Changelog

Source: NEWS.md

codecheck (development version)

codecheck 0.22.0

Certificate Automation and Validation

• New feature: Automatic certificate ID retrieval from GitHub issues
  • get_certificate_from_github_issue(): Searches codecheckers/register issues by author names
  • is_placeholder_certificate(): Detects placeholder certificate IDs and report DOIs
  • update_certificate_from_github(): Auto-updates certificate IDs from matching GitHub issues
  • validate_certificate_for_rendering(): Displays visual warnings in PDF for placeholder values
  • Certificate template now automatically attempts to retrieve certificate IDs during rendering
• New feature: YAML validation and field completion
  • validate_yaml_syntax(): Validates YAML syntax before parsing
  • complete_codecheck_yml(): Analyzes and adds missing mandatory/optional fields
  • Both functions integrated into certificate template
• New feature: External metadata validation via CrossRef and ORCID APIs
  • validate_codecheck_yml_crossref(): Validates paper metadata against CrossRef
  • validate_codecheck_yml_orcid(): Validates author/codechecker names against ORCID records
  • validate_contents_references(): Unified wrapper combining both validations
  • Integrated into certificate template with strict mode to fail rendering on mismatches

Lifecycle Journal Integration

• New feature: Automatic metadata population from Lifecycle Journal (addresses #82)
  • get_lifecycle_metadata(): Retrieves article metadata via CrossRef API
  • update_codecheck_yml_from_lifecycle(): Auto-populates codecheck.yml with paper metadata
  • Smart field updates with preview mode and diff view before applying changes

Bug Fixes

• Critical fix: Fixed set_zenodo_certificate() to use correct zen4R API signatures
  • deleteFile() now uses deleteFile(recordId, filename) instead of deleteFile(fileId, recordId)
  • uploadFile() now uses uploadFile(path, record) with record object instead of record ID
  • Fixes “cannot coerce type ‘environment’ to vector of type ‘character’” error
• Fixed ORCID icon hyperlinks in PDF certificates using academicons package
  • Replaced complex tikz/svg implementation with simple \aiOrcid from academicons
  • Moved \usepackage{hyperref} to load after other packages to avoid conflicts
  • ORCID icons are now clickable links that work reliably across PDF viewers
• Fixed latex_summary_of_metadata() and latex_summary_of_manifest() to handle NULL/empty fields
• Fixed get_or_create_zenodo_record() to call correct function (get_zenodo_id())
• Critical fix: Fixed upload_zenodo_metadata() to properly set alternate identifiers per Zenodo curation policy
  • Certificate ID now correctly added as alternate identifiers (not related identifiers)
  • Two alternate identifier entries as required by policy:
    • URL schema: http://cdchck.science/register/certs/<CERT ID>
    • Other schema: cdchck.science/register/certs/<CERT ID> (without protocol)
  • Sets metadata$alternate_identifiers directly with proper structure
  • Related identifiers now only include paper (reviews) and repository (isSupplementedBy)
  • Paper DOI uses scheme=“doi” and relation_type=“reviews”
  • Repository URL uses scheme=“url” and relation_type=“issupplementedby”
• Code quality: Refactored DOI placeholder detection to eliminate code duplication
  • Created internal is_doi_placeholder() helper function
  • Now used by both is_placeholder_certificate() and get_or_create_zenodo_record()
  • Centralized placeholder detection logic for easier maintenance
• Code quality: Fixed R CMD check warnings
  • Added utils::globalVariables() declaration for NSE variables used in dplyr/data.table operations
  • Fixed incorrect parameter name in update_certificate_from_github() call (state vs issue_state)
  • Resolved all “no visible binding for global variable” warnings
• Code quality: Reorganized package structure for better maintainability
  • Split monolithic R/codecheck.R (2365 lines) into 7 focused files:
    • R/workspace.R (73 lines): Workspace creation and initialization
    • R/manifest.R (74 lines): File operations and manifest handling
    • R/latex.R (177 lines): LaTeX rendering utilities
    • R/zenodo.R (530 lines): Zenodo integration
    • R/lifecycle.R (238 lines): Lifecycle Journal integration
    • R/validation.R (1103 lines): Validation functions
    • R/github.R (162 lines): GitHub integration
  • All roxygen documentation, imports, and exports preserved
  • All 604 tests pass after refactoring

Enhancements

• Refactored Zenodo certificate upload: set_zenodo_certificate() renamed to upload_zenodo_certificate()
  • New feature: Can now upload additional files alongside the certificate via additional_files parameter
  • New feature: Automatically uploads certificate source file (.Rmd or .qmd) by default
    • Detects source file by looking for same base name as certificate PDF with .Rmd or .qmd extension
    • Tries .Rmd first, then .qmd if .Rmd not found (supports both R Markdown and Quarto)
    • Can be disabled with upload_source = FALSE parameter
    • Provides informative messages when source file is found/not found
    • Smart source file replacement: Checks for existing source files on Zenodo record
      • Prompts user before deleting existing .Rmd or .qmd files (when warn=TRUE)
      • Auto-deletes existing source files when warn=FALSE
      • Handles multiple existing source files (deletes all before uploading new one)
      • Case-insensitive detection (.Rmd, .rmd, .qmd, .QMD all detected)
  • Certificate is always uploaded first to ensure it becomes the preview file for the Zenodo record
  • Source file uploaded second (if found and enabled), followed by any additional files
  • set_zenodo_certificate() retained as an alias for backward compatibility
  • Returns list with certificate result, source result, and additional_files results
  • Improved API: Parameter renamed from zen to zenodo for clarity
  • Flexible record input: Now accepts either a record ID (string/numeric) or a Zenodo record object
  • When a record object is provided, skips unnecessary API fetch for better performance
• Smart certificate upload: upload_zenodo_certificate() checks for existing certificate files before uploading
  • Automatically detects existing PDF files on Zenodo record
  • Prompts user whether to delete existing files and upload new one, or abort operation
  • New warn parameter (default TRUE) for interactive prompting; set FALSE for automated/non-interactive contexts
  • Shows file details (name, size) before deletion
  • Handles multiple PDF files and provides clear feedback during deletion/upload
  • Comprehensive error handling with graceful degradation
  • Comprehensive test suite with 52 tests covering all scenarios including source file upload and replacement
• Automatic YAML updating: get_or_create_zenodo_record() now automatically updates codecheck.yml with Zenodo DOI
  • When creating a new Zenodo record, automatically updates the report field in codecheck.yml
  • Detects empty or placeholder values (FIXME, TODO, placeholder, XXXXX, etc.) and updates automatically
  • For non-placeholder values, asks user confirmation before overwriting (when warn=TRUE)
  • Handles NULL report field gracefully
  • 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”)
  • Description includes certificate summary as required by policy
  • Adds related identifier for original paper with “reviews” relation (scheme=“doi”, relation_type=“reviews”, resource_type=“publication-article”)
  • Adds related identifier for code repository with “isSupplementedBy” relation (scheme=“url”, relation_type=“issupplementedby”, resource_type=auto-detected)
  • Adds two alternate identifiers for certificate ID (URL and Other schemas) - correctly uses alternate_identifiers field per curation policy
  • Smart repository type detection: Automatically detects if repository is software (GitHub, GitLab, Codeberg, etc.) or dataset (DataCite DOI)
  • Configurable resource types: New resource_types parameter allows overriding defaults via named list (paper, repository)
  • Prints confidence level messages for low/medium confidence detections to allow user verification
  • Validates required fields (certificate ID, warns for missing summary)
  • Handles NULL/empty repository gracefully
  • Extracts clean DOI from doi.org URLs
  • Comprehensive test suite with 38 tests including auto-detection and override scenarios
• Zenodo functions now load metadata from codecheck.yml by default
• DOI validation is now platform-agnostic (Zenodo, OSF, ResearchEquals, etc.)
• Removed pifont package dependency; now uses UTF-8 emoji ⚠ for warnings
• Enhanced error messages with clearer guidance
• Added ~230 new tests across all features

codecheck 0.21.0

• Added pkgdown configuration and workflow for documentation site
• Added CLAUDE.md with comprehensive guidance for AI-assisted development
• Fixed typo in get_abstract_text_crossref() (referenc → reference)
• Fixed test file error handling for missing config files
• Fixed variable scoping issues in tinytest suite
• Added launch pad link to documentation
• Added clarifying comments in core functions
• Bug fix: Fixed validate_codecheck_yml() repository URL validation - now correctly calls http_error() on response objects instead of URL strings

codecheck 0.20.0

• Renamed fields in register output for consistency
• Updated footer with improved contact information
• Removed individual maintainer references from footer

codecheck 0.19.0

• Fixed namespace issues
• Added support for specifying from-to range when rendering register

codecheck 0.18.0

• Added validation of certificate identifier format in validate_codecheck_yml()
• Ensures certificate IDs follow the NNNN-NNN pattern (e.g., “2024-001”)

codecheck 0.17.0

• Added support for certificate download from ResearchEquals platform
• Extended get_cert_link() to handle ResearchEquals DOIs

codecheck 0.16.0

• Added support for sub-paths within GitHub repositories to access codecheck.yml
• Enables accessing codecheck.yml files in subdirectories using github::org/repo|subpath syntax
• Updated check template
• Added TL;DR section to README for template usage

codecheck 0.15.0

• Added handling for PDF import in template certificate
• Improved certificate template generation

codecheck 0.14.0

• Added TU Delft Data Champion Centre (DCC) as venue
• Added eLife journal as venue
• Removed unused venue entries
• Fixed Zenodo hyperlinks in register output
• Hardened code for missing ORCIDs in codechecker field
• Added venue hyperlinks to register pages
• Fixed issue with missing codechecks column
• Reordered fields in the UI for better usability

codecheck 0.12.0

• Added support for retrieving codecheck.yml files from Zenodo records
• New repository specification: zenodo::1234567 and zenodo-sandbox::1234567
• Fixed various warnings and notes from R CMD check

codecheck 0.11.6

• Fixed JSON output to not include markdown hyperlinks
• Added tests for rendering functions

codecheck 0.11.5

• Fixed imports to reflect API changes in zen4R package
• Added templates for the codecheck report

codecheck 0.11.4

• Replaced custom url_exists() with httr::http_error()
• Improved URL validation

codecheck 0.11.3

• Added missing import in DESCRIPTION
• Added logging of cache usage for check and render operations

codecheck 0.11.2

• Fixed codechecker hyperlink generation when ORCID ID is missing

codecheck 0.11.1

• Fixed certificate pages that have no certificate preview available

codecheck 0.11.0

• Added generation of individual certificate HTML pages
• New function create_cert_md() for certificate markdown generation
• Added abstract retrieval from CrossRef and OpenAlex APIs

codecheck 0.10.1

• Fixed venue type page hyperlinks

codecheck 0.10.0

• Fixed URL links in venues and venue type tables
• Made non-register venue tables use plural naming
• Improved hyperlink consistency across all outputs

codecheck 0.9.0 / 0.8.0

• Replaced repository column in register with platform-prefixed specifications
• Added support for multiple repository platforms (GitHub, OSF, GitLab, Zenodo)

codecheck 0.7.0

• Added Amsterdam UMC as venue
• Added codecheckers extra text section
• Improved venue management

codecheck 0.6.0

• Split register by type (journal, conference, community, institution)
• Created filtered CSV files by venue and codechecker
• Refactored register rendering architecture
• Updated column width configurations
• Moved hyperlinks configuration to config.R

codecheck 0.5.0

• Initial support for multiple output formats (HTML, JSON, Markdown)
• Added JSON register output
• Improved register table rendering

codecheck 0.4.0

• Enhanced register filtering capabilities
• Added codechecker-specific register views

codecheck 0.3.0

• Improved register preprocessing
• Added remote configuration retrieval

codecheck 0.2.0

• Added register rendering functionality
• Support for multiple venues and codecheckers

codecheck 0.1.0

• Initial release
• Basic CODECHECK workspace creation
• Certificate generation support
• Integration with Zenodo for certificate uploads

codecheck 0.0.0.90xx

• Added tests using tinytest
• Added a NEWS.md file to track changes to the package