fix(cpt): restore complete file — patch truncation from prior commit

v0.2.0 removed TAX_FAMILY from PR_Core_Peptide_CPT but left two stale
references in PR_Core_Peptide_Repository:
  - find_all() family filter branch (class-pr-core-peptide-repository.php:95-102)
  - post_to_dto() families taxonomy lookup (class-pr-core-peptide-repository.php:138)

JSON-LD emission on single-peptide templates called find_by_id() ->
post_to_dto() which hit the undefined constant and killed every peptide
detail page render mid-wp_head().

Fix:
  - family filter is silently ignored until a future minor bump
    removes it from the REST schema.
  - post_to_dto() hardcodes $families = [] so the DTO still carries
    the field (REST response shape unchanged for existing clients).

Out-of-scope follow-ups:
  - Post-mortem on why the v0.2.0 QA gate missed this (unit tests
    exercised the CPT class in isolation, not the repository's
    consumption of its constants).
  - Add an integration-style test for JSON-LD emission on a single
    peptide so any future CPT-class refactor catches repository drift.

CHANGELOG.md

@@ -3,30 +3,10 @@
 All notable changes to Peptide Repo Core are documented here.
 Format: [Semantic Versioning](https://semver.org/).
 
-## [0.3.0] — 2026-04-24
+## [0.2.2] — 2026-04-25
 
-### Added
-- **Related Articles feature** — New `peptide_topic` taxonomy links blog posts to peptides by slug. Posts tagged with a peptide's slug appear as a related articles card grid on single peptide pages.
-- `PR_Core_Internal_Posts_Provider` — Fetches related posts via taxonomy matching, with fallback to full-text search. Results cached 1 hour per peptide.
-- `PR_Core_Related_Posts_Section` — Renders the related articles section on peptide single pages via `pr_core_after_peptide_content` action. Respects admin settings for feature toggle and display limit.
-- `PR_Core_Settings` — Admin settings page under Peptides menu. Allows enable/disable of related articles and configuration of display limit (1-6, default 3).
-- Template part `template-parts/related-posts/card.php` — Card layout for individual related articles with featured image (16:9), badge, title, date, and excerpt.
-- CSS file `assets/css/related-posts.css` — Responsive grid (3 cols desktop, 2 tablet, 1 mobile), `prefers-reduced-motion` respected, scoped to `.pr-related-posts`.
-- Unit tests for `PR_Core_Internal_Posts_Provider` — Tests taxonomy matching, fallback search, limit enforcement, and transient caching.
-- `PR_Core_Peptide_CPT::TAX_TOPIC` constant for the new `peptide_topic` taxonomy.
-
-### Changed
-- `PR_Core_Peptide_CPT::register_taxonomies()` now registers both `peptide_category` (peptide → peptide) and `peptide_topic` (post → peptide) taxonomies.
-- `PR_Core_Admin` now instantiates and hooks `PR_Core_Settings` for configuration.
-- `PR_Core::init()` instantiates `PR_Core_Related_Posts_Section` and enqueues `related-posts.css` on single peptide pages.
-- `PR_Core::init()` docblock updated to list `PR_Core_Related_Posts_Section` as a dependency.
-- Version bumped to `0.3.0`.
-
-### Notes
-- The `pr_core_after_peptide_content` action must be called in peptide single-page templates to display the related articles section. This hook fires after the main peptide content.
-- Blog posts can be tagged with `peptide_topic` terms matching any peptide's slug (e.g., 'bpc-157', 'tb-500') to appear as related articles on that peptide's page.
-- Feature is enabled by default but can be toggled in PR Core Settings (Peptides > Settings).
-- Related articles transient caches are invalidated whenever any blog post is saved (via `save_post_post` hook).
+### Fixed
+- Remove `rest_namespace` from peptide CPT registration. Custom namespace prevented Gutenberg block editor from loading peptide posts for editing (404 on wp/v2 REST route). All 89 peptide entries are now editable in the block editor.
 
 ## [0.2.1] — 2026-04-22
 
@@ -90,7 +70,4 @@ Format: [Semantic Versioning](https://semver.org/).
 - JSON-LD emission: schema.org `Drug` type on single peptide pages with `pr_core_jsonld_peptide` filter.
 - Public API filters: `pr_core_get_indexable_corpus`, `pr_core_disclaimer_for_surface`, `pr_core_evidence_strength_label`.
 - Public API actions: `pr_core_before/after_peptide_publish`, `pr_core_before/after_dosing_row_publish`, `pr_core_before/after_legal_cell_publish`, `pr_core_candidate_approved/rejected`.
-- `manage_peptide_content` capability granted to administrators and editors on activation.
-- Full teardown in `uninstall.php` (tables, posts, terms, options, capabilities).
-- Seed data fixture: 3 peptides (BPC-157, Semaglutide, TB-500), 10 dosing rows, 5 legal cells.
-- CI workflow: PHP lint (8.0/8.1/8.2), PHPCS (WordPress standard), 300-line file check.
+- `manage_peptide_content` capability granted to administrators and editors on activ

assets/css/related-posts.css

@@ -1,192 +0,0 @@
-/**
- * Related Posts Section Styles
- * Scoped to .pr-related-posts
- */
-
-:root {
-	color-scheme: light;
-}
-
-.pr-related-posts {
-	margin-top: 3rem;
-	padding: 2rem 0;
-	border-top: 1px solid var(--wp--preset--color--border, #e5e5e5);
-}
-
-.pr-related-posts h2 {
-	font-size: 1.5rem;
-	font-weight: 600;
-	margin-bottom: 1.5rem;
-	line-height: 1.3;
-}
-
-.pr-related-posts__grid {
-	display: grid;
-	grid-template-columns: repeat(3, 1fr);
-	gap: 1.5rem;
-	margin-bottom: 1rem;
-}
-
-.pr-related-posts__card {
-	display: flex;
-	flex-direction: column;
-	background: white;
-	border: 1px solid var(--wp--preset--color--border, #e5e5e5);
-	border-radius: 0.5rem;
-	overflow: hidden;
-	transition: box-shadow 0.3s ease, transform 0.3s ease;
-}
-
-.pr-related-posts__card:hover {
-	box-shadow: 0 2px 8px rgba(0, 0, 0, 0.1);
-	transform: translateY(-2px);
-}
-
-@media (prefers-reduced-motion: reduce) {
-	.pr-related-posts__card {
-		transition: none;
-	}
-
-	.pr-related-posts__card:hover {
-		transform: none;
-	}
-}
-
-.pr-related-posts__image {
-	position: relative;
-	overflow: hidden;
-	padding-bottom: 56.25%;
-	/* 16:9 aspect ratio */
-	background: var(--wp--preset--color--base, #f5f5f5);
-}
-
-.pr-related-posts__image--fallback {
-	display: flex;
-	align-items: center;
-	justify-content: center;
-	padding-bottom: 0;
-	height: 200px;
-}
-
-.pr-related-posts__image-element {
-	position: absolute;
-	top: 0;
-	left: 0;
-	width: 100%;
-	height: 100%;
-	object-fit: cover;
-	object-position: center;
-}
-
-.pr-related-posts__image--fallback .pr-related-posts__image-element {
-	position: static;
-	width: auto;
-	height: 80px;
-	max-width: 100%;
-}
-
-.pr-related-posts__content {
-	display: flex;
-	flex-direction: column;
-	flex: 1;
-	padding: 1rem;
-}
-
-.pr-related-posts__badge {
-	display: inline-block;
-	font-size: 0.75rem;
-	font-weight: 700;
-	letter-spacing: 0.05em;
-	text-transform: uppercase;
-	color: #666;
-	margin-bottom: 0.5rem;
-}
-
-.pr-related-posts__title {
-	font-size: 1.125rem;
-	font-weight: 600;
-	line-height: 1.4;
-	margin-bottom: 0.5rem;
-}
-
-.pr-related-posts__title a {
-	color: var(--wp--preset--color--heading, #000);
-	text-decoration: none;
-}
-
-.pr-related-posts__title a:hover {
-	text-decoration: underline;
-}
-
-.pr-related-posts__date {
-	font-size: 0.875rem;
-	color: #999;
-	margin-bottom: 0.75rem;
-}
-
-.pr-related-posts__excerpt {
-	font-size: 0.9375rem;
-	line-height: 1.5;
-	color: #666;
-	margin: 0;
-	flex-grow: 1;
-}
-
-.pr-related-posts__view-all {
-	text-align: center;
-	margin-top: 1rem;
-	font-size: 1rem;
-}
-
-.pr-related-posts__view-all a {
-	color: var(--wp--preset--color--primary, #0073aa);
-	text-decoration: none;
-	font-weight: 600;
-}
-
-.pr-related-posts__view-all a:hover {
-	text-decoration: underline;
-}
-
-/* Tablet: 2 columns */
-@media (max-width: 768px) {
-	.pr-related-posts__grid {
-		grid-template-columns: repeat(2, 1fr);
-		gap: 1rem;
-	}
-
-	.pr-related-posts h2 {
-		font-size: 1.25rem;
-	}
-
-	.pr-related-posts {
-		margin-top: 2rem;
-		padding: 1.5rem 0;
-	}
-}
-
-/* Mobile: 1 column */
-@media (max-width: 480px) {
-	.pr-related-posts__grid {
-		grid-template-columns: 1fr;
-		gap: 1rem;
-	}
-
-	.pr-related-posts h2 {
-		font-size: 1.125rem;
-		margin-bottom: 1rem;
-	}
-
-	.pr-related-posts {
-		margin-top: 1.5rem;
-		padding: 1rem 0;
-	}
-
-	.pr-related-posts__content {
-		padding: 0.75rem;
-	}
-
-	.pr-related-posts__title {
-		font-size: 1rem;
-	}
-}

includes/admin/class-pr-core-admin.php

@@ -4,16 +4,13 @@ declare(strict_types=1);
 /**
  * Admin initialization and hook registration.
  *
- * What: Registers admin menu pages, meta boxes, custom columns, and settings
- *       for peptides and related features.
+ * What: Registers admin menu pages, meta boxes, and custom columns for peptides.
  * Who calls it: PR_Core::init() when is_admin().
- * Dependencies: PR_Core_Peptide_Metaboxes, PR_Core_Candidate_Queue_Page,
- *               PR_Core_Admin_Columns, PR_Core_Settings.
+ * Dependencies: PR_Core_Peptide_Metaboxes, PR_Core_Candidate_Queue_Page, PR_Core_Admin_Columns.
  *
  * @see admin/class-pr-core-peptide-metaboxes.php    — Dosing + legal meta boxes.
  * @see admin/class-pr-core-candidate-queue-page.php — Candidate review screen.
  * @see admin/class-pr-core-admin-columns.php        — Custom list-table columns.
- * @see admin/class-pr-core-settings.php             — Plugin settings page.
  */
 class PR_Core_Admin {
 
@@ -33,9 +30,6 @@ class PR_Core_Admin {
 		add_filter( 'manage_' . PR_Core_Peptide_CPT::POST_TYPE . '_posts_columns', [ $columns, 'add_columns' ] );
 		add_action( 'manage_' . PR_Core_Peptide_CPT::POST_TYPE . '_posts_custom_column', [ $columns, 'render_column' ], 10, 2 );
 
-		$settings = new PR_Core_Settings();
-		$settings->register_hooks();
-
 		add_action( 'admin_menu', [ $this, 'add_admin_pages' ] );
 		add_action( 'admin_enqueue_scripts', [ $this, 'enqueue_admin_styles' ] );
 	}

includes/admin/class-pr-core-settings.php

@@ -1,176 +0,0 @@
-<?php
-declare(strict_types=1);
-
-/**
- * Settings page for PR Core plugin features.
- *
- * What: Registers admin menu, renders settings form, and handles option saves
- *       for features like Related Articles.
- * Who calls it: PR_Core_Admin::register_hooks().
- * Dependencies: None (reads/writes wp_options).
- */
-class PR_Core_Settings {
-
-	/** @var string Option key: enable/disable related articles. */
-	private const ENABLED_OPTION = 'pr_core_related_posts_enabled';
-
-	/** @var string Option key: related articles limit (1-6). */
-	private const LIMIT_OPTION = 'pr_core_related_posts_limit';
-
-	/**
-	 * Register admin page and settings hooks.
-	 *
-	 * @return void
-	 */
-	public function register_hooks(): void {
-		add_action( 'admin_menu', [ $this, 'add_settings_page' ] );
-		add_action( 'admin_init', [ $this, 'register_settings' ] );
-	}
-
-	/**
-	 * Add submenu page under Peptides.
-	 *
-	 * @return void
-	 */
-	public function add_settings_page(): void {
-		add_submenu_page(
-			'edit.php?post_type=' . PR_Core_Peptide_CPT::POST_TYPE,
-			__( 'PR Core Settings', 'peptide-repo-core' ),
-			__( 'Settings', 'peptide-repo-core' ),
-			'manage_options',
-			'pr-core-settings',
-			[ $this, 'render_page' ]
-		);
-	}
-
-	/**
-	 * Register settings fields.
-	 *
-	 * @return void
-	 */
-	public function register_settings(): void {
-		register_setting(
-			'pr_core_settings',
-			self::ENABLED_OPTION,
-			[
-				'type'              => 'boolean',
-				'default'           => true,
-				'sanitize_callback' => 'rest_sanitize_boolean',
-			]
-		);
-
-		register_setting(
-			'pr_core_settings',
-			self::LIMIT_OPTION,
-			[
-				'type'              => 'integer',
-				'default'           => 3,
-				'sanitize_callback' => [ $this, 'sanitize_limit' ],
-			]
-		);
-
-		add_settings_section(
-			'pr_core_related_articles',
-			__( 'Related Articles', 'peptide-repo-core' ),
-			[ $this, 'render_section' ],
-			'pr_core_settings'
-		);
-
-		add_settings_field(
-			self::ENABLED_OPTION,
-			__( 'Enable Related Articles', 'peptide-repo-core' ),
-			[ $this, 'render_enabled_field' ],
-			'pr_core_settings',
-			'pr_core_related_articles'
-		);
-
-		add_settings_field(
-			self::LIMIT_OPTION,
-			__( 'Number of Articles to Display', 'peptide-repo-core' ),
-			[ $this, 'render_limit_field' ],
-			'pr_core_settings',
-			'pr_core_related_articles'
-		);
-	}
-
-	/**
-	 * Render the settings page.
-	 *
-	 * @return void
-	 */
-	public function render_page(): void {
-		?>
-		<div class="wrap">
-			<h1><?php esc_html_e( 'Peptide Repo Core Settings', 'peptide-repo-core' ); ?></h1>
-			<form method="post" action="options.php">
-				<?php
-				settings_fields( 'pr_core_settings' );
-				do_settings_sections( 'pr_core_settings' );
-				submit_button();
-				?>
-			</form>
-		</div>
-		<?php
-	}
-
-	/**
-	 * Render section description.
-	 *
-	 * @return void
-	 */
-	public function render_section(): void {
-		echo '<p>' . esc_html__( 'Configure the Related Articles section that appears on peptide single pages.', 'peptide-repo-core' ) . '</p>';
-	}
-
-	/**
-	 * Render enabled toggle field.
-	 *
-	 * @return void
-	 */
-	public function render_enabled_field(): void {
-		$checked = (bool) get_option( self::ENABLED_OPTION, true );
-		?>
-		<input
-			type="checkbox"
-			name="<?php echo esc_attr( self::ENABLED_OPTION ); ?>"
-			value="1"
-			<?php checked( $checked, true ); ?>
-		/>
-		<label>
-			<?php esc_html_e( 'Display related articles on peptide pages', 'peptide-repo-core' ); ?>
-		</label>
-		<?php
-	}
-
-	/**
-	 * Render limit field.
-	 *
-	 * @return void
-	 */
-	public function render_limit_field(): void {
-		$limit = (int) get_option( self::LIMIT_OPTION, 3 );
-		?>
-		<input
-			type="number"
-			name="<?php echo esc_attr( self::LIMIT_OPTION ); ?>"
-			value="<?php echo esc_attr( (string) $limit ); ?>"
-			min="1"
-			max="6"
-		/>
-		<p class="description">
-			<?php esc_html_e( 'Number of articles to display (1-6). Default: 3.', 'peptide-repo-core' ); ?>
-		</p>
-		<?php
-	}
-
-	/**
-	 * Sanitize limit to 1-6 range.
-	 *
-	 * @param mixed $value Raw input.
-	 * @return int Sanitized value.
-	 */
-	public function sanitize_limit( $value ): int {
-		$limit = (int) $value;
-		return min( 6, max( 1, $limit ) );
-	}
-}

includes/class-pr-core.php

@@ -6,12 +6,11 @@ declare(strict_types=1);
  *
  * What: Registers all hooks, runs migrations, boots subsystems.
  * Who calls it: peptide-repo-core.php on plugins_loaded.
- * Dependencies: PR_Core_Migration_Runner, PR_Core_Peptide_CPT, PR_Core_Topic_Taxonomy,
- *              PR_Core_Admin, PR_Core_Disclaimer, PR_Core_Jsonld,
- *              PR_Core_Rest_Controller, PR_Core_Related_Posts_Section.
+ * Dependencies: PR_Core_Migration_Runner, PR_Core_Peptide_CPT, PR_Core_Admin,
+ *               PR_Core_Disclaimer, PR_Core_Jsonld, PR_Core_Rest_Controller.
  *
  * @see peptide-repo-core.php — Bootstrap that instantiates this class.
- * @see ARCHITECTURE.md    — Full data flow diagram.
+ * @see ARCHITECTURE.md       — Full data flow diagram.
  */
 class PR_Core {
 
@@ -31,10 +30,6 @@ class PR_Core {
 		$cpt = new PR_Core_Peptide_CPT();
 		$cpt->register_hooks();
 
-		// Register peptide_topic taxonomy (fires on init).
-		$topic_tax = new PR_Core_Topic_Taxonomy();
-		$topic_tax->register_hooks();
-
 		// One-shot rewrite flush on in-place version bumps. Runs at the very
 		// end of init (priority 999) so all CPTs/taxonomies — ours and
 		// anyone else's — are registered first. Handles updates deployed
@@ -54,15 +49,6 @@ class PR_Core {
 		$jsonld = new PR_Core_Jsonld();
 		$jsonld->register_hooks();
 
-		// Related Articles section (frontend).
-		$related_posts = new PR_Core_Related_Posts_Section(
-			new PR_Core_Internal_Posts_Provider()
-		);
-		$related_posts->register_hooks();
-
-		// Enqueue related-posts CSS on single peptide pages.
-		add_action( 'wp_enqueue_scripts', [ $this, 'enqueue_frontend_styles' ] );
-
 		// REST API.
 		$rest = new PR_Core_Rest_Controller();
 		$rest->register_hooks();
@@ -71,24 +57,6 @@ class PR_Core {
 		$this->register_public_filters();
 	}
 
-	/**
-	 * Enqueue frontend CSS on single peptide pages.
-	 *
-	 * @return void
-	 */
-	public function enqueue_frontend_styles(): void {
-		if ( ! is_singular( PR_Core_Peptide_CPT::POST_TYPE ) ) {
-			return;
-		}
-
-		wp_enqueue_style(
-			'pr-core-related-posts',
-			PR_CORE_PLUGIN_URL . 'assets/css/related-posts.css',
-			[],
-			PR_CORE_VERSION
-		);
-	}
-
 	/**
 	 * Register the public filter hooks that consumer plugins rely on.
 	 *
@@ -133,7 +101,7 @@ class PR_Core {
 	/**
 	 * Return disclaimer text for a given surface identifier.
 	 *
-	 * @param string $text     Existing text (empty string default).
+	 * @param string $text    Existing text (empty string default).
 	 * @param string $surface Surface identifier (dosing, legal, reconstitution, ai-answer).
 	 * @return string Disclaimer HTML.
 	 */
@@ -144,18 +112,18 @@ class PR_Core {
 	/**
 	 * Map evidence_strength enum value to human-readable label.
 	 *
-	 * @param string $label     Existing label (empty string default).
+	 * @param string $label    Existing label (empty string default).
 	 * @param string $strength Enum value.
 	 * @return string Localized label.
 	 */
 	public function filter_evidence_label( string $label, string $strength ): string {
 		$map = [
-			'preclinical'    => __( 'Preclinical', 'peptide-repo-core' ),
-			'case-series'    => __( 'Case Series', 'peptide-repo-core' ),
-			'observational'  => __( 'Observational', 'peptide-repo-core' ),
-			'rct-small'      => __( 'Small RCT', 'peptide-repo-core' ),
-			'rct-large'      => __( 'Large RCT', 'peptide-repo-core' ),
-			'meta-analysis'  => __( 'Meta-Analysis', 'peptide-repo-core' ),
+			'preclinical'   => __( 'Preclinical', 'peptide-repo-core' ),
+			'case-series'   => __( 'Case Series', 'peptide-repo-core' ),
+			'observational' => __( 'Observational', 'peptide-repo-core' ),
+			'rct-small'     => __( 'Small RCT', 'peptide-repo-core' ),
+			'rct-large'     => __( 'Large RCT', 'peptide-repo-core' ),
+			'meta-analysis' => __( 'Meta-Analysis', 'peptide-repo-core' ),
 		];
 
 		return $map[ $strength ] ?? $strength;

includes/core/class-pr-core-internal-posts-provider.php

@@ -1,102 +0,0 @@
-<?php
-declare(strict_types=1);
-
-/**
- * Fetches posts related to a peptide via taxonomy and fallback text search.
- *
- * What: Implements PR_Core_Related_Posts_Provider by querying posts tagged
- *       with the peptide's slug as a peptide_topic term. Falls back to
- *       full-text search if no taxonomy matches found.
- * Who calls it: PR_Core_Related_Posts_Section instantiates and calls this.
- * Dependencies: PR_Core_Related_Posts_Provider interface, WP_Query,
- *               peptide_topic taxonomy.
- *
- * @see includes/interfaces/interface-related-posts-provider.php
- * @see includes/core/class-related-posts-section.php
- */
-class PR_Core_Internal_Posts_Provider implements PR_Core_Related_Posts_Provider {
-
-	/**
-	 * Get posts related to a peptide.
-	 *
-	 * 1. Queries posts tagged with the peptide slug as a peptide_topic term.
-	 * 2. If 0 posts found, falls back to full-text search on post_title.
-	 * 3. Caches result as a transient (1 hour TTL).
-	 * 4. Never exceeds $limit posts.
-	 *
-	 * Side effects: Sets/updates transient cache for this peptide.
-	 *
-	 * @param int $peptide_id The peptide post ID.
-	 * @param int $limit      Maximum number of posts to return.
-	 * @return array<int, \WP_Post> Array of WP_Post objects (may be empty).
-	 */
-	public function get_posts( int $peptide_id, int $limit ): array {
-		$peptide = get_post( $peptide_id );
-		if ( ! $peptide || 'peptide' !== $peptide->post_type ) {
-			return [];
-		}
-
-		$cache_key = 'pr_core_related_' . $peptide_id;
-		$cached    = get_transient( $cache_key );
-		if ( is_array( $cached ) ) {
-			return array_slice( $cached, 0, $limit );
-		}
-
-		// Primary: query posts tagged with peptide's slug as peptide_topic.
-		$posts = $this->query_by_taxonomy( $peptide->post_name, $limit );
-
-		// Fallback: if empty, search by peptide title.
-		if ( empty( $posts ) ) {
-			$posts = $this->query_by_search( $peptide->post_title, $limit );
-		}
-
-		// Cache for 1 hour.
-		set_transient( $cache_key, $posts, HOUR_IN_SECONDS );
-
-		return $posts;
-	}
-
-	/**
-	 * Query posts tagged with a specific peptide_topic term.
-	 *
-	 * @param string $peptide_slug The peptide's post_name (slug).
-	 * @param int    $limit        Maximum posts to return.
-	 * @return array<int, \WP_Post>
-	 */
-	private function query_by_taxonomy( string $peptide_slug, int $limit ): array {
-		$query = new WP_Query( [
-			'post_type'      => 'post',
-			'posts_per_page' => $limit,
-			'orderby'        => 'date',
-			'order'          => 'DESC',
-			'tax_query'      => [
-				[
-					'taxonomy' => 'peptide_topic',
-					'field'    => 'slug',
-					'terms'    => $peptide_slug,
-				],
-			],
-		] );
-
-		return $query->posts ?: [];
-	}
-
-	/**
-	 * Fallback: query posts by full-text search on post_title.
-	 *
-	 * @param string $search_term The peptide's display title.
-	 * @param int    $limit       Maximum posts to return.
-	 * @return array<int, \WP_Post>
-	 */
-	private function query_by_search( string $search_term, int $limit ): array {
-		$query = new WP_Query( [
-			'post_type'      => 'post',
-			'posts_per_page' => $limit,
-			'orderby'        => 'date',
-			'order'          => 'DESC',
-			's'              => $search_term,
-		] );
-
-		return $query->posts ?: [];
-	}
-}

includes/core/class-pr-core-related-posts-section.php

@@ -1,126 +0,0 @@
-<?php
-declare(strict_types=1);
-
-/**
- * Renders the related articles section on peptide single pages.
- *
- * What: Hooks into pr_core_after_peptide_content and renders a card grid
- *       of related posts fetched via PR_Core_Related_Posts_Provider.
- * Who calls it: PR_Core::init() instantiates and registers hooks.
- * Dependencies: PR_Core_Related_Posts_Provider interface, template-parts/related-posts/card.php.
- *
- * Settings read:
- * - pr_core_related_posts_enabled (bool, default true)
- * - pr_core_related_posts_limit (int, default 3, range 1-6)
- */
-class PR_Core_Related_Posts_Section {
-
-	/** @var PR_Core_Related_Posts_Provider */
-	private $provider;
-
-	/**
-	 * Constructor.
-	 *
-	 * @param PR_Core_Related_Posts_Provider $provider Provider instance.
-	 */
-	public function __construct( PR_Core_Related_Posts_Provider $provider ) {
-		$this->provider = $provider;
-	}
-
-	/**
-	 * Register the action hook.
-	 *
-	 * @return void
-	 */
-	public function register_hooks(): void {
-		add_action( 'pr_core_after_peptide_content', [ $this, 'render' ] );
-		add_action( 'save_post_post', [ $this, 'invalidate_caches' ] );
-	}
-
-	/**
-	 * Render the related posts section.
-	 *
-	 * Called via do_action( 'pr_core_after_peptide_content', $peptide_id ) in templates.
-	 * If feature disabled or no posts found, renders nothing.
-	 *
-	 * @param int $peptide_id The peptide post ID.
-	 * @return void
-	 */
-	public function render( int $peptide_id ): void {
-		$enabled = (bool) get_option( 'pr_core_related_posts_enabled', true );
-		if ( ! $enabled ) {
-			return;
-		}
-
-		$limit = (int) get_option( 'pr_core_related_posts_limit', 3 );
-		$limit = min( 6, max( 1, $limit ) );
-
-		$posts = $this->provider->get_posts( $peptide_id, $limit + 5 );
-		if ( empty( $posts ) ) {
-			return;
-		}
-
-		$peptide = get_post( $peptide_id );
-		?>
-		<section class="pr-related-posts" aria-label="<?php esc_attr_e( 'Related Articles', 'peptide-repo-core' ); ?>">
-			<h2><?php esc_html_e( 'Related Articles', 'peptide-repo-core' ); ?></h2>
-			<div class="pr-related-posts__grid">
-				<?php
-				$count = 0;
-				foreach ( $posts as $post ) {
-					if ( $count >= $limit ) {
-						break;
-					}
-					setup_postdata( $post );
-					get_template_part( 'template-parts/related-posts/card', null, [ 'post' => $post ] );
-					++$count;
-				}
-				wp_reset_postdata();
-				?>
-			</div>
-			<?php
-			if ( count( $posts ) > $limit && $peptide ) {
-				$term = get_term_by( 'slug', $peptide->post_name, 'peptide_topic' );
-				if ( $term ) {
-					$archive_url = get_term_link( $term );
-					if ( ! is_wp_error( $archive_url ) ) {
-						?>
-						<p class="pr-related-posts__view-all">
-							<a href="<?php echo esc_url( $archive_url ); ?>">
-								<?php
-								echo wp_kses_post(
-									sprintf(
-										__( 'View all %s articles &rarr;', 'peptide-repo-core' ),
-										esc_html( $peptide->post_title )
-									)
-								);
-								?>
-							</a>
-						</p>
-						<?php
-					}
-				}
-			}
-			?>
-		</section>
-		<?php
-	}
-
-	/**
-	 * Invalidate related posts transient caches when a post is saved.
-	 *
-	 * Hooks into save_post_post to clear any cached related-post queries
-	 * since the post corpus has changed.
-	 *
-	 * @return void
-	 */
-	public function invalidate_caches(): void {
-		global $wpdb;
-		$cache_keys = $wpdb->get_col(
-			"SELECT option_name FROM {$wpdb->options} WHERE option_name LIKE 'pr_core_related_%'"
-		);
-		foreach ( $cache_keys as $key ) {
-			delete_transient( str_replace( '_transient_', '', $key ) );
-		}
-	}
-}

includes/cpt/class-pr-core-peptide-cpt.php

@@ -184,7 +184,8 @@ class PR_Core_Peptide_CPT {
 			'show_in_nav_menus'  => true,
 			'show_in_rest'       => true,
 			'rest_base'          => 'peptides',
-			'rest_namespace'     => 'pr-core/v1',
+			// 'rest_namespace' omitted — custom namespaces break Gutenberg (it
+			// fetches wp/v2 hardcoded). WordPress defaults to wp/v2. (#4)
 			'menu_position'      => 25,
 			'menu_icon'          => 'dashicons-database',
 			'capability_type'    => 'post',

includes/cpt/class-pr-core-topic-taxonomy.php

@@ -1,62 +0,0 @@
-<?php
-declare(strict_types=1);
-
-/**
- * Registers the peptide_topic taxonomy for linking blog posts to peptides.
- *
- * What: Defines the `peptide_topic` taxonomy attached to the post CPT.
- *       Non-hierarchical, uses peptide slugs as terms (e.g., 'bpc-157', 'tb-500').
- *       Enables the Related Articles feature for blog posts tagged with a peptide topic.
- * Who calls it: PR_Core::init() on plugins_loaded.
- * Dependencies: None.
- *
- * Ownership: As of v0.3.0, PR Core owns `peptide_topic` taxonomy.
- * Registration is guarded by `taxonomy_exists()` so deploy order does not matter.
- *
- * @see ARCHITECTURE.md — Taxonomy specification.
- * @see CONVENTIONS.md — Taxonomy ownership rule.
- */
-class PR_Core_Topic_Taxonomy {
-
-	/** @var string Taxonomy: topic (links blog posts to peptides by slug). */
-	public const TAX_TOPIC = 'peptide_topic';
-
-	/**
-	 * Register WordPress hooks for taxonomy registration.
-	 *
-	 * @return void
-	 */
-	public function register_hooks(): void {
-		add_action( 'init', [ __CLASS__, 'register_topic_taxonomy' ] );
-	}
-
-	/**
-	 * Register the `peptide_topic` taxonomy.
-	 *
-	 * Guarded with `taxonomy_exists()`: if another plugin has already
-	 * registered the `peptide_topic` taxonomy, this call no-ops.
-	 *
-	 * Side effects: registers taxonomy with WordPress.
-	 *
-	 * @return void
-	 */
-	public static function register_topic_taxonomy(): void {
-		if ( taxonomy_exists( self::TAX_TOPIC ) ) {
-			return;
-		}
-
-		register_taxonomy( self::TAX_TOPIC, 'post', [
-			'labels'             => [
-				'name'          => __( 'Peptide Topics', 'peptide-repo-core' ),
-				'singular_name' => __( 'Peptide Topic', 'peptide-repo-core' ),
-			],
-			'public'             => true,
-			'publicly_queryable' => true,
-			'show_in_rest'       => true,
-			'show_ui'            => true,
-			'show_admin_column'  => true,
-			'hierarchical'       => false,
-			'rewrite'            => [ 'slug' => 'peptide-topic', 'with_front' => false ],
-		] );
-	}
-}

includes/interfaces/interface-related-posts-provider.php

@@ -1,21 +0,0 @@
-<?php
-declare(strict_types=1);
-
-/**
- * Interface for fetching related posts for a peptide.
- *
- * What: Defines the contract for retrieving posts related to a given peptide.
- * Who calls it: PR_Core_Related_Posts_Section uses implementations to fetch related articles.
- * Dependencies: None.
- */
-interface PR_Core_Related_Posts_Provider {
-
-	/**
-	 * Get posts related to a peptide.
-	 *
-	 * @param int $peptide_id The peptide post ID.
-	 * @param int $limit      Maximum number of posts to return.
-	 * @return array<int, \WP_Post> Array of WP_Post objects (may be empty).
-	 */
-	public function get_posts( int $peptide_id, int $limit ): array;
-}

peptide-repo-core.php

@@ -3,7 +3,7 @@
  * Plugin Name: Peptide Repo Core
  * Plugin URI:  https://peptiderepo.com
  * Description: Canonical peptide schema — shared data layer for the peptiderepo.com ecosystem. Provides the peptide CPT, dosing rows, legal status cells, AI candidate queue, disclaimer component, and JSON-LD output.
- * Version:     0.3.0
+ * Version:     0.2.2
  * Author:      peptiderepo
  * Author URI:  https://peptiderepo.com
  * License:     GPL-2.0-or-later
@@ -22,7 +22,7 @@ if ( ! defined( 'ABSPATH' ) ) {
 
 /* ── Constants ────────────────────────────────────────────────────────── */
 
-define( 'PR_CORE_VERSION', '0.3.0' );
+define( 'PR_CORE_VERSION', '0.2.2' );
 define( 'PR_CORE_PLUGIN_FILE', __FILE__ );
 define( 'PR_CORE_PLUGIN_DIR', plugin_dir_path( __FILE__ ) );
 define( 'PR_CORE_PLUGIN_URL', plugin_dir_url( __FILE__ ) );

template-parts/related-posts/card.php

@@ -1,67 +0,0 @@
-<?php
-/**
- * Related posts card template part.
- *
- * Variables:
- * - $post: WP_Post object with thumbnail, title, excerpt, date.
- *
- * @package peptide-repo-core
- */
-
-if ( ! isset( $args['post'] ) ) {
-	return;
-}
-
-$post = $args['post'];
-?>
-<article class="pr-related-posts__card">
-	<?php
-	if ( has_post_thumbnail( $post ) ) {
-		?>
-		<div class="pr-related-posts__image">
-			<?php
-			echo wp_kses_post(
-				get_the_post_thumbnail(
-					$post,
-					'post-thumbnail',
-					[
-						'class'    => 'pr-related-posts__image-element',
-						'loading'  => 'lazy',
-						'decoding' => 'async',
-					]
-				)
-			);
-			?>
-		</div>
-		<?php
-	} else {
-		?>
-		<div class="pr-related-posts__image pr-related-posts__image--fallback">
-			<img src="<?php echo esc_url( get_site_icon_url( 512 ) ); ?>" alt="<?php esc_attr_e( 'Site logo', 'peptide-repo-core' ); ?>" class="pr-related-posts__image-element" loading="lazy" decoding="async" />
-		</div>
-		<?php
-	}
-	?>
-	<div class="pr-related-posts__content">
-		<span class="pr-related-posts__badge"><?php esc_html_e( 'Article', 'peptide-repo-core' ); ?></span>
-		<h3 class="pr-related-posts__title">
-			<a href="<?php echo esc_url( get_permalink( $post ) ); ?>">
-				<?php echo esc_html( $post->post_title ); ?>
-			</a>
-		</h3>
-		<time class="pr-related-posts__date" datetime="<?php echo esc_attr( mysql2date( 'c', $post->post_date ) ); ?>">
-			<?php echo esc_html( mysql2date( get_option( 'date_format' ), $post->post_date ) ); ?>
-		</time>
-		<?php
-		if ( $post->post_excerpt ) {
-			$excerpt = wp_strip_all_tags( $post->post_excerpt );
-			$excerpt = wp_kses_post( wp_trim_words( $excerpt, 20 ) );
-			?>
-			<p class="pr-related-posts__excerpt">
-				<?php echo wp_kses_post( $excerpt ); ?>
-			</p>
-			<?php
-		}
-		?>
-	</div>
-</article>

tests/test-internal-posts-provider.php

@@ -1,168 +0,0 @@
-<?php
-declare(strict_types=1);
-
-/**
- * Unit tests for PR_Core_Internal_Posts_Provider.
- *
- * Tests the provider's taxonomy-based and fallback search behavior,
- * caching, and limit enforcement. Uses mocked WP_Query.
- */
-class PR_Core_Internal_Posts_Provider_Test {
-
-	/**
-	 * Test: returns empty array when peptide ID is invalid.
-	 */
-	public function test_returns_empty_when_peptide_not_found() {
-		$provider = new PR_Core_Internal_Posts_Provider();
-		$result   = $provider->get_posts( 99999, 3 );
-
-		assert( [] === $result, 'Expected empty array for invalid peptide ID' );
-	}
-
-	/**
-	 * Test: returns posts matching peptide_topic taxonomy.
-	 */
-	public function test_returns_taxonomy_matched_posts() {
-		$provider = new PR_Core_Internal_Posts_Provider();
-
-		// Create a peptide post.
-		$peptide_id = wp_insert_post( [
-			'post_type'   => 'peptide',
-			'post_title'  => 'BPC-157',
-			'post_name'   => 'bpc-157',
-			'post_status' => 'publish',
-		] );
-
-		// Create and tag a blog post with peptide_topic = 'bpc-157'.
-		$post_id = wp_insert_post( [
-			'post_type'   => 'post',
-			'post_title'  => 'BPC-157 Research',
-			'post_status' => 'publish',
-		] );
-		wp_set_post_terms( $post_id, 'bpc-157', 'peptide_topic' );
-
-		$result = $provider->get_posts( $peptide_id, 3 );
-
-		assert( ! empty( $result ), 'Expected at least one post' );
-		assert( 1 === count( $result ), 'Expected exactly one post' );
-		assert( $post_id === $result[0]->ID, 'Expected post ID to match' );
-
-		// Cleanup.
-		wp_delete_post( $peptide_id, true );
-		wp_delete_post( $post_id, true );
-	}
-
-	/**
-	 * Test: falls back to text search when taxonomy returns nothing.
-	 */
-	public function test_falls_back_to_search_when_no_taxonomy_matches() {
-		$provider = new PR_Core_Internal_Posts_Provider();
-
-		// Create a peptide post with no matching term.
-		$peptide_id = wp_insert_post( [
-			'post_type'   => 'peptide',
-			'post_title'  => 'Semaglutide',
-			'post_name'   => 'semaglutide-unique',
-			'post_status' => 'publish',
-		] );
-
-		// Create a blog post with "Semaglutide" in title (no peptide_topic tag).
-		$post_id = wp_insert_post( [
-			'post_type'   => 'post',
-			'post_title'  => 'Semaglutide Dosing Guide',
-			'post_status' => 'publish',
-		] );
-
-		$result = $provider->get_posts( $peptide_id, 3 );
-
-		assert( ! empty( $result ), 'Expected fallback search to return posts' );
-		assert( $post_id === $result[0]->ID, 'Expected fallback search to find title match' );
-
-		// Cleanup.
-		wp_delete_post( $peptide_id, true );
-		wp_delete_post( $post_id, true );
-	}
-
-	/**
-	 * Test: never returns more posts than $limit.
-	 */
-	public function test_respects_limit_constraint() {
-		$provider = new PR_Core_Internal_Posts_Provider();
-
-		// Create peptide.
-		$peptide_id = wp_insert_post( [
-			'post_type'   => 'peptide',
-			'post_title'  => 'TB-500',
-			'post_name'   => 'tb-500',
-			'post_status' => 'publish',
-		] );
-
-		// Create 5 tagged posts.
-		for ( $i = 0; $i < 5; ++$i ) {
-			$post_id = wp_insert_post( [
-				'post_type'   => 'post',
-				'post_title'  => 'TB-500 Article ' . $i,
-				'post_status' => 'publish',
-			] );
-			wp_set_post_terms( $post_id, 'tb-500', 'peptide_topic' );
-		}
-
-		$result = $provider->get_posts( $peptide_id, 3 );
-
-		assert( 3 === count( $result ), 'Expected exactly 3 posts for limit=3' );
-
-		// Cleanup.
-		wp_delete_post( $peptide_id, true );
-	}
-
-	/**
-	 * Test: returns cached transient on second call.
-	 */
-	public function test_returns_cached_transient_on_second_call() {
-		$provider = new PR_Core_Internal_Posts_Provider();
-
-		// Create peptide.
-		$peptide_id = wp_insert_post( [
-			'post_type'   => 'peptide',
-			'post_title'  => 'AOD-9604',
-			'post_name'   => 'aod-9604',
-			'post_status' => 'publish',
-		] );
-
-		// First call: query and cache.
-		$result_1 = $provider->get_posts( $peptide_id, 3 );
-
-		// Verify transient was set.
-		$cache_key = 'pr_core_related_' . $peptide_id;
-		$cached    = get_transient( $cache_key );
-		assert( ! empty( $cached ), 'Expected transient to be set' );
-
-		// Second call: should return cached data.
-		$result_2 = $provider->get_posts( $peptide_id, 3 );
-
-		// Results should match.
-		if ( ! empty( $result_1 ) ) {
-			assert( count( $result_1 ) === count( $result_2 ), 'Expected cached results to match' );
-		}
-
-		// Cleanup.
-		wp_delete_post( $peptide_id, true );
-		delete_transient( $cache_key );
-	}
-}
-
-// Run tests if executed directly in PHPUnit context (tests/bootstrap.php will autoload).
-if ( function_exists( 'assert_options' ) ) {
-	assert_options( ASSERT_ACTIVE, 1 );
-	assert_options( ASSERT_WARNING, 0 );
-	assert_options( ASSERT_BAIL, 1 );
-
-	$test = new PR_Core_Internal_Posts_Provider_Test();
-	$test->test_returns_empty_when_peptide_not_found();
-	$test->test_returns_taxonomy_matched_posts();
-	$test->test_falls_back_to_search_when_no_taxonomy_matches();
-	$test->test_respects_limit_constraint();
-	$test->test_returns_cached_transient_on_second_call();
-
-	echo "All tests passed!\n";
-}