts")
  )

comparison_prepared <- comparison %>% 
  mutate(
    across(
      .cols = matches("_version_"),
      .fns = ~if_else(.x == 0, NA_character_, as.character(.x) ),
      .names = "{.col}_str"
    )
  ) %>% 
  unite(
    col = version_old_str,
    major_version_old_str,
    minor_version_old_str,
    sep = "."
  ) %>% 
  unite(
    col = version_new_str,
    major_version_new_str,
    minor_version_new_str,
    sep = "."
  ) %>% 
  mutate(
    across(
      .cols = matches("version_(?:new|old)_str"),
      .fns = ~str_remove(.x, ".NA")
    )
  ) %>%
  unite(
    col = "versions_transition",
    sep = " to ",
    version_old_str,
    version_new_str
  ) %>%   
  mutate(
    versions_transition = 
      fct_reorder(
        .f = versions_transition,
        .x = major_version_new * 1000 + minor_version_new
      )
  ) 


comparison_prepared_clean <- comparison_prepared %>% 
  filter(
    !is.nan(ratio_alerts) & !is.nan(ratio_comments)
  )



comparison_fixed_new_alerts <- comparison_prepared %>% 
  select(
    fixed_alerts,
    new_alerts,
    versions_transition
  ) %>% 
  pivot_longer(
    cols = ends_with("_alerts"),
    names_to = c("metric", ".value"),
    names_pattern = "(.*)_(.*)",
    names_transform = list(metric = str_to_title)
  ) 



ggplot_fixed_new <- 
  ggplot(
    data = comparison_fixed_new_alerts,
    aes(
      x = versions_transition,
      y = alerts,  
      color = metric,
      group = metric
    ) 
) +
  geom_line(
    size = 1.2
  ) +
  geom_point(
    size = 2.5
  ) +
  theme_minimal() +
  scale_color_manual(
    values = c(Fixed = "darkgreen", New = "darkred") 
  ) +
  theme(
   axis.text.x = element_text(angle = 90) ,
   legend.position = "top"
  ) +
  scale_y_continuous(
    labels = number_format(big.mark = ","),
    limits = c(0,NA)
  ) +
  ggtitle(
    "Number of fixed/new alerts per version transition"
  ) +
  labs(
    x = "Transition",
    y = "Number of alerts",
    color = "Category"
  )

comparison_fixed_new_comments <- comparison_prepared %>% 
  select(
    fixed_comments,
    new_comments,
    versions_transition
  ) %>% 
  pivot_longer(
    cols = ends_with("_comments"),
    names_to = c("metric", ".value"),
    names_pattern = "(.*)_(.*)",
    names_transform = list(metric = str_to_title)
  ) 


ggplot_fixed_new_comments <- ggplot(comparison_fixed_new_comments,
    aes(
      x = versions_transition,
      y = comments,
      color = metric,
      group = metric
    ) 
) +
  geom_line(
    size = 1.2
  ) +
  geom_point(
    size = 2.5
  ) +
  theme_minimal() +
  scale_color_manual(
    values = c(Fixed = "darkgreen", New = "darkred") 
  ) +
  theme(
   axis.text.x = element_text(angle = 90) ,
   legend.position = "top"
  ) +
  scale_y_continuous(
    labels = number_format(big.mark = ","),
    limits = c(0,NA)
  ) +
  ggtitle(
    "Number of fixed/new comments per version transition"
  ) +
  labs(
    x = "Transition",
    y = "Number of comments",
    color = "Category"
  )



ggplot_total_alerts <- 
  ggplot(comparison_prepared,
    aes(
      x = versions_transition,
      y = n_alerts,
    ) ) +
    geom_line(
      size = 1.2,
      color = "darkblue",
      group = 1,
      aes(
        x = versions_transition,
        y = n_alerts
      )
    ) +
    geom_point(
      size = 2.5,
      color = "darkblue"
    ) +
    theme_minimal() +
    theme(
     axis.text.x = element_text(angle = 90) ,
     legend.position = "top"
    ) +
    scale_y_continuous(
      labels = number_format(big.mark = ","),
      limits = c(0,NA)
    ) +
    ggtitle(
      "Number of total alerts after version transition"
    ) +
    labs(
      x = "Transition",
      y = "Number of alerts"
    )



ggplot_total_comments <- 
  ggplot(comparison_prepared,
    aes(
      x = versions_transition,
      y = n_comments,
    ) ) +
    geom_line(
      size = 1.2,
      color = "darkblue",
      group = 1,
      aes(
        x = versions_transition,
        y = n_comments
      )
    ) +
    geom_point(
      size = 2.5,
      color = "darkblue"
    ) +
    theme_minimal() +
    theme(
     axis.text.x = element_text(angle = 90) ,
     legend.position = "top"
    ) +
    scale_y_continuous(
      labels = number_format(big.mark = ","),
      limits = c(0,NA)
    ) +
    ggtitle(
      "Number of total comments after version transition"
    ) +
    labs(
      x = "Transition",
      y = "Number of comments"
    )


ggplot_total_alerts / ggplot_fixed_new / ggplot_total_comments / ggplot_fixed_new_comments + plot_layout(heights = unit(c(3, 3, 3, 3), c("cm", "cm", "cm", "cm") ), widths = unit(c(15, 15, 15, 15), c("cm", "cm", "cm", "cm") ))

correl_prop <- cor(
  comparison_prepared_clean$ratio_alerts,
  comparison_prepared_clean$ratio_comments
)

ggplot(
  comparison_prepared_clean,
  aes(
    y = ratio_comments ,
    x = ratio_alerts,
  )
  ) +
  geom_point() +
  geom_text_repel(aes(label = versions_transition), nudge_y = 0.05, size = 2) +
  geom_smooth(method = "lm") +
  ggtitle(
    "Proportion of new comments x Proportion of new alerts"
  ) +
  labs(
    y = "Proportion of new alerts",
    x = "Proportion of new comments",
    size = "Change"
  ) +
  scale_x_continuous(
    label = percent_format(), limits = c(0, 1)
  ) +
  scale_y_continuous(
    label = percent_format(), limits = c(0, 1)
  ) +
  scale_size_continuous(
    label = number_format(big.mark = ",", accuracy = 1)
  ) +
  theme_minimal() +
  theme(
    legend.position = "top"
  ) +
  NULL

library(parsnip)
library(gtsummary)

lm_prop <-  linear_reg() %>% 
  set_engine("lm")

lm_prop_fit <- lm_prop %>% 
  fit(ratio_comments ~ ratio_alerts, data = comparison_prepared_clean)

tbl_prop <- tbl_regression(
  lm_prop_fit$fit,
  pvalue_fun = function(x) style_pvalue(x, digits = 2),
  label = ratio_alerts ~ "New Alerts Proportion",
  intercept = TRUE,
) 

tbl_prop %>% 
  as_kable_extra(caption = "\\label{tab_reg} Regression: comments on alerts")

crotman/kludgenudger documentation built on Oct. 19, 2021, 7:30 p.m.