peptide-repo-core/CHANGELOG.md

Changelog

All notable changes to Peptide Repo Core are documented here. Format: Semantic Versioning.

[0.2.2] — 2026-04-25

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

Fixed

• P1 hotfix: fatal Undefined constant PR_Core_Peptide_CPT::TAX_FAMILY on every peptide page. The v0.2.0 release removed TAX_FAMILY from PR_Core_Peptide_CPT but left two stale references in PR_Core_Peptide_Repository (the family filter branch in find_all() and the families lookup in post_to_dto()). JSON-LD emission on single-peptide templates called find_by_id(), which called post_to_dto(), which hit the undefined constant and killed page rendering mid-wp_head(). QA gate on 874f93b missed this because the unit tests cover the CPT class in isolation, not the repository's consumption of its constants. Post-mortem + QA checklist update to follow.

Changed

• PR_Core_Peptide_Repository::find_all() — family filter is now silently ignored rather than throwing. Next minor bump will remove it from the REST schema.
• PR_Core_Peptide_DTO::$families is preserved but always populated as []. Keeps REST response shape stable for existing clients; will be dropped with a release note.

[0.2.0] — 2026-04-22

Changed (BREAKING)

• CPT renamed from pr_peptide to peptide. Consolidates with PSA's existing peptide CPT which owns the 89 canonical peptide posts on production.
• Taxonomy renamed from pr_peptide_category to peptide_category. Same reason.
• CPT args harmonized as superset of PSA + prior PR Core registration (supports now includes thumbnail + revisions + custom-fields).
• Defensive registration: guards with post_type_exists() / taxonomy_exists() so PSA's parallel registration no-ops cleanly during the PSA v4.5.0 transition.

Added

• PR_Core_Activator::maybe_flush_on_version_change() — one-shot rewrite flush on in-place version bumps (hooked at init priority 999). Eliminates the need for a manual wp rewrite flush after updates that change CPT/taxonomy slugs.
• _pr_core_authored post-meta flag contract — peptide posts created via PR Core UI carry this flag; uninstall.php uses it to scope teardown to plugin-owned posts only.
• Lightweight unit-test harness (tests/bootstrap.php + tests/unit/test-peptide-cpt.php) that exercises CPT/taxonomy guards and args payload shape without a PHPUnit + wp-env dependency. Wired into the existing PHP-lint CI job.

Removed

• pr_peptide_family taxonomy — never populated, never surfaced in UI.
• All pr_peptide* CPT-slug-derived references (constants, docblock mentions, uninstall string literals).
• Blanket DELETE FROM posts WHERE post_type = 'pr_peptide' on uninstall. Replaced with a join-on-_pr_core_authored selective delete so PSA-authored peptide posts are never destroyed by PR Core teardown.
• Taxonomy-term cleanup on uninstall. peptide_category is shared ownership post-v0.2.0; term data the site still needs is preserved.

Fixed

• Production peptide detail pages (all 89) were 404'ing due to a rewrite slug collision between PSA's peptide CPT and PR Core's pr_peptide CPT both claiming /peptides/%postname%/. PR Core v0.1.1's empty pr_peptide CPT was winning the rewrite resolution. This release consolidates both to a single peptide CPT owned by PR Core.

Notes

• Scope of the pr_peptide* scrub is intentionally narrow: CPT-slug-derived identifiers only. Class names (PR_Core_Peptide_CPT), file names (class-pr-core-peptide-cpt.php), plugin constants (PR_CORE_VERSION), option keys (pr_core_*), and the REST namespace (pr-core/v1) are the plugin's own namespace, not the CPT slug, and are preserved verbatim.
• PR Core-defined meta keys (display_name, aliases, evidence_strength, editorial_review_status, …) are gated by manage_peptide_content. The activator grants this capability to administrator and editor roles on activation. Prod sites where the activation hook never fired (v0.1.1 was deployed manually) will receive the grant on next wp plugin activate peptide-repo-core. Follow-up thread to decide whether a dedicated peptide_editor role is more appropriate than extending core editor.

[0.1.1] — 2026-04-19

Fixed

• Fatal error on activation: NAMESPACE is a PHP reserved keyword. Renamed to REST_NAMESPACE in the REST controller.
• Fatal error: autoloader cannot resolve PR_Core class. Class name equals the autoloader prefix exactly, producing wrong filename. Added explicit require_once in bootstrap (same pattern as PRAutoBlogger).

[0.1.0] — 2026-04-17

Added

• pr_peptide custom post type with REST API, archive, and taxonomies (pr_peptide_category, pr_peptide_family).
• Post-meta fields: display_name, aliases, molecular_formula, molecular_weight, cas_number, drugbank_id, chembl_id, evidence_strength, editorial_review_status, last_editorial_review_at, medical_editor_id.
• Custom table pr_dosing_rows with schema migration 0001 — high-cardinality dosing data with citation tracking, evidence strength, and supersede (soft-delete) pattern.
• Custom table pr_legal_cells with schema migration 0002 — per-country legal status with unique constraint on peptide x country (active).
• Custom table pr_ai_candidate_queue with schema migration 0003 — AI-extracted dosing candidates awaiting human review.
• Migration runner with sequential versioning (pr_core_schema_version option, PR_CORE_TARGET_SCHEMA_VERSION constant).
• Typed DTOs: PR_Core_Peptide_DTO, PR_Core_Dosing_Row_DTO, PR_Core_Legal_Cell_DTO, PR_Core_Candidate_DTO.
• Repository classes: PR_Core_Peptide_Repository, PR_Core_Dosing_Repository, PR_Core_Legal_Repository, PR_Core_Candidate_Queue_Repository.
• REST API (pr-core/v1): list/get peptides, list/create dosing rows, list/create legal cells.
• Admin UI: Scientific Identifiers meta box, Dosing Data meta box (read-only), Legal Status meta box (read-only), custom list-table columns (Evidence, Editorial, Dosing Rows).
• AI Candidate Queue admin page with approve/reject workflow (copies approved rows to dosing table).
• Shared disclaimer component: [pr_disclaimer surface="dosing"] shortcode, PR_Core_Disclaimer::render() static method, pr_core_disclaimer_for_surface filter.
• 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 activ