feat: create R project with minimum functions

.Rbuildignore

+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

+
+################################################################################
+# R template from:
+# https://raw.githubusercontent.com/github/gitignore/main/R.gitignore
+# Downloaded the 2023-08-31 11:51:25
+################################################################################
+
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+.RDataTmp
+
+# 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/
+
+# translation temp files
+po/*~
+
+# RStudio Connect folder
+rsconnect/

DESCRIPTION

+Package: fairify
+Title: Produce FAIR reports with Rmarkdown and data in the cloud
+Version: 0.0.0.9000
+Authors@R: 
+    person("David", "Dorchies", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6595-7984"), email = "david.dorchies@inrae.fr")
+Description: R-package proposing a framework to apply FAIR principles based on reports created using the bookdown R-package and published as a website (e.g. gitlab pages) and data located on a owncloud/nextcloud server.
+License: AGPL (>= 3)
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3

NAMESPACE

+# Generated by roxygen2: do not edit by hand
+
+export("%>%")
+export(add_gitignore)
+export(getDataPath)
+export(iconv_filename)
+export(loadConfig)
+importFrom(magrittr,"%>%")

R/add_gitignore.R

+#' Add .gitignore file suitable for R project
+#'
+#' @inheritParams utils:download.file
+#'
+#' @return `NULL`, this function is used for side effect.
+#' @export
+#'
+#' @examples
+#' tmpfile <- tempfile()
+#' add_gitignore(destfile = tmpfile)
+#' readLines(tmpfile)
+add_gitignore <- function(url = "https://raw.githubusercontent.com/github/gitignore/main/R.gitignore",
+                          destfile = ".gitignore") {
+  stopifnot(download.file(url, destfile) == 0)
+  header <- add_comment_block("R template from:",
+                              url,
+                              paste("Downloaded the", Sys.time()))
+  s <- readLines(destfile)
+  s <- c(header, s)
+  writeLines(s, destfile)
+}
+
+add_comment <- function(x, comment_tag = "#") {
+  paste(comment_tag, x)
+}
+
+add_comment_block <- function(..., comment_tag = "#", line_len) {
+  x <- list(...)
+  c("",
+    strrep(comment_tag, 80),
+    sapply(x, add_comment, comment_tag = comment_tag),
+    strrep(comment_tag, 80),
+    "")
+}

R/getDataPath.R

+#' Give the complete path of the data and cache data on local disk
+#'
+#' @description
+#' It supports Nextcloud public links in case of using cloud. In this case,
+#' this function can download the file in a temporary
+#' folder and returns the path of the downloaded file.
+#' This functionality is useful for `read_excel` from the package *readxl*
+#' (See: https://stackoverflow.com/a/41368947/5300212).
+#'
+#' @param path [character] representing the path of the data in the database
+#' @param ... [character] path elements to add after `path`
+#' @param use_cache [logical] download the data and use cache location
+#' @param cfg a config object. Configuration to use. See [loadConfig] for details
+#' @param root [character] URL or path of the database root
+#' @param cache [character] path where downloaded files from cloud are cached (See details)
+#'
+#' @details
+#' The cache directory is by default located in the system temporary folder in a
+#' subdirectory named as the package name or the value of the environment variable
+#' "PKG_DATA_CACHE" if it is defined.
+#'
+#' @return [character] with the path of the file to read either on:
+#' - the local storage if `cfg$data$cloud == FALSE`
+#' - the cache directory if `cfg$data$cloud == FALSE` and `use_cache == TRUE`
+#' - the cloud server if `cfg$data$cloud == FALSE` and `use_cache == FALSE`
+#' @export
+#'
+getDataPath <- function(path,
+                        ...,
+                        use_cache = TRUE,
+                        cfg = loadConfig(),
+                        root = cfg$data$path,
+                        cache = Sys.getenv("PKG_DATA_CACHE",
+                                           file.path(dirname(tempdir()),
+                                                     utils::packageName()))) {
+  path <- file.path(path, ...)
+  stopifnot(is.character(path),
+            length(path) == 1)
+
+  if (cfg$data$cloud) {
+    file <- basename(path)
+    ext <- tools::file_ext(file)
+
+    folder <- dirname(path)
+    # model of link on Nextcloud https://nextcloud.inrae.fr/s/QbwR7yCo2HSDCb9/download?path=hydrometrie&files=Hydrometrie_site.csv
+    query <- file.path(root, "download")
+    query <- urltools::param_set(query,
+                                 key = "path",
+                                 value = urltools::url_encode(folder))
+    query <- urltools::param_set(query,
+                                 key = "files",
+                                 value = urltools::url_encode(file))
+
+    if (use_cache) {
+      exdir <- cache
+      if (folder != ".") {
+        exdir <- file.path(exdir, folder)
+      }
+      dir.create(exdir, showWarnings = FALSE, recursive = TRUE)
+      path <- file.path(exdir, file)
+      if (!file.exists(path)) {
+        if (cfg$data$cloud)
+          message("Download from URL: ", query)
+        resp <- httr::GET(query,
+                          httr::write_disk(path))
+        if (!identical(httr::status_code(resp), 200L)) {
+          stop("Error ", httr::status_code(resp), " on query ", query)
+        }
+        if (ext == "") {
+          # Folder in ZIP format
+          zipfile <- paste(path, "zip", sep = ".")
+          file.rename(path, zipfile)
+          utils::unzip(zipfile, exdir = exdir)
+        }
+      }
+      return(path)
+    } else {
+      return(query)
+    }
+  } else {
+    return(file.path(root, path))
+  }
+}

R/iconv_filename.R

+#' Convert a string to a compatible file name
+#'
+#' It removes accents and converts spaces and other special characters to an underscore.
+#'
+#' @param name [character] string to convert
+#'
+#' @return The converted [character] string.
+#' @export
+#'
+#' @examples
+#' iconv_filename("We don't like (wéïrd) àcçênts. And other things like $?€#%")
+iconv_filename <- function(name) {
+  s <-purge_string(name)
+  s <- gsub(" +", "_", s)
+  s <- gsub("?", "", s, fixed = TRUE)
+  gsub('(_)\\1+', '\\1', s)
+}

R/loadConfig.R

+#' Read default configuration of the package and complete it with eventual user config
+#'
+#' @param userFile location of the user config YML file
+#' @param pathDefaultCfg The location of the default configuration (located in "inst/config.yml" of the package by default)
+#'
+#' @return A configuration as it is returned by [config::get]
+#' @export
+#'
+#' @examples
+#' cfg <- loadConfig()
+#' str(cfg)
+loadConfig <- function(userFile = "config.yml", pathDefaultCfg = system.file("config.yml", package = "TalanoaHydro")) {
+  cfg <- config::get(file = pathDefaultCfg)
+  if (file.exists(userFile)) {cfg = config::merge(cfg,config::get(file = userFile))}
+  # By default results are written in the DB if the DB is local
+  if (is.null(cfg$data$write_results)) cfg$data$write_results <- !cfg$data$cloud
+  cfg
+}

R/utils-pipe.R

+#' Pipe operator
+#'
+#' See \code{magrittr::\link[magrittr:pipe]{\%>\%}} for details.
+#'
+#' @name %>%
+#' @rdname pipe
+#' @keywords internal
+#' @export
+#' @importFrom magrittr %>%
+#' @usage lhs \%>\% rhs
+#' @param lhs A value or the magrittr placeholder.
+#' @param rhs A function call using the magrittr semantics.
+#' @return The result of calling `rhs(lhs)`.
+NULL

fairify.Rproj

+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

man/add_gitignore.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/add_gitignore.R
+\name{add_gitignore}
+\alias{add_gitignore}
+\title{Add .gitignore file suitable for R project}
+\usage{
+add_gitignore(
+  url = "https://raw.githubusercontent.com/github/gitignore/main/R.gitignore",
+  destfile = ".gitignore"
+)
+}
+\value{
+\code{NULL}, this function is used for side effect.
+}
+\description{
+Add .gitignore file suitable for R project
+}
+\examples{
+tmpfile <- tempfile()
+add_gitignore(destfile = tmpfile)
+readLines(tmpfile)
+}

man/getDataPath.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/getDataPath.R
+\name{getDataPath}
+\alias{getDataPath}
+\title{Give the complete path of the data and cache data on local disk}
+\usage{
+getDataPath(
+  path,
+  ...,
+  use_cache = TRUE,
+  cfg = loadConfig(),
+  root = cfg$data$path,
+  cache = Sys.getenv("PKG_DATA_CACHE", file.path(dirname(tempdir()),
+    utils::packageName()))
+)
+}
+\arguments{
+\item{path}{\link{character} representing the path of the data in the database}
+
+\item{...}{\link{character} path elements to add after \code{path}}
+
+\item{use_cache}{\link{logical} download the data and use cache location}
+
+\item{cfg}{a config object. Configuration to use. See \link{loadConfig} for details}
+
+\item{root}{\link{character} URL or path of the database root}
+
+\item{cache}{\link{character} path where downloaded files from cloud are cached (See details)}
+}
+\value{
+\link{character} with the path of the file to read either on:
+\itemize{
+\item the local storage if \code{cfg$data$cloud == FALSE}
+\item the cache directory if \code{cfg$data$cloud == FALSE} and \code{use_cache == TRUE}
+\item the cloud server if \code{cfg$data$cloud == FALSE} and \code{use_cache == FALSE}
+}
+}
+\description{
+It supports Nextcloud public links in case of using cloud. In this case,
+this function can download the file in a temporary
+folder and returns the path of the downloaded file.
+This functionality is useful for \code{read_excel} from the package \emph{readxl}
+(See: https://stackoverflow.com/a/41368947/5300212).
+}
+\details{
+The cache directory is by default located in the system temporary folder in a
+subdirectory named as the package name or the value of the environment variable
+"PKG_DATA_CACHE" if it is defined.
+}

man/iconv_filename.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/iconv_filename.R
+\name{iconv_filename}
+\alias{iconv_filename}
+\title{Convert a string to a compatible file name}
+\usage{
+iconv_filename(name)
+}
+\arguments{
+\item{name}{\link{character} string to convert}
+}
+\value{
+The converted \link{character} string.
+}
+\description{
+It removes accents and converts spaces and other special characters to an underscore.
+}
+\examples{
+iconv_filename("We don't like (wéïrd) àcçênts. And other things like $?€#\%")
+}

man/loadConfig.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/loadConfig.R
+\name{loadConfig}
+\alias{loadConfig}
+\title{Read default configuration of the package and complete it with eventual user config}
+\usage{
+loadConfig(
+  userFile = "config.yml",
+  pathDefaultCfg = system.file("config.yml", package = "TalanoaHydro")
+)
+}
+\arguments{
+\item{userFile}{location of the user config YML file}
+
+\item{pathDefaultCfg}{The location of the default configuration (located in "inst/config.yml" of the package by default)}
+}
+\value{
+A configuration as it is returned by \link[config:get]{config::get}
+}
+\description{
+Read default configuration of the package and complete it with eventual user config
+}
+\examples{
+cfg <- loadConfig()
+str(cfg)
+}

man/pipe.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils-pipe.R
+\name{\%>\%}
+\alias{\%>\%}
+\title{Pipe operator}
+\usage{
+lhs \%>\% rhs
+}
+\arguments{
+\item{lhs}{A value or the magrittr placeholder.}
+
+\item{rhs}{A function call using the magrittr semantics.}
+}
+\value{
+The result of calling \code{rhs(lhs)}.
+}
+\description{
+See \code{magrittr::\link[magrittr:pipe]{\%>\%}} for details.
+}
+\keyword{internal}