feat: Add Shiny app structure thanks to golem R package (https://thinkr-open.github.io/golem/)

.Rbuildignore

+^.*\.Rproj$
+^\.Rproj\.user$
+^data-raw$
+dev_history.R
+^dev$
+$run_dev.*
+^LICENSE\.md$
+^CODE_OF_CONDUCT\.md$

.gitignore

+###############################################################################
+
+# Project-specific
+
+# Man pages generated by Roxygen
+man/*.Rd
+/.vscode/
+/NAMESPACE
+
+###############################################################################
+
+# https://raw.githubusercontent.com/github/gitignore/master/R.gitignore
+
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+# pkgdown site
+docs/
+
+inst/doc

CODE_OF_CONDUCT.md

+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards
+of acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies
+when an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at [INSERT CONTACT
+METHOD]. All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0,
+available at https://www.contributor-covenant.org/version/2/0/
+code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at https://
+www.contributor-covenant.org/translations.

DESCRIPTION

+Package: irmara
+Title: Interactive Reservoir MAnagement Risk Assessment
+Version: 0.0.0.9000
+Authors@R: person('David', 'Dorchies', email = 'david.dorchies@inrae.fr', role = c('cre', 'aut'))
+Description: IRMaRA is a R Shiny interface providing probability of failure of flood and drought objective at key locations downstream of the 4 lakes regulating the Seine River.
+License: AGPL-3
+Imports: 
+    config,
+    golem,
+    shiny,
+    processx,
+    attempt,
+    DT,
+    glue,
+    htmltools
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.1.0
+URL: https://gitlab.irstea.fr/in-wop/irmara
+BugReports: https://gitlab.irstea.fr/in-wop/irmara/issues
+Suggests: 
+    testthat

NEWS.md

+# irmara 0.0.0.9000
+
+* Added a `NEWS.md` file to track changes to the package.

R/app_config.R

+#' Access files in the current app
+#' 
+#' @param ... Character vector specifying directory and or file to
+#'     point to inside the current package.
+#' 
+#' @noRd
+app_sys <- function(...){
+  system.file(..., package = "irmara")
+}
+
+
+#' Read App Config
+#' 
+#' @param value Value to retrieve from the config file. 
+#' @param config R_CONFIG_ACTIVE value. 
+#' @param use_parent Logical, scan the parent directory for config file.
+#'     
+#' @importFrom config get
+#' 
+#' @noRd
+get_golem_config <- function(
+  value, 
+  config = Sys.getenv("R_CONFIG_ACTIVE", "default"), 
+  use_parent = TRUE
+){
+  config::get(
+    value = value, 
+    config = config, 
+    # Modify this if your config file is somewhere else:
+    file = app_sys("golem-config.yml"), 
+    use_parent = use_parent
+  )
+}
+

R/app_server.R

+#' The application server-side
+#' 
+#' @param input,output,session Internal parameters for {shiny}. 
+#'     DO NOT REMOVE.
+#' @import shiny
+#' @noRd
+app_server <- function( input, output, session ) {
+  # List the first level callModules here
+
+}

R/app_ui.R

+#' The application User-Interface
+#' 
+#' @param request Internal parameter for `{shiny}`. 
+#'     DO NOT REMOVE.
+#' @import shiny
+#' @noRd
+app_ui <- function(request) {
+  tagList(
+    # Leave this function for adding external resources
+    golem_add_external_resources(),
+    # List the first level UI elements here 
+    fluidPage(
+      h1("irmara")
+    )
+  )
+}
+
+#' Add external Resources to the Application
+#' 
+#' This function is internally used to add external 
+#' resources inside the Shiny application. 
+#' 
+#' @import shiny
+#' @importFrom golem add_resource_path activate_js favicon bundle_resources
+#' @noRd
+golem_add_external_resources <- function(){
+  
+  add_resource_path(
+    'www', app_sys('app/www')
+  )
+ 
+  tags$head(
+    favicon(),
+    bundle_resources(
+      path = app_sys('app/www'),
+      app_title = 'irmara'
+    )
+    # Add here other external resources
+    # for example, you can add shinyalert::useShinyalert() 
+  )
+}
+

R/golem_utils_server.R

+#' Inverted versions of in, is.null and is.na
+#' 
+#' @noRd
+#' 
+#' @examples
+#' 1 %not_in% 1:10
+#' not_null(NULL)
+`%not_in%` <- Negate(`%in%`)
+
+not_null <- Negate(is.null)
+
+not_na <- Negate(is.na)
+
+#' Removes the null from a vector
+#' 
+#' @noRd
+#' 
+#' @example 
+#' drop_nulls(list(1, NULL, 2))
+drop_nulls <- function(x){
+  x[!sapply(x, is.null)]
+}
+
+#' If x is `NULL`, return y, otherwise return x
+#' 
+#' @param x,y Two elements to test, one potentially `NULL`
+#' 
+#' @noRd
+#' 
+#' @examples
+#' NULL %||% 1
+"%||%" <- function(x, y){
+  if (is.null(x)) {
+    y
+  } else {
+    x
+  }
+}
+
+#' If x is `NA`, return y, otherwise return x
+#' 
+#' @param x,y Two elements to test, one potentially `NA`
+#' 
+#' @noRd
+#' 
+#' @examples
+#' NA %||% 1
+"%|NA|%" <- function(x, y){
+  if (is.na(x)) {
+    y
+  } else {
+    x
+  }
+}
+
+#' Typing reactiveValues is too long
+#' 
+#' @inheritParams reactiveValues
+#' @inheritParams reactiveValuesToList
+#' 
+#' @noRd
+rv <- shiny::reactiveValues
+rvtl <- shiny::reactiveValuesToList
+

R/golem_utils_ui.R

+#' Turn an R list into an HTML list
+#'
+#' @param list An R list
+#' @param class a class for the list
+#' 
+#' @return an HTML list
+#' @noRd
+#' 
+#' @examples
+#' list_to_li(c("a","b"))
+#'
+#' @importFrom htmltools tags tagAppendAttributes tagList
+list_to_li <- function(list, class = NULL){
+  if (is.null(class)){
+    tagList(
+      lapply(
+        list, 
+        tags$li
+      )
+    )
+  } else {
+    res <- lapply(
+      list, 
+      tags$li
+    )
+    res <- lapply(
+      res, 
+      function(x) {
+        tagAppendAttributes(
+          x, 
+          class = class
+        )
+      }
+    )
+    tagList(res)
+  }
+  
+}
+
+#' @importFrom htmltools tags tagAppendAttributes tagList
+list_to_p <- function(list, class = NULL){
+  if (is.null(class)){
+    tagList(
+      lapply(
+        list, 
+        tags$p
+      )
+    )
+  } else {
+    res <- lapply(
+      list, 
+      tags$p
+    )
+    res <- lapply(
+      res, 
+      function(x) { 
+        tagAppendAttributes(
+          x, 
+          class = class
+        )
+      }
+    )
+    tagList(res)
+  }
+  
+}
+
+#' @importFrom htmltools tags tagAppendAttributes tagList
+named_to_li <- function(list, class = NULL){
+  if(is.null(class)){
+    res <- mapply(
+      function(x, y){
+        tags$li(
+          HTML(
+            sprintf("<b>%s:</b> %s", y, x)
+          )
+        )
+      },
+      list, 
+      names(list), 
+      SIMPLIFY = FALSE
+    )
+    tagList(res)
+  } else {
+    res <- mapply(
+      function(x, y){
+        tags$li(
+          HTML(
+            sprintf("<b>%s:</b> %s", y, x)
+          )
+        )
+      },
+      list,
+      names(list), 
+      SIMPLIFY = FALSE
+    )
+    res <- lapply(
+      res, 
+      function(x) {
+        tagAppendAttributes(
+          x, 
+          class = class
+        )
+      }
+    )
+    tagList(res)
+  }
+}
+
+#' Remove a tag attribute
+#'
+#' @param tag the tag
+#' @param ... the attributes to remove
+#'
+#' @return a new tag
+#' @noRd
+#' 
+#' @examples
+#' a <- shiny::tags$p(src = "plop", "pouet")
+#' tagRemoveAttributes(a, "src")
+tagRemoveAttributes <- function(tag, ...) {
+  attrs <- as.character(list(...))
+  for (i in seq_along(attrs)) {
+    tag$attribs[[ attrs[i] ]] <- NULL
+  }
+  tag
+}
+
+#' Hide or display a tag
+#' 
+#' @param tag the tag
+#' 
+#' @return a tag
+#' @noRd
+#' 
+#' @examples
+#' ## Hide
+#' a <- shiny::tags$p(src = "plop", "pouet")
+#' undisplay(a)
+#' b <- shiny::actionButton("go_filter", "go")
+#' undisplay(b)
+#' 
+#' @importFrom htmltools tagList
+undisplay <- function(tag) {
+  # if not already hidden
+  if (
+    !is.null(tag$attribs$style) && 
+    !grepl("display:\\s+none", tag$attribs$style)
+  ) {
+    tag$attribs$style <- paste(
+      "display: none;", 
+      tag$attribs$style
+    )
+  } else {
+    tag$attribs$style <- "display: none;"
+  }
+  tag
+}
+
+#' @importFrom htmltools tagList
+display <- function(tag) {
+  if (
+    !is.null(tag$attribs$style) && 
+    grepl("display:\\s+none", tag$attribs$style)
+  ) {
+    tag$attribs$style <- gsub(
+      "(\\s)*display:(\\s)*none(\\s)*(;)*(\\s)*", 
+      "", 
+      tag$attribs$style
+    )
+  }
+  tag
+}
+
+#' Hide an elements by calling jquery hide on it
+#' 
+#' @param id the id of the element to hide
+#' 
+#' @noRd
+#' 
+#' @importFrom htmltools tags
+jq_hide <- function(id) {
+  tags$script(sprintf("$('#%s').hide()", id))
+}
+
+#' Add a red star at the end of the text
+#'
+#' Adds a red star at the end of the text
+#' (for example for indicating mandatory fields).
+#'
+#' @param text the HTLM text to put before the red star
+#'
+#' @return an html element
+#' @noRd
+#' 
+#' @examples
+#' with_red_star("Enter your name here")
+#' 
+#' @importFrom htmltools tags HTML
+with_red_star <- function(text) {
+  htmltools::tags$span(
+    HTML(
+      paste0(
+        text,
+        htmltools::tags$span(
+          style = "color:red", "*"
+        )
+      )
+    )
+  )
+}
+
+
+
+#' Repeat tags$br
+#'
+#' @param times the number of br to return
+#'
+#' @return the number of br specified in times
+#' @noRd
+#' 
+#' @examples
+#' rep_br(5)
+#' 
+#' @importFrom htmltools HTML
+rep_br <- function(times = 1) {
+  HTML(rep("<br/>", times = times))
+}
+
+#' Create an url
+#'
+#' @param url the URL
+#' @param text the text to display
+#'
+#' @return an a tag
+#' @noRd
+#'
+#' @examples
+#' enurl("https://www.thinkr.fr", "ThinkR")
+#' 
+#' @importFrom htmltools tags
+enurl <- function(url, text){
+  tags$a(href = url, text)
+}
+
+#' Columns wrappers
+#' 
+#' These are convenient wrappers around 
+#' `column(12, ...)`, `column(6, ...)`, `column(4, ...)`...
+#' 
+#' @noRd
+#' 
+#' @importFrom shiny column
+col_12 <- function(...){
+  column(12, ...)
+}
+
+#' @importFrom shiny column
+col_10 <- function(...){
+  column(10, ...)
+}
+