From af863009d05b74d363e8ca4e4c5080d54d38a23c Mon Sep 17 00:00:00 2001
From: David Dorchies <david.dorchies@inrae.fr>
Date: Thu, 31 Aug 2023 18:39:35 +0200
Subject: [PATCH] fix: bugs in render_reports
---
R/render_report.R | 15 ++++++++-------
R/render_reports.R | 28 +++++++++++++---------------
man/render_reports.Rd | 25 +++++++++++++++++--------
3 files changed, 38 insertions(+), 30 deletions(-)
diff --git a/R/render_report.R b/R/render_report.R
index 436e1a2..a6f215a 100644
--- a/R/render_report.R
+++ b/R/render_report.R
@@ -1,7 +1,8 @@
#' @rdname render_reports
+#' @inheritParams bookdown::render_book
#' @export
-render_report <- function(path_report,
- path_publish,
+render_report <- function(input,
+ output_dir,
output_format = Sys.getenv("BOOKDOWN_FORMAT", "bookdown::gitbook"),
clean_cache = FALSE,
...) {
@@ -11,23 +12,23 @@ render_report <- function(path_report,
if (output_format == "bookdown::pdf_book") {
if (!require("tinytex")) install.packages("tinytex")
}
+ message("output_format=", output_format)
if (clean_cache) {
- cache_dir <- list.files(path = path,
+ cache_dir <- list.files(path = input,
pattern = "_cache$",
include.dirs = TRUE,
full.names = TRUE)
unlink(cache_dir, recursive = TRUE)
}
cfg_bookdown <-
- yaml::read_yaml(file.path(path, "_bookdown.yml"))
- unlink(file.path(path, paste0(cfg_bookdown$book_filename, ".*")))
- output_dir <- file.path(path_publish, file)
+ yaml::read_yaml(file.path(input, "_bookdown.yml"))
+ unlink(file.path(input, paste0(cfg_bookdown$book_filename, ".*")))
dir.create(output_dir,
recursive = TRUE,
showWarnings = FALSE)
attached_packages <- (.packages())
- bookdown::render_book(path,
+ bookdown::render_book(input,
output_format = output_format,
output_dir = output_dir,
envir = new.env(),
diff --git a/R/render_reports.R b/R/render_reports.R
index 72fb582..78dd7bf 100644
--- a/R/render_reports.R
+++ b/R/render_reports.R
@@ -1,9 +1,9 @@
#' Render reports
#'
-#' @param path_reports [character] path for the reports
-#' @param path_report [character] report path
+#' @param reports_dir [character] path for the reports
#' @param reports [character] subfolders containing each report
-#' @param path_publish [character] rendering output path
+#' @param publish_dir [character] rendering output path relatively to the report
+#' folder which is in format `"./reports/my_report"`
#' @param output_format output format, see [bookdown::render_book]. Only
#' `"bookdown::gitbook"` and `"bookdown::pdf_book"` are currently handled
#' @param clean_cache [logical] clean Rmarkdown cache files
@@ -14,26 +14,24 @@
#' @rdname render_reports
#'
#' @examples
-render_reports <- function(path_reports = "./reports",
- reports = list.files(path_reports, pattern = "^[0-9]{2}-.*$"),
- path_publish = "./public/reports",
+render_reports <- function(reports_dir = "./reports",
+ reports = list.dirs(reports_dir),
+ publish_dir = "../../public/reports",
...) {
-
-
-
options(knitr.duplicate.label = 'allow')
- message("output_format=", output_format)
message("folder list:")
- invisible(sapply(files, message))
+ invisible(sapply(reports, message))
- for(file in files){
+ for(report in reports){
message("*******************************************************************")
- message("** RENDER ", file)
+ message("** RENDER ", report)
message("*******************************************************************")
- path <- file.path(path_reports, file)
- render_report()
+ path <-
+ render_report(input = file.path(reports_dir, report),
+ output_dir = file.path(publish_dir, report),
+ ...)
}
NULL
}
diff --git a/man/render_reports.Rd b/man/render_reports.Rd
index 25e6d56..851d69d 100644
--- a/man/render_reports.Rd
+++ b/man/render_reports.Rd
@@ -6,24 +6,31 @@
\title{Render reports}
\usage{
render_report(
- path_report,
- path_publish,
+ input,
+ output_dir,
output_format = Sys.getenv("BOOKDOWN_FORMAT", "bookdown::gitbook"),
clean_cache = FALSE,
...
)
render_reports(
- path_reports = "./reports",
- reports = list.files(path_reports, pattern = "^[0-9]{2}-.*$"),
- path_publish = "./public/reports",
+ reports_dir = "./reports",
+ reports = list.files(reports_dir, pattern = "^[0-9]{2}-.*$"),
+ publish_dir = "./public/reports",
...
)
}
\arguments{
-\item{path_report}{\link{character} report path}
+\item{input}{A directory, an input filename or multiple filenames. For a
+directory, \file{index.Rmd} will be used if it exists in this (book)
+project directory. For filenames, if \code{preview = TRUE}, only files
+specified in this argument are rendered, otherwise all R Markdown files
+specified by the book are rendered.}
-\item{path_publish}{\link{character} rendering output path}
+\item{output_dir}{The output directory. If \code{NULL}, a field named
+\code{output_dir} in the configuration file \file{_bookdown.yml} will be
+used (possibly not specified, either, in which case a directory name
+\file{_book} will be used).}
\item{output_format}{output format, see \link[bookdown:render_book]{bookdown::render_book}. Only
\code{"bookdown::gitbook"} and \code{"bookdown::pdf_book"} are currently handled}
@@ -32,9 +39,11 @@ render_reports(
\item{...}{Parameters passed to \link{render_report} and \link[bookdown:render_book]{bookdown::render_book}}
-\item{path_reports}{\link{character} path for the reports}
+\item{reports_dir}{\link{character} path for the reports}
\item{reports}{\link{character} subfolders containing each report}
+
+\item{publish_dir}{\link{character} rendering output path}
}
\value{
\code{NULL}, this function is used for side effect.
--
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