From 1cea776586ecedb9d712b097be0be9b540a80631 Mon Sep 17 00:00:00 2001
From: David Dorchies <david.dorchies@inrae.fr>
Date: Fri, 8 Mar 2024 17:53:03 +0100
Subject: [PATCH 1/3] feat(add_report): change template strategy - remove copy
of templates in create_reports - create reports folder if needed - check
template existence - add .template_dependencies file
Refs #23
---
R/add_report.R | 29 ++++++++++++++++++++++++-----
R/create_reports.R | 16 ----------------
tests/testthat/test-add_report.R | 24 +++++++++++++++---------
3 files changed, 39 insertions(+), 30 deletions(-)
diff --git a/R/add_report.R b/R/add_report.R
index c202398..0aedbba 100644
--- a/R/add_report.R
+++ b/R/add_report.R
@@ -12,15 +12,31 @@
#' @inherit create_reports examples
#'
add_report <- function(name,
- template = "inrae",
+ template = "fairify:inrae",
lang = "english",
path = pkgload::pkg_path()) {
- if (!all(dir.exists(file.path(path, c("reports", "templates"))))) {
- stop("Report structure not found, call `create_reports` first!")
+ # reports folder handling
+ if (!dir.exists(file.path(path, "reports"))) {
+ message("Creating reports folder in: ", path, "...")
+ create_reports(path)
}
- if (!dir.exists(file.path(path, "templates", template))) {
- stop("Template\"", template, "\" not found in ", file.path(path, "templates"))
+ # Checking template existence
+ if (!grepl("^[a-zA-Z0-9_]*\\:[a-zA-Z0-9_]*$", template)) {
+ stop("`template` should be in the format `[package]:[template_name]`")
}
+ template_location <- strsplit(template, ":", fixed = TRUE)[[1]]
+ if (!dir.exists(system.file("templates", package = template_location[1]))) {
+ stop("'templates' folder not found in the package '", template_location[1], "'\n",
+ "Complete folder: ",system.file("templates", package = template_location[1]))
+ }
+ template_folder <- system.file(file.path("templates", template_location[2]),
+ package = template_location[1])
+ if (!dir.exists(template_folder)) {
+ stop("template '", template_location[2],"'' not found in the package '", template_location[1], "'\n",
+ "Complete folder: ", template_folder)
+ }
+
+ # Creating report
destpath <- file.path(path, "reports", name)
if (dir.exists(destpath))
stop("The folder ",
@@ -52,6 +68,7 @@ add_report <- function(name,
append = TRUE
)
+ # Setting template in tex files
lapply(c("in_header", "before_body", "after_body"), function(x) {
tex_content <- sprintf("\\input{../../templates/%s/%s}", template, x)
if (x == "in_header") {
@@ -70,6 +87,8 @@ add_report <- function(name,
"% Add your own settings below to append or overwrite template settings")
writeLines(tex_content, file.path(destpath, sprintf("%s.tex", x)))
})
+ # Setting template dependency
+ writeLines(template, file.path(destpath, ".template_dependencies"))
tinytex_install_babel_language_support(lang)
diff --git a/R/create_reports.R b/R/create_reports.R
index a082b44..2bc5a4a 100644
--- a/R/create_reports.R
+++ b/R/create_reports.R
@@ -18,22 +18,6 @@
#' report_path <- add_report("my_report", path = path)
#' list.files(report_path)
create_reports <- function(path = ".", overwrite = FALSE, git = TRUE) {
- # Copy templates
- if (dir.exists(file.path(path, "templates"))) {
- if (overwrite) {
- warning("Folder ", file.path(path, "templates"), " is overwritten")
- } else {
- stop("Folder ", file.path(path, "templates"), " already exists")
- }
- }
-
- ok <- file.copy(
- from = pkg_sys("templates"),
- to = path,
- recursive = TRUE
- )
- if (!ok) stop("Error when copying 'templates' folder to ", path)
-
# Create reports folder
reports_path <- file.path(path, "reports")
dir.create(reports_path, showWarnings = FALSE)
diff --git a/tests/testthat/test-add_report.R b/tests/testthat/test-add_report.R
index 3396919..0df00e2 100644
--- a/tests/testthat/test-add_report.R
+++ b/tests/testthat/test-add_report.R
@@ -1,7 +1,7 @@
-test_that("add_report should raise error if reports does not exists", {
+test_that("add_report should raise message if reports does not exists", {
path <- tempfile(pattern = "dir")
dir.create(path, recursive = TRUE)
- expect_error(add_report("test", path = path))
+ expect_message(add_report("test", path = path))
unlink(path, recursive = TRUE)
})
@@ -9,7 +9,12 @@ test_that("add_report should raise error if template does not exists", {
path <- tempfile(pattern = "dir")
dir.create(path, recursive = TRUE)
create_reports(path)
- expect_error(add_report("test", template = "wrong_template", path = path))
+ expect_error(add_report("test", template = "wrong_syntax", path = path),
+ regexp = "format")
+ expect_error(add_report("test", template = "ggplot2:inrae", path = path),
+ regexp = "templates")
+ expect_error(add_report("test", template = "fairify:wrong_template", path = path),
+ regexp = "template")
unlink(path, recursive = TRUE)
})
@@ -18,11 +23,12 @@ test_that("add_report should create a report", {
dir.create(path, recursive = TRUE)
create_reports(path)
add_report("test", path = path)
- expect_true(
- all(file.exists(
- file.path(path,
- "reports/test",
- list.files(pkg_sys("bookdown_template")))
- )))
+ sapply(file.path(path,
+ "reports/test",
+ c(list.files(pkg_sys("bookdown_template")),
+ ".template_dependencies")),
+ function(x) expect_true(file.exists(!!x)))
+ expect_equal(readLines(file.path(path, "reports/test/.template_dependencies")),
+ "fairify:inrae")
unlink(path, recursive = TRUE)
})
--
GitLab
From 4a2d1986e40d480160c9e4a7c91325dda40f73dc Mon Sep 17 00:00:00 2001
From: David Dorchies <david.dorchies@inrae.fr>
Date: Sat, 9 Mar 2024 18:25:00 +0100
Subject: [PATCH 2/3] feat: use templates from package data
- templates are copied from package inst/templates during render
- handling of dependencies between templates
- setup.R is template dependant now
- _output.yml is also template dependant and completed recursively through dependency chain
Refs #23
---
R/add_report.R | 72 +++++++++++++------
R/create_reports.R | 3 +-
R/render_report.R | 50 +++++++++++++
R/render_reports.R | 2 +-
inst/bookdown_template/setup.R | 7 --
inst/reports_gitignore.txt | 2 +-
.../basic}/_output.yml | 5 +-
inst/templates/{ => basic}/setup.R | 0
inst/templates/inrae/.template_dependencies | 1 +
inst/templates/inrae/_output.yml | 6 ++
inst/templates/inrae/after_body.tex | 2 +-
inst/templates/inrae/backcover_inrae.tex | 6 +-
inst/templates/inrae/cover.tex | 6 +-
inst/templates/inrae/in_header.tex | 7 +-
inst/templates/inrae/preamble.tex | 6 +-
inst/templates/inrae/setup.R | 1 +
.../templates/umr_geau/.template_dependencies | 2 +
inst/templates/umr_geau/after_body.tex | 2 +-
inst/templates/umr_geau/in_header.tex | 16 ++++-
inst/templates/umr_geau/setup.R | 1 +
man/add_report.Rd | 2 +-
man/create_reports.Rd | 4 +-
tests/testthat/test-add_report.R | 11 +--
tests/testthat/test-create_reports.R | 4 +-
tests/testthat/test-render_reports.R | 7 +-
25 files changed, 157 insertions(+), 68 deletions(-)
delete mode 100644 inst/bookdown_template/setup.R
rename inst/{bookdown_template => templates/basic}/_output.yml (58%)
rename inst/templates/{ => basic}/setup.R (100%)
create mode 100644 inst/templates/inrae/.template_dependencies
create mode 100644 inst/templates/inrae/_output.yml
create mode 100644 inst/templates/inrae/setup.R
create mode 100644 inst/templates/umr_geau/.template_dependencies
create mode 100644 inst/templates/umr_geau/setup.R
diff --git a/R/add_report.R b/R/add_report.R
index 0aedbba..b771981 100644
--- a/R/add_report.R
+++ b/R/add_report.R
@@ -12,7 +12,7 @@
#' @inherit create_reports examples
#'
add_report <- function(name,
- template = "fairify:inrae",
+ template = "fairify:basic",
lang = "english",
path = pkgload::pkg_path()) {
# reports folder handling
@@ -21,20 +21,7 @@ add_report <- function(name,
create_reports(path)
}
# Checking template existence
- if (!grepl("^[a-zA-Z0-9_]*\\:[a-zA-Z0-9_]*$", template)) {
- stop("`template` should be in the format `[package]:[template_name]`")
- }
- template_location <- strsplit(template, ":", fixed = TRUE)[[1]]
- if (!dir.exists(system.file("templates", package = template_location[1]))) {
- stop("'templates' folder not found in the package '", template_location[1], "'\n",
- "Complete folder: ",system.file("templates", package = template_location[1]))
- }
- template_folder <- system.file(file.path("templates", template_location[2]),
- package = template_location[1])
- if (!dir.exists(template_folder)) {
- stop("template '", template_location[2],"'' not found in the package '", template_location[1], "'\n",
- "Complete folder: ", template_folder)
- }
+ template_location <- get_template_location(template)
# Creating report
destpath <- file.path(path, "reports", name)
@@ -70,7 +57,7 @@ add_report <- function(name,
# Setting template in tex files
lapply(c("in_header", "before_body", "after_body"), function(x) {
- tex_content <- sprintf("\\input{../../templates/%s/%s}", template, x)
+ tex_content <- sprintf("\\input{templates/%s/%s}", template_location[2], x)
if (x == "in_header") {
tex_content <- c(
sprintf("\\usepackage[%s]{babel}", lang),
@@ -79,18 +66,63 @@ add_report <- function(name,
)
babel_lang_tex <- sprintf("templates/basic/babel_%s.tex", lang)
if (file.exists(pkg_sys(babel_lang_tex))) {
- tex_content <- c(tex_content, sprintf("\\input{../../%s}", babel_lang_tex))
+ tex_content <- c(tex_content, sprintf("\\input{%s}", babel_lang_tex))
}
}
tex_content <- c(tex_content,
- "\n",
- "% Add your own settings below to append or overwrite template settings")
+ "\n% Add your own settings below to append or overwrite template settings")
writeLines(tex_content, file.path(destpath, sprintf("%s.tex", x)))
})
# Setting template dependency
writeLines(template, file.path(destpath, ".template_dependencies"))
-
+ # Setting the setup R script
+ cat(NULL, file = file.path(destpath, ".here"))
+ writeLines(
+ c(sprintf("source(here::here(\"templates/%s/setup.R\"))\n", template_location[2]),
+ "# pkgload::load_all() # Uncomment to load current fairyfied project code and data\n",
+ "# Add your own settings below to append or overwrite template settings"),
+ file.path(destpath, "setup.R")
+ )
+ # Setting up the _output.yml file from templates
+ write_output_yml(destpath)
+ # Babel language support installation
tinytex_install_babel_language_support(lang)
return(destpath)
}
+
+write_output_yml <- function(path) {
+ template_dependencies <- get_template_dependencies(path)
+ template_paths <- sapply(template_dependencies, function(x) {
+ get_template_location(x)["path"]
+ })
+ output_paths <- file.path(template_paths, "_output.yml")
+
+ output <- NULL
+ for(output_path in output_paths) {
+ if (file.exists(output_path)) {
+ template_output <- yaml::read_yaml(output_path)
+ output <- config::merge(output, template_output)
+ }
+ }
+ yaml::write_yaml(output, file.path(path, "_output.yml"))
+}
+
+get_template_dependencies <- function(path) {
+ dep_chain <- NULL
+ i <- 0
+ while(file.exists(file.path(path, ".template_dependencies"))) {
+ dep_chain <- rbind(dep_chain,
+ data.frame(path = unname(path),
+ template = readLines(
+ file.path(path, ".template_dependencies")
+ )))
+ i <- i + 1
+ path <- get_template_location(dep_chain$template[i])["path"]
+ }
+ if (!is.null(dep_chain)) {
+ return(unique(rev(dep_chain$template)))
+ } else {
+ return(NULL)
+ }
+}
diff --git a/R/create_reports.R b/R/create_reports.R
index 2bc5a4a..8836679 100644
--- a/R/create_reports.R
+++ b/R/create_reports.R
@@ -1,7 +1,6 @@
#' Set reports folder structure
#'
#' @param path Destination folder for reports and templates
-#' @param overwrite Allow overwriting templates folder
#' @param git add gitignore file suitable for TeX and HTML reports
#'
#' @return The path to the created reports folder.
@@ -17,7 +16,7 @@
#' # Add a new report
#' report_path <- add_report("my_report", path = path)
#' list.files(report_path)
-create_reports <- function(path = ".", overwrite = FALSE, git = TRUE) {
+create_reports <- function(path = ".", git = TRUE) {
# Create reports folder
reports_path <- file.path(path, "reports")
dir.create(reports_path, showWarnings = FALSE)
diff --git a/R/render_report.R b/R/render_report.R
index 98fcd45..c6563e0 100644
--- a/R/render_report.R
+++ b/R/render_report.R
@@ -27,10 +27,13 @@ render_report <- function(input,
full.names = TRUE)
unlink(cache_dir, recursive = TRUE)
}
+ on.exit({unlink(file.path(input, "templates"), recursive = TRUE)})
+ copy_templates(input)
cfg_bookdown <-
yaml::read_yaml(file.path(input, "_bookdown.yml"))
unlink(file.path(input, paste0(cfg_bookdown$book_filename, ".*")))
attached_packages <- (.packages())
+ here:::do_refresh_here(input)
bookdown::render_book(input,
output_format = output_format,
output_dir = output_dir,
@@ -44,3 +47,50 @@ render_report <- function(input,
character.only = TRUE))
invisible()
}
+
+copy_templates <- function(input) {
+ if (file.exists(input) && !dir.exists(input)) {
+ # Remove index.Rmd or whatever the file to get the folder
+ template <- basename(template)
+ }
+ templates_path <- file.path(input, "templates")
+ dir.create(templates_path, showWarnings = FALSE)
+ template_dependencies <- get_template_dependencies(input)
+ templates <- lapply(template_dependencies, function(x) {
+ get_template_location(x)
+ })
+ sapply(templates, function(template) {
+ ok <- file.copy(
+ from = template["path"],
+ to = templates_path,
+ recursive = TRUE
+ )
+ if (!ok) stop("Error when copying template '", template["name"], "'\n",
+ "From: ", template["path"], "\n",
+ "To: ", templates_path)
+ })
+ invisible()
+}
+
+get_template_location <- function(template, err_msg = "") {
+ if (!grepl("^[a-zA-Z0-9_]*\\:[a-zA-Z0-9_]*$", template)) {
+ stop(err_msg,
+ "`template` should be in the format `[package]:[template_name]`, ",
+ "found: ", template)
+ }
+ template_location <- strsplit(template, ":", fixed = TRUE)[[1]]
+ names(template_location) <- c("pkg", "name")
+ if (!dir.exists(system.file("templates", package = template_location[1]))) {
+ stop(err_msg,
+ "'templates' folder not found in the package '", template_location[1], "'\n",
+ "Complete folder: ",system.file("templates", package = template_location[1]))
+ }
+ template_folder <- system.file(file.path("templates", template_location[2]),
+ package = template_location[1])
+ if (!dir.exists(template_folder)) {
+ stop(err_msg,
+ "template '", template_location[2],"'' not found in the package '", template_location[1], "'\n",
+ "Complete folder: ", template_folder)
+ }
+ return(c(template_location, path = template_folder))
+}
diff --git a/R/render_reports.R b/R/render_reports.R
index 62011a1..02245e0 100644
--- a/R/render_reports.R
+++ b/R/render_reports.R
@@ -25,7 +25,7 @@ render_reports <- function(reports_dir = file.path(pkgload::pkg_path(), "reports
invisible(sapply(reports, message))
for(report in reports){
- message("*******************************************************************")
+ message("\n*******************************************************************")
message("** RENDER ", report)
message("*******************************************************************")
render_report(input = file.path(reports_dir, report),
diff --git a/inst/bookdown_template/setup.R b/inst/bookdown_template/setup.R
deleted file mode 100644
index ff3ca7a..0000000
--- a/inst/bookdown_template/setup.R
+++ /dev/null
@@ -1,7 +0,0 @@
-# Global report configuration
-source("../../templates/setup.R")
-
-# Add below specific configuration for this report
-
-# Load this package and its configuration
-# library(myPackage)
diff --git a/inst/reports_gitignore.txt b/inst/reports_gitignore.txt
index 0c4b87e..2fb2f5a 100644
--- a/inst/reports_gitignore.txt
+++ b/inst/reports_gitignore.txt
@@ -1,5 +1,6 @@
myBook.*
*/_book
+*/templates
*/*_files
*/*_cache
*/config.yml
@@ -10,4 +11,3 @@ myBook.*
*.wrt
*.rds
*.pdf
-
diff --git a/inst/bookdown_template/_output.yml b/inst/templates/basic/_output.yml
similarity index 58%
rename from inst/bookdown_template/_output.yml
rename to inst/templates/basic/_output.yml
index b231b09..3689c5f 100644
--- a/inst/bookdown_template/_output.yml
+++ b/inst/templates/basic/_output.yml
@@ -1,11 +1,8 @@
bookdown::gitbook:
- css: style.css
config:
toc:
- before: |
- <li><a href="./"><img src="../../templates/inrae/bloc_etat.png" width = "130"></a></li>
after: |
- <li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
+ <li>Published with <a href="https://forgemia.inra.fr/umr-g-eau/fairify" target="blank">fairify</a> and <a href="https://github.com/rstudio/bookdown" target="blank">bookdown</a></li>
download: ["pdf"]
bookdown::pdf_book:
includes:
diff --git a/inst/templates/setup.R b/inst/templates/basic/setup.R
similarity index 100%
rename from inst/templates/setup.R
rename to inst/templates/basic/setup.R
diff --git a/inst/templates/inrae/.template_dependencies b/inst/templates/inrae/.template_dependencies
new file mode 100644
index 0000000..775b482
--- /dev/null
+++ b/inst/templates/inrae/.template_dependencies
@@ -0,0 +1 @@
+fairify:basic
diff --git a/inst/templates/inrae/_output.yml b/inst/templates/inrae/_output.yml
new file mode 100644
index 0000000..d23c54d
--- /dev/null
+++ b/inst/templates/inrae/_output.yml
@@ -0,0 +1,6 @@
+bookdown::gitbook:
+ css: style.css
+ config:
+ toc:
+ before: |
+ <li><img src="templates/inrae/bloc_etat.png" width = "130"></li>
diff --git a/inst/templates/inrae/after_body.tex b/inst/templates/inrae/after_body.tex
index 84aab12..1b3c304 100644
--- a/inst/templates/inrae/after_body.tex
+++ b/inst/templates/inrae/after_body.tex
@@ -8,7 +8,7 @@
\cleartobackcover
-\input{../../templates/inrae/backcover_inrae}
+\input{templates/inrae/backcover_inrae}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% END AFTER_BODY.TEX
diff --git a/inst/templates/inrae/backcover_inrae.tex b/inst/templates/inrae/backcover_inrae.tex
index b259edf..4b00d51 100644
--- a/inst/templates/inrae/backcover_inrae.tex
+++ b/inst/templates/inrae/backcover_inrae.tex
@@ -11,7 +11,7 @@
\begin{center}
\color{inrae}
- \includegraphics{../../templates/inrae/chevron.png}
+ \includegraphics{templates/inrae/chevron.png}
\vspace{3mm}
@@ -23,7 +23,7 @@
\vspace{5.5mm}
Rejoignez-nous sur :\\
- \includegraphics{../../templates/inrae/reseaux_sociaux.png}\\
+ \includegraphics{templates/inrae/reseaux_sociaux.png}\\
\textbf{\website}
\vspace{27mm}
@@ -34,7 +34,7 @@
\vspace{3cm}
- \includegraphics{../../templates/inrae/logo_inrae_dos_bas.png}
+ \includegraphics{templates/inrae/logo_inrae_dos_bas.png}
\end{center}
\thispagestyle{empty}
diff --git a/inst/templates/inrae/cover.tex b/inst/templates/inrae/cover.tex
index 7108ded..016644f 100644
--- a/inst/templates/inrae/cover.tex
+++ b/inst/templates/inrae/cover.tex
@@ -2,14 +2,14 @@
\thispagestyle{empty}
\tikz[remember picture,overlay] \node[opacity=1,inner sep=0pt] at (current page.center) {
- \includegraphics[width=\paperwidth]{../../templates/inrae/inrae_fond_page.jpg}
+ \includegraphics[width=\paperwidth]{templates/inrae/inrae_fond_page.jpg}
};
\vspace{-1cm}%
\hfill%
\begin{minipage}[t][6cm][t]{0.20\textwidth}
\begin{center}
- \input{../../templates/inrae/logos}
+ \input{templates/inrae/logos}
\end{center}
\end{minipage}
@@ -21,7 +21,7 @@
\vspace{1cm}
-\includegraphics{../../templates/inrae/chevron.png}\\
+\includegraphics{templates/inrae/chevron.png}\\
\vspace{-3mm}
diff --git a/inst/templates/inrae/in_header.tex b/inst/templates/inrae/in_header.tex
index e41bcde..3e69a6b 100644
--- a/inst/templates/inrae/in_header.tex
+++ b/inst/templates/inrae/in_header.tex
@@ -2,21 +2,20 @@
% BEGIN PREAMBLE.TEX
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\newcommand{\insertfirstlogo}{\includegraphics[width=4cm]{../../templates/inrae/logo_inrae_couv_haut.png}}
\newcommand{\insertsecondlogo}{}
\newcommand{\insertthirdlogo}{}
\newcommand{\insertfourthlogo}{}
\newcommand{\insertcoverimage}{}
-\input{../../templates/basic/in_header}
-\input{../../templates/inrae/preamble.tex}
+\input{templates/basic/in_header}
+\input{templates/inrae/preamble.tex}
% Première de couverture
\usepackage{tikz}
\usepackage{titling}
\makeatletter
\def\maketitle{%
-\input{../../templates/inrae/cover.tex}
+\input{templates/inrae/cover.tex}
}
\makeatother
diff --git a/inst/templates/inrae/preamble.tex b/inst/templates/inrae/preamble.tex
index 467e03d..bdd5128 100644
--- a/inst/templates/inrae/preamble.tex
+++ b/inst/templates/inrae/preamble.tex
@@ -67,7 +67,7 @@
%\let\marginpar\oldmarginpar
% Definition des couleurs
-\RequirePackage{../../templates/inrae/inraecolors}
+\RequirePackage{templates/inrae/inraecolors}
% Pourquoi les couleurs chargées depuis "inraecolors" ne sont-elles pas disponibles pour \hypersetup ci-dessous ?
\definecolor{titreColor}{HTML}{008C8E} % inraeDark
@@ -110,7 +110,7 @@
\setlength{\parskip}{0.5em}
% Format des titres utilisés dans le préambule du rapport (Auteurs, résumé...)
-\newcommand{\titrepreambule}[1]{
+\newcommand{\titrepreamble}[1]{
\vspace{2\baselineskip}
{\sffamily\Large\color{titreColor}\scshape{#1}}
\vspace{\baselineskip}}
@@ -134,4 +134,4 @@
% Acronymes
\usepackage[printonlyused,withpage]{acronym}
-\newcommand{\insertfirstlogo}{\includegraphics[width=3.5cm]{../../templates/inrae/logo_inrae_couv_haut.png}}
+\newcommand{\insertfirstlogo}{\includegraphics[width=3.5cm]{templates/inrae/logo_inrae_couv_haut.png}}
diff --git a/inst/templates/inrae/setup.R b/inst/templates/inrae/setup.R
new file mode 100644
index 0000000..67ef853
--- /dev/null
+++ b/inst/templates/inrae/setup.R
@@ -0,0 +1 @@
+source(here::here("templates/basic/setup.R"))
diff --git a/inst/templates/umr_geau/.template_dependencies b/inst/templates/umr_geau/.template_dependencies
new file mode 100644
index 0000000..345bf38
--- /dev/null
+++ b/inst/templates/umr_geau/.template_dependencies
@@ -0,0 +1,2 @@
+fairify:inrae
+fairify:basic
diff --git a/inst/templates/umr_geau/after_body.tex b/inst/templates/umr_geau/after_body.tex
index 44cc7cd..b697b2a 100644
--- a/inst/templates/umr_geau/after_body.tex
+++ b/inst/templates/umr_geau/after_body.tex
@@ -1 +1 @@
-\input{../../templates/inrae/after_body}
+\input{templates/inrae/after_body}
diff --git a/inst/templates/umr_geau/in_header.tex b/inst/templates/umr_geau/in_header.tex
index 9a9b524..354dc18 100644
--- a/inst/templates/umr_geau/in_header.tex
+++ b/inst/templates/umr_geau/in_header.tex
@@ -4,9 +4,19 @@
%\usepackage[french]{babel}
-\newcommand{\insertsecondlogo}{\includegraphics[width=4cm]{../../templates/umr_geau/logo_umr_geau.png}}
+\newcommand{\insertsecondlogo}{\includegraphics[width=4cm]{templates/umr_geau/logo_umr_geau.png}}
\newcommand{\insertthirdlogo}{}
\newcommand{\insertfourthlogo}{}
+\newcommand{\insertcoverimage}{}
+
+% Première de couverture
+\usepackage{tikz}
+\usepackage{titling}
+\makeatletter
+\def\maketitle{%
+\input{templates/inrae/cover.tex}
+}
+\makeatother
\newcommand{\service}{UMR G-EAU}
\newcommand{\site}{
@@ -22,8 +32,8 @@
\url{www.inrae.fr}
}
-\input{../../templates/basic/in_header}
-\input{../../templates/inrae/preambule_inrae.tex}
+\input{templates/basic/in_header}
+\input{templates/inrae/preamble.tex}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% END PREAMBLE.TEX
diff --git a/inst/templates/umr_geau/setup.R b/inst/templates/umr_geau/setup.R
new file mode 100644
index 0000000..ce24fd2
--- /dev/null
+++ b/inst/templates/umr_geau/setup.R
@@ -0,0 +1 @@
+source(here::here("templates/inrae/setup.R"))
diff --git a/man/add_report.Rd b/man/add_report.Rd
index 7af2577..27b30e0 100644
--- a/man/add_report.Rd
+++ b/man/add_report.Rd
@@ -6,7 +6,7 @@
\usage{
add_report(
name,
- template = "inrae",
+ template = "fairify:basic",
lang = "english",
path = pkgload::pkg_path()
)
diff --git a/man/create_reports.Rd b/man/create_reports.Rd
index f61a6aa..107ace1 100644
--- a/man/create_reports.Rd
+++ b/man/create_reports.Rd
@@ -4,13 +4,11 @@
\alias{create_reports}
\title{Set reports folder structure}
\usage{
-create_reports(path = ".", overwrite = FALSE, git = TRUE)
+create_reports(path = ".", git = TRUE)
}
\arguments{
\item{path}{Destination folder for reports and templates}
-\item{overwrite}{Allow overwriting templates folder}
-
\item{git}{add gitignore file suitable for TeX and HTML reports}
}
\value{
diff --git a/tests/testthat/test-add_report.R b/tests/testthat/test-add_report.R
index 0df00e2..b9822c7 100644
--- a/tests/testthat/test-add_report.R
+++ b/tests/testthat/test-add_report.R
@@ -8,7 +8,6 @@ test_that("add_report should raise message if reports does not exists", {
test_that("add_report should raise error if template does not exists", {
path <- tempfile(pattern = "dir")
dir.create(path, recursive = TRUE)
- create_reports(path)
expect_error(add_report("test", template = "wrong_syntax", path = path),
regexp = "format")
expect_error(add_report("test", template = "ggplot2:inrae", path = path),
@@ -21,14 +20,16 @@ test_that("add_report should raise error if template does not exists", {
test_that("add_report should create a report", {
path <- tempfile(pattern = "dir")
dir.create(path, recursive = TRUE)
- create_reports(path)
- add_report("test", path = path)
+ add_report("test", template = "fairify:umr_geau", path = path)
sapply(file.path(path,
"reports/test",
c(list.files(pkg_sys("bookdown_template")),
- ".template_dependencies")),
+ ".template_dependencies",
+ "_output.yml")),
function(x) expect_true(file.exists(!!x)))
expect_equal(readLines(file.path(path, "reports/test/.template_dependencies")),
- "fairify:inrae")
+ "fairify:umr_geau")
+ output_yml <- yaml::read_yaml(file.path(path, "reports/test/_output.yml"))
+ expect_true(grepl("templates/inrae", output_yml$`bookdown::gitbook`$config$toc$before))
unlink(path, recursive = TRUE)
})
diff --git a/tests/testthat/test-create_reports.R b/tests/testthat/test-create_reports.R
index dcec0e2..f8bd485 100644
--- a/tests/testthat/test-create_reports.R
+++ b/tests/testthat/test-create_reports.R
@@ -3,8 +3,6 @@ test_that("create_reports works", {
dir.create(path, recursive = TRUE)
expect_equal(create_reports(path),
file.path(path, "reports"))
- expect_true(all(dir.exists(file.path(path, c("reports", "templates")))))
- expect_error(create_reports(path))
- expect_warning(create_reports(path, overwrite = TRUE))
+ expect_true(all(dir.exists(file.path(path, "reports"))))
unlink(path, recursive = TRUE)
})
diff --git a/tests/testthat/test-render_reports.R b/tests/testthat/test-render_reports.R
index 40e20ae..4e753b8 100644
--- a/tests/testthat/test-render_reports.R
+++ b/tests/testthat/test-render_reports.R
@@ -2,15 +2,16 @@ test_that("render_reports works for all templates", {
path <- helper_create_fairify()
dfC <-
expand.grid(
- template = list.dirs(file.path(path, "templates"), full.names = FALSE)[-1],
- lang = c("french", "english")
+ template = list.dirs(pkg_sys("templates"), full.names = FALSE)[-1],
+ lang = c("french", "english"),
+ stringsAsFactors = FALSE
)
mapply(
FUN =
function(template, lang, path) {
add_report(
paste("my_report", template, lang, sep = "_"),
- template = template,
+ template = paste0("fairify:",template),
lang = lang,
path = path
)
--
GitLab
From 54d1c38e97d13c8ad197b701561f4a296c115f7a Mon Sep 17 00:00:00 2001
From: David Dorchies <david.dorchies@inrae.fr>
Date: Sat, 9 Mar 2024 18:30:46 +0100
Subject: [PATCH 3/3] fix: missing dependency package here
For fixing working directory to the report directory when rendering a report
Refs #23
---
DESCRIPTION | 1 +
1 file changed, 1 insertion(+)
diff --git a/DESCRIPTION b/DESCRIPTION
index 46c59ea..d0e6598 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -15,6 +15,7 @@ Imports:
devtools,
dplyr,
gert,
+ here,
httr,
jsonlite,
magrittr,
--
GitLab