From 43daa194508726230ad4b81eebb4cda318cb3268 Mon Sep 17 00:00:00 2001
From: David Dorchies <david.dorchies@inrae.fr>
Date: Tue, 26 Mar 2024 18:44:10 +0100
Subject: [PATCH 1/5] feat: add_article
Refs #29
---
DESCRIPTION | 2 ++
NAMESPACE | 1 +
R/add_article.R | 44 +++++++++++++++++++++++++++++++
R/add_report.R | 6 ++---
R/create_reports.R | 9 ++++++-
R/list_reports.R | 9 ++++++-
R/render_report.R | 23 ++++++++++++----
man/add_article.Rd | 38 ++++++++++++++++++++++++++
man/create_reports.Rd | 2 +-
tests/testthat/test-add_article.R | 23 ++++++++++++++++
10 files changed, 145 insertions(+), 12 deletions(-)
create mode 100644 R/add_article.R
create mode 100644 man/add_article.Rd
create mode 100644 tests/testthat/test-add_article.R
diff --git a/DESCRIPTION b/DESCRIPTION
index ea0976f..f4e591a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -23,6 +23,7 @@ Imports:
pkgload,
readr,
rlang,
+ rticles,
stringr,
this.path,
urltools,
@@ -31,6 +32,7 @@ Imports:
yaml,
zlib
Suggests:
+ rmarkdown,
testthat (>= 3.0.0),
tinytex
Config/testthat/edition: 3
diff --git a/NAMESPACE b/NAMESPACE
index ba18baf..43ac795 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,6 +1,7 @@
# Generated by roxygen2: do not edit by hand
export("%>%")
+export(add_article)
export(add_gitignore)
export(add_report)
export(build_site)
diff --git a/R/add_article.R b/R/add_article.R
new file mode 100644
index 0000000..e17d3ce
--- /dev/null
+++ b/R/add_article.R
@@ -0,0 +1,44 @@
+#' Add a new article in a fairify project
+#'
+#' This function prepares an article with a template provided by the **rticles**
+#' package.
+#'
+#' @details
+#' This function uses [rmardown::draft] for creating the new document based on
+#' a template, so its uses is theoritically not limited to the templates
+#' provided by the **rticles** package.
+#'
+#' @inheritParams add_report
+#' @inheritParams rmarkdown::draft
+#'
+#' @return Used for side effect.
+#' @export
+#'
+#' @examples
+add_article <- function(name,
+ template,
+ package = "rticles",
+ path = pkgload::pkg_path(),
+ edit = FALSE) {
+ stopifnot(template %in% rticles::journals())
+
+ # reports folder handling
+ check_reports_folder(path)
+
+ destpath <- file.path(path, "reports", name)
+ if (dir.exists(destpath))
+ stop("The folder ",
+ destpath,
+ " exists already. Delete it first or choose another.")
+ dir.create(destpath)
+
+ owd <- setwd(destpath)
+ on.exit(setwd(owd))
+ rmarkdown::draft("index.Rmd",
+ template = template,
+ package = package,
+ create_dir = FALSE,
+ edit = edit)
+
+ invisible()
+}
diff --git a/R/add_report.R b/R/add_report.R
index a71d30a..4db5cc7 100644
--- a/R/add_report.R
+++ b/R/add_report.R
@@ -16,10 +16,8 @@ add_report <- function(name,
lang = "english",
path = pkgload::pkg_path()) {
# reports folder handling
- if (!dir.exists(file.path(path, "reports"))) {
- message("Creating reports folder in: ", path, "...")
- create_reports(path)
- }
+ check_reports_folder(path)
+
# Checking template existence
template_location <- get_template_location(template)
diff --git a/R/create_reports.R b/R/create_reports.R
index 8836679..59979a2 100644
--- a/R/create_reports.R
+++ b/R/create_reports.R
@@ -16,7 +16,7 @@
#' # Add a new report
#' report_path <- add_report("my_report", path = path)
#' list.files(report_path)
-create_reports <- function(path = ".", git = TRUE) {
+create_reports <- function(path = pkgload::pkg_path(), git = TRUE) {
# Create reports folder
reports_path <- file.path(path, "reports")
dir.create(reports_path, showWarnings = FALSE)
@@ -29,3 +29,10 @@ create_reports <- function(path = ".", git = TRUE) {
}
invisible(file.path(path, "reports"))
}
+
+check_reports_folder <- function(path) {
+ if (!dir.exists(file.path(path, "reports"))) {
+ message("Creating reports folder in: ", path, "...")
+ create_reports(path)
+ }
+}
diff --git a/R/list_reports.R b/R/list_reports.R
index ad8ded2..5544346 100644
--- a/R/list_reports.R
+++ b/R/list_reports.R
@@ -46,7 +46,14 @@ get_report_header <- function(path, index = "index.Rmd") {
f <- file.path(path, index)
if (file.exists(f)) {
l <- read_rmd(file.path(path, index))
- return(l$header)
+ header <- lapply(l$header, function(x) {
+ if (!is.list(x)) {
+ return(x)
+ } else {
+ return(NULL)
+ }
+ })
+ return(header)
} else {
warning("File ", f, " not found, the folder ", basename(path), " is ignored")
return(NULL)
diff --git a/R/render_report.R b/R/render_report.R
index 005c03f..48a686e 100644
--- a/R/render_report.R
+++ b/R/render_report.R
@@ -24,15 +24,19 @@ render_report <- function(input,
on.exit({setwd(owd)})
input <- getwd()
- add_before_chapter_script(input)
+ if (file.exists(file.path(input, "_bookdown.yml"))) {
+ add_before_chapter_script(input)
+ }
if (output_format == "bookdown::pdf_book") {
if (!requireNamespace("tinytex", quietly = TRUE))
install.packages("tinytex")
- babel_lang <-
- yaml::read_yaml("_bookdown.yml")$babel_lang
- if (!is.null(babel_lang)) {
- tinytex_install_babel_language_support(babel_lang)
+ if (file.exists(file.path(input, "_bookdown.yml"))) {
+ babel_lang <-
+ yaml::read_yaml("_bookdown.yml")$babel_lang
+ if (!is.null(babel_lang)) {
+ tinytex_install_babel_language_support(babel_lang)
+ }
}
}
message("output_format=", output_format)
@@ -52,6 +56,15 @@ render_report <- function(input,
fun = bookdown::render_book,
args = args
)
+ output_index <- file.path(output_dir,
+ paste0("index.",
+ ifelse(output_format == "bookdown::pdf_book",
+ "pdf",
+ "html")))
+ output_main <- sub("index", "_main", output_index)
+ if (file.exists(output_main)) {
+ file.rename(output_main, output_index)
+ }
invisible()
}
diff --git a/man/add_article.Rd b/man/add_article.Rd
new file mode 100644
index 0000000..9200ff5
--- /dev/null
+++ b/man/add_article.Rd
@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/add_article.R
+\name{add_article}
+\alias{add_article}
+\title{Add a new article in a fairify project}
+\usage{
+add_article(
+ name,
+ template,
+ package = "rticles",
+ path = pkgload::pkg_path(),
+ edit = FALSE
+)
+}
+\arguments{
+\item{name}{Name of the report (sub-folder name in "reports")}
+
+\item{template}{The report template chosen between the folders located in
+the "templates" folder of the fairify project}
+
+\item{package}{(Optional) Name of package where the template is located.}
+
+\item{path}{Path of the fairify project}
+
+\item{edit}{\code{TRUE} to edit the template immediately}
+}
+\value{
+Used for side effect.
+}
+\description{
+This function prepares an article with a template provided by the \strong{rticles}
+package.
+}
+\details{
+This function uses \link[rmardown:draft]{rmardown::draft} for creating the new document based on
+a template, so its uses is theoritically not limited to the templates
+provided by the \strong{rticles} package.
+}
diff --git a/man/create_reports.Rd b/man/create_reports.Rd
index 107ace1..06e7c63 100644
--- a/man/create_reports.Rd
+++ b/man/create_reports.Rd
@@ -4,7 +4,7 @@
\alias{create_reports}
\title{Set reports folder structure}
\usage{
-create_reports(path = ".", git = TRUE)
+create_reports(path = pkgload::pkg_path(), git = TRUE)
}
\arguments{
\item{path}{Destination folder for reports and templates}
diff --git a/tests/testthat/test-add_article.R b/tests/testthat/test-add_article.R
new file mode 100644
index 0000000..50e7a38
--- /dev/null
+++ b/tests/testthat/test-add_article.R
@@ -0,0 +1,23 @@
+path <- helper_create_fairify()
+add_article(name = "myarticle",
+ template = "rjournal",
+ path = path)
+
+test_that("add_article works", {
+ expect_true(file.exists(file.path(path, "reports/myarticle/index.Rmd")))
+})
+
+test_that("render_reports works with articles", {
+ render_reports(reports_dir = file.path(path, "reports"),
+ output_format = "bookdown::gitbook")
+ render_reports(reports_dir = file.path(path, "reports"),
+ output_format = "bookdown::pdf_book")
+})
+
+test_that("list_reports works with articles", {
+ expect_equal(nrow(list_reports(file.path(path, "reports"))), 1)
+})
+
+test_that("build_site works with articles", {
+ fairify::build_site(pkg = path)
+})
--
GitLab
From 25e533b5ad5cf6d781c8c4d05d0772c4f14d2b09 Mon Sep 17 00:00:00 2001
From: David Dorchies <david.dorchies@inrae.fr>
Date: Tue, 26 Mar 2024 18:44:31 +0100
Subject: [PATCH 2/5] docs: improve add_article doc
Refs #29
---
R/add_article.R | 10 +++++-----
R/create_reports.R | 4 ++++
man/add_article.Rd | 19 +++++++++++++++++--
man/add_report.Rd | 4 ++++
man/create_reports.Rd | 4 ++++
5 files changed, 34 insertions(+), 7 deletions(-)
diff --git a/R/add_article.R b/R/add_article.R
index e17d3ce..5a7e34f 100644
--- a/R/add_article.R
+++ b/R/add_article.R
@@ -4,17 +4,18 @@
#' package.
#'
#' @details
-#' This function uses [rmardown::draft] for creating the new document based on
+#' This function uses [rmarkdown::draft] for creating the new document based on
#' a template, so its uses is theoritically not limited to the templates
#' provided by the **rticles** package.
#'
#' @inheritParams add_report
#' @inheritParams rmarkdown::draft
#'
-#' @return Used for side effect.
+#' @return The path of the added article
#' @export
#'
-#' @examples
+#' @inherit create_reports examples
+#'
add_article <- function(name,
template,
package = "rticles",
@@ -39,6 +40,5 @@ add_article <- function(name,
package = package,
create_dir = FALSE,
edit = edit)
-
- invisible()
+ return(destpath)
}
diff --git a/R/create_reports.R b/R/create_reports.R
index 59979a2..b4073dd 100644
--- a/R/create_reports.R
+++ b/R/create_reports.R
@@ -16,6 +16,10 @@
#' # Add a new report
#' report_path <- add_report("my_report", path = path)
#' list.files(report_path)
+#'
+#' # Add a new article
+#' article_path <- add_article("my_article", template = "rjournal", path = path)
+#' list.files(article_path)
create_reports <- function(path = pkgload::pkg_path(), git = TRUE) {
# Create reports folder
reports_path <- file.path(path, "reports")
diff --git a/man/add_article.Rd b/man/add_article.Rd
index 9200ff5..a4124eb 100644
--- a/man/add_article.Rd
+++ b/man/add_article.Rd
@@ -25,14 +25,29 @@ the "templates" folder of the fairify project}
\item{edit}{\code{TRUE} to edit the template immediately}
}
\value{
-Used for side effect.
+The path of the added article
}
\description{
This function prepares an article with a template provided by the \strong{rticles}
package.
}
\details{
-This function uses \link[rmardown:draft]{rmardown::draft} for creating the new document based on
+This function uses \link[rmarkdown:draft]{rmarkdown::draft} for creating the new document based on
a template, so its uses is theoritically not limited to the templates
provided by the \strong{rticles} package.
}
+\examples{
+# Create structure for reports
+path <- tempfile(pattern = "report-example")
+dir.create(path)
+create_reports(path, git = FALSE)
+list.files(path, recursive = TRUE)
+
+# Add a new report
+report_path <- add_report("my_report", path = path)
+list.files(report_path)
+
+# Add a new article
+article_path <- add_article("my_article", template = "rjournal", path = path)
+list.files(article_path)
+}
diff --git a/man/add_report.Rd b/man/add_report.Rd
index 27b30e0..da84182 100644
--- a/man/add_report.Rd
+++ b/man/add_report.Rd
@@ -37,4 +37,8 @@ list.files(path, recursive = TRUE)
# Add a new report
report_path <- add_report("my_report", path = path)
list.files(report_path)
+
+# Add a new article
+article_path <- add_article("my_article", template = "rjournal", path = path)
+list.files(article_path)
}
diff --git a/man/create_reports.Rd b/man/create_reports.Rd
index 06e7c63..76ab98f 100644
--- a/man/create_reports.Rd
+++ b/man/create_reports.Rd
@@ -27,4 +27,8 @@ list.files(path, recursive = TRUE)
# Add a new report
report_path <- add_report("my_report", path = path)
list.files(report_path)
+
+# Add a new article
+article_path <- add_article("my_article", template = "rjournal", path = path)
+list.files(article_path)
}
--
GitLab
From d3744e634f82c8d4676b4ed379c583ec59147c4b Mon Sep 17 00:00:00 2001
From: David Dorchies <david.dorchies@inrae.fr>
Date: Tue, 26 Mar 2024 21:26:58 +0100
Subject: [PATCH 3/5] refactor: role of render_report_setup
Refs #29
---
R/add_report.R | 2 +-
R/render_report.R | 31 +++++++++++++++++++++----------
2 files changed, 22 insertions(+), 11 deletions(-)
diff --git a/R/add_report.R b/R/add_report.R
index 4db5cc7..e9436a0 100644
--- a/R/add_report.R
+++ b/R/add_report.R
@@ -76,7 +76,7 @@ add_report <- function(name,
file.path(destpath, "_fairify.yml"))
# Setting the setup R script
writeLines(
- c("# Fairify configuration: don't change the following line",
+ c("# This script is run before every chapter",
"fairify::render_report_setup(this.path::this.dir())",
"# pkgload::load_all() # Uncomment to load current fairyfied project code and data\n",
"# Add your own settings below to append or overwrite template settings"),
diff --git a/R/render_report.R b/R/render_report.R
index 48a686e..e90a4a8 100644
--- a/R/render_report.R
+++ b/R/render_report.R
@@ -24,7 +24,7 @@ render_report <- function(input,
on.exit({setwd(owd)})
input <- getwd()
- if (file.exists(file.path(input, "_bookdown.yml"))) {
+ if (file.exists(file.path(input, "setup.R"))) {
add_before_chapter_script(input)
}
@@ -46,6 +46,21 @@ render_report <- function(input,
unlink(file.path(input, c(".Rprofile", "templates")),
recursive = TRUE)
}, add = TRUE)
+ if (clean_cache) {
+ clean_cache_report(input)
+ }
+ file_bookdown <- file.path(input, "_bookdown.yml")
+ book_filename <- NULL
+ if (file.exists(file_bookdown)) {
+ book_filename <-
+ yaml::read_yaml(file_bookdown)$book_filename
+ }
+ if (is.null(book_filename)) book_filename <- "_main"
+ unlink(file.path(input, paste0(book_filename, ".*")))
+ file_fairify <- file.path(input, "_fairify.yml")
+ if (file.exists(file_fairify)) {
+ copy_templates(input)
+ }
args <- list(
input = file.path(input, input_index),
output_format = output_format,
@@ -72,16 +87,12 @@ render_report <- function(input,
#' @rdname render_reports
#' @export
render_report_setup <- function(input = getwd(), clean_cache = FALSE) {
- if (clean_cache) {
- clean_cache_report(input)
- }
- copy_templates(input)
- cfg_bookdown <-
- yaml::read_yaml(file.path(input, "_bookdown.yml"))
- unlink(file.path(input, paste0(cfg_bookdown$book_filename, ".*")))
options(knitr.duplicate.label = "allow")
- template <- yaml::read_yaml(file.path(input, "_fairify.yml"))$template
- source_template_setup(template)
+ file_fairify <- file.path(input, "_fairify.yml")
+ if (file.exists(file_fairify)) {
+ template <- yaml::read_yaml(file_fairify)$template
+ source_template_setup(template)
+ }
}
copy_templates <- function(input) {
--
GitLab
From 316c7a591e89c48ed82c4f2f27092232cd1f6811 Mon Sep 17 00:00:00 2001
From: David Dorchies <david.dorchies@inrae.fr>
Date: Tue, 26 Mar 2024 21:27:29 +0100
Subject: [PATCH 4/5] fix: list_reports for articles
Refs #29
---
R/list_reports.R | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/R/list_reports.R b/R/list_reports.R
index 5544346..a3ba392 100644
--- a/R/list_reports.R
+++ b/R/list_reports.R
@@ -48,7 +48,7 @@ get_report_header <- function(path, index = "index.Rmd") {
l <- read_rmd(file.path(path, index))
header <- lapply(l$header, function(x) {
if (!is.list(x)) {
- return(x)
+ return(paste(x, collapse = ", "))
} else {
return(NULL)
}
--
GitLab
From 9d3cd1e88612ddf3e7a11995ad20dd6bfa1287c4 Mon Sep 17 00:00:00 2001
From: David Dorchies <david.dorchies@inrae.fr>
Date: Tue, 26 Mar 2024 21:28:05 +0100
Subject: [PATCH 5/5] fix: filenames for having pdf link in gitbook
Refs #29
---
R/render_report.R | 9 ++-------
tests/testthat/test-add_article.R | 3 +++
2 files changed, 5 insertions(+), 7 deletions(-)
diff --git a/R/render_report.R b/R/render_report.R
index e90a4a8..d57c1fe 100644
--- a/R/render_report.R
+++ b/R/render_report.R
@@ -71,14 +71,9 @@ render_report <- function(input,
fun = bookdown::render_book,
args = args
)
- output_index <- file.path(output_dir,
- paste0("index.",
- ifelse(output_format == "bookdown::pdf_book",
- "pdf",
- "html")))
- output_main <- sub("index", "_main", output_index)
+ output_main <- file.path(output_dir, "_main.html")
if (file.exists(output_main)) {
- file.rename(output_main, output_index)
+ file.rename(output_main, file.path(output_dir, "index.html"))
}
invisible()
diff --git a/tests/testthat/test-add_article.R b/tests/testthat/test-add_article.R
index 50e7a38..c098309 100644
--- a/tests/testthat/test-add_article.R
+++ b/tests/testthat/test-add_article.R
@@ -10,8 +10,10 @@ test_that("add_article works", {
test_that("render_reports works with articles", {
render_reports(reports_dir = file.path(path, "reports"),
output_format = "bookdown::gitbook")
+ expect_true(file.exists(file.path(path, "public/reports/myarticle/index.html")))
render_reports(reports_dir = file.path(path, "reports"),
output_format = "bookdown::pdf_book")
+ expect_true(file.exists(file.path(path, "public/reports/myarticle/_main.pdf")))
})
test_that("list_reports works with articles", {
@@ -20,4 +22,5 @@ test_that("list_reports works with articles", {
test_that("build_site works with articles", {
fairify::build_site(pkg = path)
+ expect_true(file.exists(file.path(path, "public/index.html")))
})
--
GitLab