setup.R

# Learnitdown configuration and functions
learnitdown <- list(
  baseurl = "https://wp.sciviews.org", # The base URL for the site
  imgbaseurl =
    "https://filedn.com/lzGVgfOGxb6mHFQcRn9ueUb/sdd-umons", # The base URL for external (big) images
  shiny_imgdir = "images/shinyapps",   # The Shiny image directory (screenshots)
  svbox = 2024,                        # The SciViews Box version used
  rstudio = "start_rstudio2024.html",  # Run Rstudio from the box
  package = "BioDataScience1",         # Associated package for the exercises
  institutions = "UMONS",              # Known institutions
  courses = c(
    "S-BIOG-006",                      # SDD1 Q1 Mons
    "S-BIOG-027" #,                      # SDD1 Q2 Mons
    #"S-BIOG-921"                       # SDD1 Charleroi
  ),
  courses_names = c(
    "Science des Données Biologiques I : visualisation à l'UMONS",
    "Science des Données Biologiques I : inférence à l'UMONS" #,
    #"Bio-Informatique et Science des Données à Charleroi"
  ),
  acad_year = "2024-2025",               # The academic year
  YY = 24,                               # The academic year short id
  W = as.Date("2024-09-08") + (0:37)*7,  # Sundays before each academic week
  Q1 = as.Date("2024-09-08") + (0:15)*7, # There are 15 weeks at Q1
  Q2 = as.Date("2025-02-02") + c(0:11, 14:16)*7 # Q2 starts 02/02 w22 but w33-34 are holidays
)

# We use glue() often for variables replacement from learnitdown, so, we
# define the `!` operator for character objects to glue the string
# Cons: it slightly slows down the usual `!` operator (10x slower)
`!` <- function(x) {
  if (is.character(x)) {
    as.character(glue::glue_data(learnitdown, x))
  } else {# Usual ! operator
    .Primitive('!')(x)
  }
}

# Examples:
#!"svbox{svbox} is for academic year {acad_year}"
#  -> svbox2024 is for academic year 2024-2025
#microbenchmark::microbenchmark(!TRUE, .Primitive('!')(TRUE), .Primitive('!'))

# Unary + binary + is nice too, but it slows down additions!
# We use glue() often for variables replacement from learnitdown, so, we
# redefine the unary and binary `+` operators for character objects
#`+` <- function(e1, e2) {
#  if (missing(e2)) {# Unary operator
#    if (inherits(e1, "character")) {
#      glue::glue_data(learnitdown, e1)
#    } else {# Usual + operator
#      .Primitive("+")(e1)
#    }
#      glue::glue_data(learnitdown, e1)
#  } else {# Binary operator
#    if (inherits(e1, "character")) {
#      glue::as_glue(paste0(e1, glue::glue_data(learnitdown, e2)))
#    } else {# Usual + operator
#      .Primitive("+")(e1, e2)
#    }
#  }
#}
# Examples:
#+"svbox{svbox} is for academic year {acad_year}"
#  -> svbox2024 is for academic year 2024-2025
#+"svbox{svbox}" + " is for" + " academic year {acad_year}"
#  -> same result
# With the new R 4.0 character strings syntax:
#+r"("{courses[1]}" est le cours de {courses_names[1]})"
#  -> "S-BIOG-015" est le cours de Science des Données Biologiques II à l'UMONS
# Date are better defined according to the academic calendar. So, W[1]+1 is
# monday of first week and W[15]+5 is friday of last Q1 week
#+"Q1 starts {W[1]+1} 08:15:00 and ends {W[15]+5} 17:45:00"
#  -> Q1 starts 2021-09-13 08:15:00 and ends 2021-12-24 17:45:00

## Big images (animated gifs, ...) are stored externally, refer them this way:
#
# `r img("sub_dir", "image_name.gif")`
# or to add a caption (use ''' instead of ` if you need it in your caption):
# # `r img("sub_dir", "image_name.gif", caption = "A nice picture.")`

## h5p(), launch_shiny(), learnr() & assignation() for exercises blocks, use:
#
# `r h5p(x, toc = "Short description")`
#
# `r launch_shiny(url, toc = "Short description")`
#
# `r learnr(id, title = "...", toc = "Short description")`
#
#```{r assign_A01Ia_markdown, echo=FALSE, results='asis'}
#if (exists("assignment"))
#  assignment("A01Ia_markdown", part = NULL,
#    url = "https://github.com/BioDataScience-Course/A01Ia_markdown",
#    course.ids = c(
#      'S-BIOG-015'         = +"A01Ia_{YY}M_markdown",
#      'S-BIOG-937-958-959' = +"A01Ia_{YY}C_markdown",
#      'late_mons'          = +"A01Ia_{YY}M_markdown"),
#    course.urls = c(
#      'S-BIOG-015'         = "https://classroom.github.com/a/...",
#      'S-BIOG-937-958-959' = "https://classroom.github.com/a/...",
#      'late_mons'          = "https://classroom.github.com/a/..."),
#    course.starts = c(
#      'S-BIOG-015'         = +"{W[1]+1} 08:00:00",
#      'S-BIOG-937-958-959' = NA, # Nondefined date, or just ignore it
#      'sdd1late'           = +"{W[1]+1} 08:00:00"),
#    course.ends = c(
#      'S-BIOG-015'         = +"{W[3]+5} 23:59:59",
#      'sdd1late'           = +"{W[5]+5} 23:59:59"),
#    term = "Q1", level = 3,
#    toc = "Réalisation d'un premier document en Markdown")
#```
# Use assignment2() for group assignment, and challenge() or challenge2()
# for assignments that are linked to challenges
#
# Then, at the end of the module, create the exercises toc with:
#
# `r show_ex_toc()`
#
# Use `r learnitdown::clean_ex_toc()` at the beginning of index.Rmd to
# make sure the ex dir is clean when the book compiles

img <- function(..., caption = "") {
  path <- paste(learnitdown$imgbaseurl, ..., sep = "/")
  # Cannot use ` inside R code => use ''' instead
  caption <- gsub("'''", "`", caption)
  paste0("![", caption, "](", path, ")")
}

h5p <- function(id, toc = "", ...)
  learnitdown::h5p(id, toc = toc, baseurl = learnitdown$baseurl,
    toc.def = "Exercice H5P {id}",
    h5p.img = "images/list-h5p.png",
    h5p.link = paste(learnitdown$baseurl, "h5p", sep = "/"), ...)

launch_shiny <- function(url, toc = "", fun = paste(learnitdown$package, "run_app", sep = "::"),
  #ENalt1 = "*Click to start the Shiny application*",
  alt1 = "*Cliquez pour lancer l'application Shiny.*",
  #ENalt2 = "*Click to start or [run `{run.cmd}`]({run.url}{run.arg}) in RStudio.*",
  alt2 = "*Cliquez pour lancer ou [exécutez dans RStudio]({run.url}{run.arg}){{target=\"_blank\"}} `{run.cmd}`.*", ...)
  learnitdown::launch_shiny(url = url, toc = toc, imgdir = learnitdown$shiny_imgdir,
    fun = fun, alt1 = alt1, alt2 = alt2, toc.def = "Application Shiny {app}",
    run.url = paste(learnitdown$baseurl, "/", learnitdown$rstudio,  "?runrcode=", sep = ""),
    app.img = "images/list-app.png",
    app.link = paste(learnitdown$baseurl, "shiny_app", sep = "/"), ...)

launch_report <- function(module, course = "S-BIOG-006", toc = NULL, fun = NULL,
  #ENalt1 = "*Click to see the progress report.*",
  alt1 = "*Cliquez pour visualiser le rapport de progression.*",
  #ENalt2 = "*Click to calculate your progress report for this module.*",
  alt2 = "*Cliquez pour calculer votre rapport de progression pour ce module.*",
  height = 800, ...)
  learnitdown::launch_shiny(url =
      paste0("https://sdd.umons.ac.be/sdd-progress-report?course=", course,
        "&module=", module),
    toc = toc, imgdir = learnitdown$shiny_imgdir,
    fun = fun, alt1 = alt1, alt2 = alt2, toc.def = "Progress report {app}",
    run.url = paste(learnitdown$baseurl, "/", learnitdown$rstudio,  "?runrcode=", sep = ""),
    app.img = "images/list-app.png",
    app.link = paste(learnitdown$baseurl, "shiny_app", sep = "/"), height = height, ...)

# Note: not used yet!
launch_learnr <- function(url, toc = "", fun = paste(learnitdown$package, "run", sep = "::"), ...)
  launch_shiny(url = url, toc = toc, fun = fun, ...)

learnr <- function(id, title = NULL, toc = "", package = learnitdown$package,
text = "Effectuez maintenant les exercices du tutoriel")
  learnitdown::learnr(id = id, title = title, package = package, toc = toc,
    text = text, toc.def = "Tutoriel {id}",
    rstudio.url = paste(learnitdown$baseurl, learnitdown$rstudio, sep = "/"),
    tuto.img = "images/list-tuto.png",
    tuto.link = paste(learnitdown$baseurl, "tutorial", sep = "/"))

# Note: use course.urls = c(`S-BIOG-006` = "classroom url1", `S-BIOG-921` = "classroom url2"), and url = link to Github template repository for the assignment
assignment <- function(name, url, course.ids = NULL, course.urls = NULL,
  course.starts = NULL, course.ends = NULL, part = NULL, toc = "", clone = TRUE,
  level = 3, n = 1, type = "ind. github", acad_year = !"{acad_year}",
  term = "Q1", texts = learnitdown::assignment_fr())
  learnitdown::assignment(name = name, url = url, course.ids = course.ids,
    course.urls = course.urls, course.starts = course.starts,
    course.ends = course.ends, part = part,
    course.names = stats::setNames(learnitdown$courses_names,
      learnitdown$courses), toc = toc, clone = clone, level = level, n = n,
    type = type, acad_year = acad_year, term = term, texts = texts,
    assign.img = "images/list-assign.png",
    assign.link = paste(learnitdown$baseurl, "github_assignment", sep = "/"),
    template = "assignment_fr.html", baseurl = learnitdown$baseurl)

assignment2 <- function(name, url, course.ids = NULL, course.urls = NULL,
  course.starts = NULL, course.ends = NULL, part = NULL, toc = "", clone = TRUE,
  level = 4, n = 2, type = "group github", acad_year = !"{acad_year}",
  term = "Q1", texts = learnitdown::assignment2_fr())
  learnitdown::assignment2(name = name, url = url, course.ids = course.ids,
    course.urls = course.urls, course.starts = course.starts,
    course.ends = course.ends, part = part,
    course.names = stats::setNames(learnitdown$courses_names,
      learnitdown$courses), toc = toc, clone = clone, level = level, n = n,
    type = type, acad_year = acad_year, term = term, texts = texts,
    assign.img = "images/list-assign2.png",
    assign.link = paste(learnitdown$baseurl, "github_assignment", sep = "/"),
    template = "assignment_fr.html", baseurl = learnitdown$baseurl)

challenge <- function(name, url, course.ids = NULL, course.urls = NULL,
  course.starts = NULL, course.ends = NULL, part = NULL, toc = "", clone = TRUE,
  level = 3, n = 1, type = "ind. challenge", acad_year = !"{acad_year}",
  term = "Q1", texts = learnitdown::challenge_fr())
  learnitdown::challenge(name = name, url = url, course.ids = course.ids,
    course.urls = course.urls, course.starts = course.starts,
    course.ends = course.ends, part = part,
    course.names = stats::setNames(learnitdown$courses_names,
      learnitdown$courses), toc = toc, clone = clone, level = level, n = n,
    type = type, acad_year = acad_year, term = term, texts = texts,
    assign.img = "images/list-challenge.png",
    assign.link = paste(learnitdown$baseurl, "github_challenge", sep = "/"),
    template = "assignment_fr.html", baseurl = learnitdown$baseurl)

challenge2 <- function(name, url, course.ids = NULL, course.urls = NULL,
  course.starts = NULL, course.ends = NULL, part = NULL, toc = "", clone = TRUE,
  level = 4, n = 2, type = "group challenge", acad_year = !"{acad_year}",
  term = "Q1", texts = learnitdown::challenge2_fr())
  learnitdown::challenge2(name = name, url = url, course.ids = course.ids,
    course.urls = course.urls, course.starts = course.starts,
    course.ends = course.ends, part = part,
    course.names = stats::setNames(learnitdown$courses_names,
      learnitdown$courses), toc = toc, clone = clone, level = level, n = n,
    type = type, acad_year = acad_year, term = term, texts = texts,
    assign.img = "images/list-challenge2.png",
    assign.link = paste(learnitdown$baseurl, "github_challenge", sep = "/"),
    template = "assignment_fr.html", baseurl = learnitdown$baseurl)

# Note: use `r learnitdown::clean_ex_toc()` at the beginning of index.Rmd to
# make sure the ex dir is clean when the book compiles.
show_ex_toc <- function(header = "", clear.it = TRUE)
  learnitdown::show_ex_toc(header = header, clear.it = clear.it)

# Include javascript and css code for {learnitdown} additional features
# in style.css and header.html, respectively
learnitdown::learnitdown_init(
  baseurl = learnitdown$baseurl,
  #EN hide.code.msg = "See the code",
  hide.code.msg = "Voir le code",
  institutions = learnitdown$institutions,
  courses = learnitdown$courses)

# Knitr default options
knitr::opts_chunk$set(comment = "#", fig.align = "center")