Enhances Zenodo integration (include community submission), fix some R CMD check stuff

Author: nuest

.Rbuildignore

@@ -13,3 +13,4 @@
 ^CONTRIBUTING\.md$
 ^CLAUDE\.md$
 ^\.claude$
+^LICENSE\.md$

DESCRIPTION

@@ -24,7 +24,8 @@ Authors@R:
            comment = c(ORCID = "0000-0002-1322-1553"))
        )
 Description: This contains helper functions for codecheckers for conducting CODECHECKs, e.g., authoring CODECHECK certificates (<https://codecheck.org.uk>), and the rendering of the CODECHECK Register (<https://codecheck.org.uk/register/>).
-License: MIT + file LICENSE
+License: MIT
+License_is_FOSS: yes
 Depends: R (>= 4.0.0), gh, R.cache, parsedate
 Imports: 
     dplyr,

LICENSE LICENSE.mdLICENSE renamed to LICENSE.md

@@ -1,6 +1,6 @@
-MIT License
+# MIT License
 
-Copyright (c) 2020 CODECHECK
+Copyright (c) 2025 codecheck authors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

NEWS.md

@@ -103,6 +103,12 @@
   - Preserves all other fields in codecheck.yml during update
   - New yml_file parameter allows specifying alternate YAML file location
   - Comprehensive test suite with 31 tests using mocked Zenodo API
+* **Automatic CODECHECK community submission**: `get_or_create_zenodo_record()` now automatically submits new records to the CODECHECK community
+  - Newly created Zenodo records are automatically submitted to https://zenodo.org/communities/codecheck/
+  - Uses zen4R's `createReviewRequest()` and `submitRecordForReview()` methods
+  - Record will be added to the community after publication
+  - Graceful error handling if community submission fails - provides warning with manual instructions
+  - Ensures all CODECHECK certificates are discoverable in the central community
 * **Zenodo curation policy compliance**: `upload_zenodo_metadata()` now fully complies with CODECHECK Zenodo community curation policy
   - Publisher set to "CODECHECK Community on Zenodo" (was "CODECHECK")
   - Resource type set to "publication-report" (was "publication-preprint")

R/github.R

@@ -22,7 +22,7 @@
 ##'     \item{issue_number}{The GitHub issue number (if found)}
 ##'     \item{was_placeholder}{Logical indicating if original was a placeholder}
 ##'   }
-##' @author Daniel Nüst
+##' @author Daniel Nuest
 ##' @importFrom yaml read_yaml write_yaml
 ##' @export
 ##' @examples
@@ -60,7 +60,7 @@ update_certificate_from_github <- function(yml_file = "codecheck.yml",
 
   # Check if we should proceed
   if (!is_placeholder && !force) {
-    message("\n⚠ Certificate ID is already set and is not a placeholder.")
+    message("\n\u26a0 Certificate ID is already set and is not a placeholder.")
     message("Use force = TRUE to update anyway.")
     message(rep("=", 80), "\n")
 
@@ -79,13 +79,13 @@ update_certificate_from_github <- function(yml_file = "codecheck.yml",
   result <- tryCatch({
     get_certificate_from_github_issue(yml_file, state = issue_state)
   }, error = function(e) {
-    message("✖ Error retrieving from GitHub: ", e$message)
+    message("\u2716 Error retrieving from GitHub: ", e$message)
     return(NULL)
   })
 
   # Check if we found a result
   if (is.null(result)) {
-    message("\n✖ No certificate found in GitHub issues")
+    message("\n\u2716 No certificate found in GitHub issues")
     message(rep("=", 80), "\n")
 
     return(invisible(list(
@@ -98,7 +98,7 @@ update_certificate_from_github <- function(yml_file = "codecheck.yml",
 
   # Check if we have a certificate
   if (is.null(result$certificate)) {
-    message("\n✖ No certificate ID found in matching issues")
+    message("\n\u2716 No certificate ID found in matching issues")
     if (!is.null(result$message)) {
       message("Reason: ", result$message)
     }
@@ -113,7 +113,7 @@ update_certificate_from_github <- function(yml_file = "codecheck.yml",
   }
 
   # We have a certificate!
-  message("\n✓ Found certificate: ", result$certificate)
+  message("\n\u2713 Found certificate: ", result$certificate)
   message("  Issue #", result$issue_number, ": ", result$title)
   if (!is.null(result$matched_author)) {
     message("  Matched author: ", result$matched_author)
@@ -137,17 +137,17 @@ update_certificate_from_github <- function(yml_file = "codecheck.yml",
     # Write back to file
     tryCatch({
       yaml::write_yaml(metadata, yml_file)
-      message("✓ Successfully updated ", yml_file)
+      message("\u2713 Successfully updated ", yml_file)
       message("  Certificate ID: ", result$certificate)
       message("  From GitHub issue #", result$issue_number)
 
       updated <- TRUE
     }, error = function(e) {
-      message("✖ Failed to write file: ", e$message)
+      message("\u2716 Failed to write file: ", e$message)
       updated <- FALSE
     })
   } else {
-    message("\n⚠ No changes applied. Use apply_update = TRUE to save changes.")
+    message("\n\u26a0 No changes applied. Use apply_update = TRUE to save changes.")
     updated <- FALSE
   }
 

R/lifecycle.R

@@ -16,7 +16,7 @@
 ##'     \item{reference}{The DOI URL}
 ##'     \item{date}{Publication date}
 ##'   }
-##' @author Daniel Nüst
+##' @author Daniel Nuest
 ##' @importFrom httr GET content status_code
 ##' @importFrom jsonlite fromJSON
 ##' @export
@@ -107,7 +107,7 @@ get_lifecycle_metadata <- function(identifier) {
 ##'   non-empty fields. If \code{FALSE} (default), only populate empty or
 ##'   placeholder fields.
 ##' @return Invisibly returns the updated metadata list
-##' @author Daniel Nüst
+##' @author Daniel Nuest
 ##' @importFrom yaml read_yaml write_yaml
 ##' @export
 ##' @examples
@@ -225,9 +225,9 @@ update_codecheck_yml_from_lifecycle <- function(identifier,
 
     if (apply_updates) {
       yaml::write_yaml(updated, yml_file)
-      cat("\n✓ Changes applied to ", yml_file, "\n\n", sep = "")
+      cat("\n\u2713 Changes applied to ", yml_file, "\n\n", sep = "")
     } else {
-      cat("\n⚠ No changes applied. Use apply_updates = TRUE to save changes.\n\n")
+      cat("\n\u26a0 No changes applied. Use apply_updates = TRUE to save changes.\n\n")
     }
   } else {
     cat("\nNo changes needed. All fields are already populated.\n")

R/validation.R

@@ -25,7 +25,7 @@
 ##'     \item{missing}{List of missing fields by category (mandatory, recommended, optional)}
 ##'     \item{updated}{The updated metadata list (if changes were made)}
 ##'   }
-##' @author Daniel Nüst
+##' @author Daniel Nuest
 ##' @importFrom yaml read_yaml write_yaml
 ##' @export
 ##' @examples
@@ -246,9 +246,9 @@ complete_codecheck_yml <- function(yml_file = "codecheck.yml",
 
     if (apply_updates) {
       yaml::write_yaml(updated, yml_file)
-      cat("\n✓ Changes applied to ", yml_file, "\n\n", sep = "")
+      cat("\n\u2713 Changes applied to ", yml_file, "\n\n", sep = "")
     } else {
-      cat("\n⚠ No changes applied. Use apply_updates = TRUE to save changes.\n\n")
+      cat("\n\u26a0 No changes applied. Use apply_updates = TRUE to save changes.\n\n")
     }
   } else {
     if (add_mandatory || add_optional) {
@@ -287,7 +287,7 @@ complete_codecheck_yml <- function(yml_file = "codecheck.yml",
 ##'     \item{issues}{Character vector of any issues found}
 ##'     \item{crossref_metadata}{The metadata retrieved from CrossRef (if available)}
 ##'   }
-##' @author Daniel Nüst
+##' @author Daniel Nuest
 ##' @importFrom httr GET content status_code
 ##' @export
 ##' @examples
@@ -394,7 +394,7 @@ validate_codecheck_yml_crossref <- function(yml_file = "codecheck.yml",
       issues <- c(issues, issue)
       warning(issue)
     } else {
-      message("✓ Title matches CrossRef metadata")
+      message("\u2713 Title matches CrossRef metadata")
     }
   }
 
@@ -447,7 +447,7 @@ validate_codecheck_yml_crossref <- function(yml_file = "codecheck.yml",
           issues <- c(issues, issue)
           warning(issue)
         } else {
-          message("✓ Author ", i, " name matches: ", local_author$name)
+          message("\u2713 Author ", i, " name matches: ", local_author$name)
         }
       }
 
@@ -465,11 +465,11 @@ validate_codecheck_yml_crossref <- function(yml_file = "codecheck.yml",
             issues <- c(issues, issue)
             warning(issue)
           } else {
-            message("✓ Author ", i, " ORCID matches: ", local_orcid)
+            message("\u2713 Author ", i, " ORCID matches: ", local_orcid)
           }
         } else {
           msg <- paste0("Author ", i, " has ORCID in local file but not in CrossRef")
-          message("ℹ ", msg)
+          message("\u2139 ", msg)
         }
       }
     }
@@ -479,13 +479,13 @@ validate_codecheck_yml_crossref <- function(yml_file = "codecheck.yml",
   valid <- length(issues) == 0
 
   if (!valid) {
-    message("\n⚠ Validation completed with ", length(issues), " issue(s)")
+    message("\n\u26a0 Validation completed with ", length(issues), " issue(s)")
     if (strict) {
       stop("Validation failed with ", length(issues), " issue(s):\n",
            paste(issues, collapse = "\n"))
     }
   } else {
-    message("\n✓ All validations passed!")
+    message("\n\u2713 All validations passed!")
   }
 
   invisible(list(
@@ -513,7 +513,7 @@ validate_codecheck_yml_crossref <- function(yml_file = "codecheck.yml",
 ##'     \item{valid}{Logical indicating if all checks passed}
 ##'     \item{issues}{Character vector of any issues found}
 ##'   }
-##' @author Daniel Nüst
+##' @author Daniel Nuest
 ##' @importFrom rorcid orcid_person
 ##' @export
 ##' @examples
@@ -624,10 +624,10 @@ validate_codecheck_yml_orcid <- function(yml_file = "codecheck.yml",
             issues <- c(issues, issue)
             warning(issue)
           } else {
-            message("✓ Author ", i, " name matches ORCID: ", author$name, " (", author$ORCID, ")")
+            message("\u2713 Author ", i, " name matches ORCID: ", author$name, " (", author$ORCID, ")")
           }
         } else {
-          message("ℹ Could not retrieve ORCID record for author ", i, ": ", author$ORCID)
+          message("\u2139 Could not retrieve ORCID record for author ", i, ": ", author$ORCID)
         }
       }
     }
@@ -653,7 +653,7 @@ validate_codecheck_yml_orcid <- function(yml_file = "codecheck.yml",
           next
         }
 
-        message("✓ Codechecker ", i, ": ", checker$name)
+        message("\u2713 Codechecker ", i, ": ", checker$name)
 
         # Validate ORCID if present
         if (!is.null(checker$ORCID)) {
@@ -690,10 +690,10 @@ validate_codecheck_yml_orcid <- function(yml_file = "codecheck.yml",
               issues <- c(issues, issue)
               warning(issue)
             } else {
-              message("✓ Codechecker ", i, " ORCID matches: ", checker$name, " (", checker$ORCID, ")")
+              message("\u2713 Codechecker ", i, " ORCID matches: ", checker$name, " (", checker$ORCID, ")")
             }
           } else {
-            message("ℹ Could not retrieve ORCID record for codechecker ", i, ": ", checker$ORCID)
+            message("\u2139 Could not retrieve ORCID record for codechecker ", i, ": ", checker$ORCID)
           }
         }
       }
@@ -704,13 +704,13 @@ validate_codecheck_yml_orcid <- function(yml_file = "codecheck.yml",
   valid <- length(issues) == 0
 
   if (!valid) {
-    message("\n⚠ ORCID validation completed with ", length(issues), " issue(s)")
+    message("\n\u26a0 ORCID validation completed with ", length(issues), " issue(s)")
     if (strict) {
       stop("ORCID validation failed with ", length(issues), " issue(s):\n",
            paste(issues, collapse = "\n"))
     }
   } else {
-    message("\n✓ All ORCID validations passed!")
+    message("\n\u2713 All ORCID validations passed!")
   }
 
   invisible(list(
@@ -739,7 +739,7 @@ validate_codecheck_yml_orcid <- function(yml_file = "codecheck.yml",
 ##'     \item{crossref_result}{Results from CrossRef validation (if performed)}
 ##'     \item{orcid_result}{Results from ORCID validation (if performed)}
 ##'   }
-##' @author Daniel Nüst
+##' @author Daniel Nuest
 ##' @export
 ##' @examples
 ##' \dontrun{
@@ -805,7 +805,7 @@ validate_contents_references <- function(yml_file = "codecheck.yml",
     if (!is.null(orcid_result)) total_issues <- total_issues + length(orcid_result$issues)
 
     message("\n", rep("=", 80))
-    message("⚠ VALIDATION SUMMARY: ", total_issues, " issue(s) found")
+    message("\u26a0 VALIDATION SUMMARY: ", total_issues, " issue(s) found")
     message(rep("=", 80))
 
     if (strict) {
@@ -818,7 +818,7 @@ validate_contents_references <- function(yml_file = "codecheck.yml",
     }
   } else {
     message("\n", rep("=", 80))
-    message("✓ ALL VALIDATIONS PASSED!")
+    message("\u2713 ALL VALIDATIONS PASSED!")
     message(rep("=", 80))
   }
 
@@ -874,7 +874,7 @@ is_doi_placeholder <- function(report_doi) {
 ##'   for placeholder patterns.
 ##' @return Logical value: TRUE if certificate or DOI is a placeholder, FALSE otherwise.
 ##'   If strict=TRUE and either is a placeholder, stops with an error instead.
-##' @author Daniel Nüst
+##' @author Daniel Nuest
 ##' @export
 ##' @examples
 ##' \dontrun{
@@ -988,7 +988,7 @@ is_placeholder_certificate <- function(yml_file = "codecheck.yml",
 ##' @param display_warning Logical. If TRUE (default), displays a warning box in
 ##'   the rendered output when certificate or DOI is a placeholder.
 ##' @return Invisibly returns TRUE if certificate and DOI are valid, FALSE if any placeholder
-##' @author Daniel Nüst
+##' @author Daniel Nuest
 ##' @export
 ##' @examples
 ##' \dontrun{
@@ -1066,7 +1066,7 @@ validate_certificate_for_rendering <- function(yml_file = "codecheck.yml",
     if (display_warning) {
       cat("\\begin{center}\n")
       cat("\\fcolorbox{red}{yellow}{\\parbox{0.9\\textwidth}{\\centering\n")
-      cat("\\textbf{\\Large \\textcolor{red}{⚠} WARNING \\textcolor{red}{⚠}}\\\\\n")
+      cat("\\textbf{\\Large \\textcolor{red}{\u26a0} WARNING \\textcolor{red}{\u26a0}}\\\\\n")
       cat("\\vspace{0.2cm}\n")
 
       # Display each warning part