small update to check template

Author: nuest

R/codecheck.R

@@ -189,10 +189,10 @@ as_latex_url  <- function(x) {
 ##' @export
 latex_summary_of_metadata <- function(metadata) {
   summary_entries = list(
-    "Title" =            metadata$paper$title,
-    "Authors" =          .names(metadata$paper$authors),
-    "Reference" =        as_latex_url(metadata$paper$reference),
-    "Codechecker" =      .names(metadata$codechecker),
+    "Title of checked publication" =            metadata$paper$title,
+    "Author(s)" =       .names(metadata$paper$authors),
+    "Reference" =       as_latex_url(metadata$paper$reference),
+    "Codechecker(s)" =  .names(metadata$codechecker),
     "Date of check" =   metadata$check_time,
     "Summary" =         metadata$summary,
     "Repository" =      as_latex_url(metadata$repository))

R/utils_render_cert_md.R

@@ -170,7 +170,7 @@ get_abstract_text_crossref <- function(register_repo) {
 
   # Could not retrieve data for DOI
   else {
-    warning(paste("Failed to retrieve data for DOI", doi))
+    warning(paste("Failed to retrieve abstract text for DOI", doi))
     return(NULL)
   }
 }

inst/extdata/templates/codecheck/codecheck.Rmd

@@ -16,29 +16,30 @@ require("xtable")
 require("tibble")
 require("readr")
 options(width = 60)
-opts_chunk$set(cache=FALSE)
+opts_chunk$set(cache = FALSE)
 
-root = find_root("codecheck.yml")
+root <- find_root("codecheck.yml")
 ```
 
 ```{r codecheck_logo, echo=FALSE,results='asis'}
 latex_codecheck_logo()
 ```
 
 ```{r manifest, eval=TRUE, include=FALSE}
-metadata = codecheck_metadata(root)
-manifest = metadata$manifest
+metadata <- codecheck_metadata(root)
+manifest <- metadata$manifest
 
-dest_dir = file.path(root, "codecheck", "outputs")
+dest_dir <- file.path(root, "codecheck", "outputs")
 ## Create the outputs directory if missing
-if ( !dir.exists(dest_dir) ) {
+if (!dir.exists(dest_dir) ) {
   dir.create(dest_dir)
 }
 
-manifest_df = copy_manifest_files(root, metadata,
+manifest_df <- copy_manifest_files(root, metadata,
                                   dest_dir, keep_full_path = FALSE,
                                   overwrite = FALSE
                                   )
+# manifest_df <- list_manifest_files(root, metadata, dest_dir)
 ```
 
 ---
@@ -92,16 +93,16 @@ I suggest to the authors to consider the following suggestions for their next pu
 # Manifest files
 
 ```{r, echo=FALSE, results="asis", width=100}
-for(i in c(1:nrow(manifest_df))) {
-  path <- manifest_df[i,"dest"]
+for (i in c(1:nrow(manifest_df))) {
+  path <- manifest_df[i, "dest"]
   if(stringr::str_ends(path, "(png|pdf|jpg|jpeg)")) {
     # include graphics with knitr has to happen at top level in chunks, see https://github.com/yihui/knitr/issues/1260
     # see also https://stackoverflow.com/questions/51268623/insert-images-using-knitrinclude-graphics-in-a-for-loop
     # knitr::include_graphics(manifest_df[1, "dest"], error = TRUE)
     # Therefore, generate Markdown code here:
     cat("## ", basename(path), "\n\n")
     cat("**Comment:** ", manifest_df[i,"comment"], "\n\n")
-    cat(paste0("![", "Test ", "](", path, ")\n"))
+    cat(paste0("![", manifest_df[i,"comment"], "](", path, ")\n"))
   } else if (stringr::str_ends(path, "(Rout|txt)")) {
     cat("## ", basename(path), "\n\n")
     cat("\\scriptsize \n\n", "```txt\n")

vignettes/codecheck_overview.Rmd

@@ -51,22 +51,24 @@ create_codecheck_files()
 These create several files that need to be edited for the codecheck
 process:
 
-1. *codecheck.yml* contains the metadata for the reproduction. If
+1. `codecheck.yml` contains the metadata for the reproduction. If
   the author or someone else has already created it, double-check
   if all required information is provided - see the
   [specification](https://codecheck.org.uk/spec/config/latest/).
-2. *codecheck/codecheck.Rmd* is a suggested R Markdown script to
-	edit, along with *Makefile* and *codecheck-preamble.sty* to help
+2. `codecheck/codecheck.Rmd` is a suggested R Markdown script to
+	edit, along with `Makefile` and `codecheck-preamble.sty` to help
 	compile the PDF.
-3. *codecheck/zenodo-codecheck.R* for help in loading the certificate
+3. `codecheck/zenodo-codecheck.R` for help in loading the certificate
    to Zenodo along with the corresponding metadata.
+4. `CODECHECK_report_template.odt` and `.docx` are templates for usage with
+   common word processors - please delete if you use the `.Rmd` file.
 
-There is also a Makefile so that `make` within the codecheck folder
+There is also a Makefile so that `make` within the `codecheck/` folder
 will rebuild `codecheck.pdf`.
 
 ## Completing the metadata file *codecheck.yml*
 
-The *codecheck.yml* file contains all the relevant metadata for the
+The `codecheck.yml` file contains all the relevant metadata for the
 certificate.  Simply edit it to your needs, bearing in mind the
 specification comments at <https://codecheck.org.uk/spec/config/latest>.