bump version; update NEWS and add docs for previous commits

Author: nuest

.claude/settings.local.json

@@ -38,7 +38,8 @@
       "Bash(R -q -e:*)",
       "WebFetch(domain:info.orcid.org)",
       "WebFetch(domain:orcid.org)",
-      "WebFetch(domain:jpswalsh.github.io)"
+      "WebFetch(domain:jpswalsh.github.io)",
+      "WebFetch(domain:fontawesome.com)"
     ],
     "deny": [],
     "ask": []

CLAUDE.md

@@ -49,6 +49,63 @@ The package uses GitHub Actions for CI/CD. Check `.github/workflows/R-CMD-check.
 
 When bumping the version in `DESCRIPTION`, add a new section to `NEWS.md` with the version number and date. Follow the existing format with `# codecheck X.Y.Z` headers.
 
+## Design Principles
+
+### Separation of Concerns: Data vs. Presentation
+
+**CRITICAL PRINCIPLE**: R functions should focus on data preparation and logic, NOT HTML generation.
+
+**✅ DO**:
+- Prepare data in R functions (e.g., extract metadata, create data structures)
+- Store HTML structure in template files (`.html`, `.md` with Mustache/Whisker placeholders)
+- Use R to populate template placeholders with data values
+- Return data objects (lists, data frames, strings) from R functions
+
+**❌ DON'T**:
+- Generate HTML tags directly in R functions (e.g., `sprintf('<a href="%s">...</a>')`)
+- Build complex HTML structures using string concatenation in R
+- Mix presentation logic with data processing logic
+
+**Example of correct approach**:
+
+```r
+# R function - prepares data only
+generate_profile_data <- function(orcid) {
+  profile <- get_profile(orcid)
+  return(list(
+    has_orcid = !is.null(profile$orcid),
+    orcid = profile$orcid,
+    has_github = !is.null(profile$github_handle),
+    github_handle = profile$github_handle
+  ))
+}
+
+# Template file (profile.html) - contains HTML structure
+# <a href="https://orcid.org/{{orcid}}">
+#   <i class="ai ai-orcid"></i> {{orcid}}
+# </a>
+
+# Rendering function - combines data with template
+render_profile <- function(orcid) {
+  data <- generate_profile_data(orcid)
+  template <- readLines("profile.html")
+  whisker::render(template, data)
+}
+```
+
+**Why this matters**:
+- **Maintainability**: HTML changes don't require R code changes
+- **Testability**: R functions can be tested without parsing HTML
+- **Readability**: Templates are easier to understand than R strings with escaped HTML
+- **Collaboration**: Designers can work on templates without touching R code
+- **Consistency**: CSS classes and HTML structure remain consistent across the codebase
+
+**Current implementation**:
+- Template files in `inst/extdata/templates/` contain HTML structure
+- R functions use `whisker::render()` or `sprintf()` to fill placeholders
+- Functions like `generate_codechecker_profile_links()`, `generate_footer_build_info()`, and `generate_meta_generator_content()` return content strings without HTML wrapper tags
+- HTML wrapper tags (`<p>`, `<meta>`, etc.) are in template files
+
 ### Version Management
 
 The package follows [Semantic Versioning](https://semver.org/) (MAJOR.MINOR.PATCH):
@@ -254,7 +311,7 @@ The rendering process follows this sequence:
 - `render_register()` - Dispatches to format-specific renderer (MD, HTML, or JSON)
 - `generate_output_dir()` - Creates output directory path based on filter and subcategory
 - `generate_table_details()` - Creates metadata dict with name, slug, subcat, output_dir
-- `filter_and_drop_register_columns()` - Keeps only relevant columns per format (uses `CONFIG$REGISTER_COLUMNS`)
+- `filter_and_drop_register_columns()` - Selects and orders columns per filter and format (uses hierarchical `CONFIG$REGISTER_COLUMNS`)
 - `add_venue_hyperlinks_reg()` - Adds markdown links to venue pages
 - `add_venue_type_hyperlinks_reg()` - Adds markdown links to venue type pages
 
@@ -315,13 +372,16 @@ The rendering process follows this sequence:
 The CONFIG environment stores all configuration as lists/vectors. Key elements:
 
 **Table structure:**
-- `CONFIG$REGISTER_COLUMNS` - Columns to keep per output format (html, md, csv, json)
+- `CONFIG$REGISTER_COLUMNS` - Hierarchical column configuration: filter → file_type → columns
+  - Special filter "default" used for main register and as fallback
+  - Filter-specific configs (e.g., "venues", "codecheckers") can override defaults
+  - Supports different column orders and selections per view
+  - Example: `CONFIG$REGISTER_COLUMNS$default$html` or `CONFIG$REGISTER_COLUMNS$venues$json`
 - `CONFIG$MD_TABLE_COLUMN_WIDTHS` - Markdown column width specifications for register and non-register tables
-- `CONFIG$JSON_COLUMNS` - Column order for JSON output
+- `CONFIG$JSON_COLUMNS` - Column order for JSON output (featured.json and main register.json)
 
 **Filtering:**
 - `CONFIG$FILTER_COLUMN_NAMES` - Maps filter name to register column (venues→Venue, codecheckers→Codechecker)
-- `CONFIG$FILTER_COLUMN_NAMES_TO_DROP` - Columns to drop for specific filters
 - `CONFIG$FILTER_SUBCAT_COLUMNS` - Maps filter to subcat column (venues→Type)
 - `CONFIG$FILTER_SUBCATEGORIES` - Lists subcats per filter (venues→[community, journal, conference, institution])
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: codecheck
 Title: Helper Functions for CODECHECK Project
-Version: 0.22.0.9000
+Version: 0.23.0
 Authors@R: 
     c(person(given = "Stephen",
             family = "Eglen",

NEWS.md

@@ -1,5 +1,91 @@
+# codecheck 0.23.0 (2025-11-12)
+
+## Register Enhancements
+
+* **Navigation header with logo**: All register pages now feature a navigation header with the CODECHECK logo in the top left, which serves as a home link back to the main register. Overview pages (main register, all venues, all codecheckers) include a menu in the top right with links to "All Venues", "All Codecheckers", and "About" (linking to the main CODECHECK website) for quick navigation
+* **Breadcrumb navigation**: All register pages now include breadcrumb navigation at the top, enabling easy navigation from detail pages back to overview pages. Breadcrumbs show hierarchical paths (e.g., CODECHECK Register > Venues > Journals > GigaScience) with clickable links to parent pages (addresses codecheckers/register#108)
+* **Configurable field ordering**: Register views now support per-filter column configuration, allowing different field orders and selections for main register vs. filtered views (venues, codecheckers). Main register now displays columns in the order: Certificate, Report, Title, Venue, Type, Check date (addresses #101)
+* **Context-aware field filtering**: Filtered views automatically exclude redundant fields (e.g., venue/type columns hidden on venue-specific pages, codechecker column hidden on codechecker pages)
+* **Hierarchical column configuration**: New `CONFIG$REGISTER_COLUMNS` structure with filter-specific overrides and automatic fallback to defaults for maximum flexibility
+* **Relative asset links**: Favicon and CSS stylesheet links in HTML headers now use relative paths calculated based on each page's depth, eliminating hard-coded absolute URLs and improving portability
+* **Build metadata in footer**: All register pages now display build information in muted text at the bottom of the footer, including timestamp, package version, codecheck package commit, and register commit with GitHub links (addresses #105)
+* **Dual commit tracking**: Footer now displays both codecheck package commit and register repository commit as clickable links to respective GitHub commits
+* **Meta generator tag**: HTML pages now include a properly formatted `<meta name="generator">` tag with package version and commit information (fixed display issue)
+* **Build metadata JSON**: A `.meta.json` file is now generated at the root of the docs directory containing build metadata for both repositories
+* **Icon font usage**: Replaced inline SVG logos with academicons and Font Awesome icon fonts for ORCID, GitHub, and Zenodo for cleaner HTML and easier maintenance
+* **Template-based HTML generation**: Moved HTML structure from R functions to template files, keeping R code focused on data preparation
+* **Codechecker profile links**: Individual codechecker pages now display ORCID and GitHub profile links above the table, pulling data from the codecheckers/codecheckers repository (addresses #73)
+* **ORCID branding compliance**: Codechecker pages now use the official ORCID iD logo and display full ORCID URLs (https://orcid.org/...) as required by ORCID brand guidelines
+* **Simplified codechecker titles**: Removed ORCID identifier from codechecker page titles for cleaner display (titles now show just "Codechecks by [Name]")
+* **Zenodo community link**: Added link to CODECHECK Zenodo Community in footer of all register pages alongside the GitHub organization link
+
+## Bug Fixes
+
+* **Fixed venue label error**: Resolved "venue_label must be size 1, not 12" error by ungrouping data frame before venue_label mutation in `create_all_venues_table()`
+* **Fixed NA codechecker handling**: Codecheckers without ORCID identifiers are now properly filtered out during register rendering, preventing creation of invalid "NA" directories
+
+## New Functions
+
+* **`generate_navigation_header()`**: Generates navigation header HTML with CODECHECK logo and conditional menu (menu shown only on main register page)
+* **`generate_breadcrumb()`**: Generates Bootstrap-styled breadcrumb navigation HTML based on page context (filter type, table details, and relative path)
+* **`calculate_breadcrumb_base_path()`**: Calculates relative path to register root based on page depth for breadcrumb links
+* **`get_build_metadata()`**: Retrieves build metadata including timestamp, package version, and git commit information from both register and codecheck package repositories
+* **`generate_meta_generator_content()`**: Creates meta generator content value (replaces `generate_meta_generator_tag()` to separate content from HTML structure)
+* **`generate_footer_build_info()`**: Generates HTML for displaying build information in page footers including both codecheck and register commits with GitHub links
+* **`write_meta_json()`**: Writes build metadata to .meta.json file in specified directory
+* **`get_codecheckers_data()`**: Fetches and caches codecheckers registry from codecheckers/codecheckers repository
+* **`get_codechecker_profile()`**: Retrieves profile information (name, GitHub handle, ORCID, fields, languages) by ORCID
+* **`generate_codechecker_profile_links()`**: Generates HTML for horizontal list of profile links with icons
+
+## Documentation
+
+* **Comprehensive register rendering documentation**: Expanded CLAUDE.md with detailed documentation of the register rendering system, including:
+  - Complete rendering pipeline flow
+  - Detailed descriptions of all 13 utility files
+  - Configuration system documentation
+  - Template system details
+  - Output directory structure
+  - Important implementation details
+* **Version management guide**: Added version management section to CLAUDE.md with procedures for bumping versions and release workflow
+
 # codecheck (development version)
 
+## Certificate Page Improvements
+
+* **Fixed codechecker links**: Codechecker names on certificate pages now link to their register landing pages (e.g., `/register/codecheckers/0000-0001-2345-6789/`) instead of ORCID profiles, making it easier to see all codechecks by that person (fixes #141)
+* **Added Type and Venue links**: Certificate pages now display clickable links for both the venue type and venue name in the CODECHECK Details section, enabling easier navigation to filtered register views (e.g., `/register/venues/journals/` and `/register/venues/journals/gigascience/`) (fixes #142)
+* **Venue-based breadcrumb navigation**: Certificate pages now include breadcrumb navigation showing the venue hierarchy (e.g., CODECHECK Register > Venues > Journals > GigaScience > 2024-001), enabling easy navigation to the venue's register page with a single click
+
+## Visual Improvements
+
+* **ORCID brand color**: ORCID icons on codechecker profile pages now display in the official ORCID green (#A6CE39) for proper brand compliance
+* **Updated Zenodo icon**: Replaced the Zenodo icon with the official blue "Z" SVG from EPFL, providing a more recognizable and polished appearance in register page footers
+* **Improved icon alignment**: Applied vertical alignment adjustments (`-5px`) to Zenodo, GitHub, and ORCID icons across all register pages for better alignment with adjacent text
+
+## Infrastructure Improvements
+
+* **Local library management**: Removed all external CDN dependencies (Bootstrap, Font Awesome, Academicons) and implemented local library management system
+* **New function**: Added `setup_external_libraries()` to download and install CSS/JS libraries locally in `docs/libs/`, ensuring reproducibility and offline capability
+* **Provenance tracking**: All external libraries now include comprehensive provenance information (version, license, date configured) stored in `docs/libs/PROVENANCE.csv`
+* **Automatic setup**: Libraries are automatically downloaded during register rendering if not already present
+* **Documentation**: Generated README.md in `docs/libs/` documenting all installed libraries and their licenses
+
+## Bug Fixes
+
+* **Fixed register rendering error**: Fixed "missing value where TRUE/FALSE needed" error when rendering register pages by adding proper NULL check for table_details[["name"]]
+* **Fixed venue type hyperlinks**: Fixed venue type links in venue lists that were rendering as Markdown syntax instead of proper HTML links due to missing closing parenthesis
+
+## Venue Configuration and Label Integration
+
+* **Dynamic venue configuration**: Venue information is now loaded from a `venues.csv` file instead of being hardcoded in `config.R`, making it easier to add and manage venues
+* **GitHub label integration**: Venue lists now include GitHub issue labels for each venue, enabling direct links to open checks
+* **Enhanced JSON output**: The venues JSON at `/register/venues/index.json` now includes an "Issue label" field for each venue
+* **Open checks links**: Venue HTML pages now display links to view open GitHub issues for each venue using their corresponding label
+* **New function**: Added `load_venues_config()` to load venue configuration from CSV files with columns: `name`, `longname`, and `label`
+* **Register repository**: Created `venues.csv` in the register repository to store venue metadata and GitHub labels
+* **Test updates**: All tests updated to work with the new venue configuration system using test fixtures
+* **Breaking change**: `register_render()` now requires a `venues_file` parameter (defaults to "venues.csv" in the working directory)
+
 ## GitHub Issue Validation
 
 * **New validation function**: Added `validate_certificate_github_issue()` to verify that certificate identifiers exist in the codecheckers/register GitHub repository