peptide-search-ai/CHANGELOG.md

Changelog

All notable changes to the Peptide Search AI plugin will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[4.7.0] — 2026-06-16

Changed

• .github/workflows/ci.yml: replaced per-repo CI jobs with thin caller for the reusable peptiderepo/peptide-e2e/.github/workflows/ci.yml@main (tests: stubs, has_js: true). Adds blocking PHPCS, 300-line file-size enforcement, and phpcbf auto-commit on PRs.
• .github/workflows/deploy.yml: dropped redundant file-existence and PHP-syntax checks now covered by the reusable CI; kept PSA_VERSION constant check.
• includes/class-psa-admin.php: removed dead backward-compat proxy methods (all delegated to PSA_Admin_Page; zero external callers). File reduced from 327 → 290 lines (estate 300-line rule compliance).
• includes/class-psa-ai-generator.php: removed untested backward-compat proxies (save_peptide_meta, assign_category_term); retained build_validation_prompt and build_generation_prompt as tested proxies (AIGeneratorTest uses reflection). Section headers condensed. File 309 → 299 lines.
• includes/class-psa-search.php: removed dead backward-compat proxy methods (all delegated to PSA_Search_Handler; zero external callers). File reduced from 307 → 294 lines.
• peptide-search-ai.php: synced PSA_VERSION constant (was stuck at 4.5.0) with plugin header (was 4.6.0); both now 4.7.0.
• package.json / package-lock.json: added minimal npm manifest (no dependencies) so the reusable lint-js job can run npm ci and fall back to node --check on the three JS asset files.

[4.6.0] — 2026-04-26

Changed

• assets/css/peptide-search.css: adopted brand tokens — replaced hardcoded #2563eb blue with var(--teal-500) family; font → Inter / IBM Plex Mono
• assets/css/psa-directory.css: same token adoption; active tabs/filters → teal; dark mode active states → teal

[4.5.1] - 2026-04-23

Changed

• Plugin header: author updated to peptiderepo, Plugin URI corrected to GitHub repo URL.

[4.5.0] - 2026-04-22

Changed (BREAKING)

• Dropped registration of the peptide custom post type and peptide_category taxonomy. These are now owned by Peptide Repo Core (PR Core) v0.2.0+, the canonical peptide data layer. Existing posts and term relationships are unaffected — they continue to work with PR Core's registration.
• PSA now has a hard dependency on PR Core ≥ 0.2.0. An admin notice appears if the dependency is not met; PSA features that operate on the peptide CPT (meta boxes, admin columns, directory widget, KB renderer, search widget, single-peptide template) degrade gracefully until PR Core is updated.
• psa_activate() no longer seeds default peptide_category terms — PR Core inherits the 8 existing terms via taxonomy-name keying in wp_term_taxonomy.
• uninstall.php no longer deletes peptide posts or peptide_category terms. Those entities are owned by PR Core as of this release; removing them on PSA uninstall would break cross-plugin contracts. PSA uninstall now only removes PSA's own options, transients, and the wp_psa_api_logs table.

Added

• PSA_Dependency_Check class (includes/class-psa-dependency-check.php): verifies PR_CORE_VERSION >= 0.2.0, renders an admin notice when unmet, and is used as a boot-path gate by CPT-dependent PSA classes.
• PHPUnit coverage for PSA_Dependency_Check::is_satisfied() across undefined / 0.1.1 / 0.2.0 / 0.3.0 version scenarios plus a regression assertion that PSA_Post_Type no longer exposes register_post_type or register_taxonomy call paths.

Removed

• PSA_Post_Type::register_peptide_post_type() method.
• PSA_Post_Type::register_taxonomy() method.
• PSA_Post_Type::populate_default_categories() method and its activation hook (seeding is a data-layer concern now owned by PR Core; the 8 existing terms remain in wp_term_taxonomy).
• Note: the PSA_Post_Type::DEFAULT_CATEGORIES constant is retained — PSA still consumes it as a slug→name reference list in PSA_AI_Content::assign_category_term() and the admin "Migrate Existing Peptides to Categories" button. Its role changed from "seed list" to "consumer lookup"; the value is unchanged.

Unchanged

• Meta boxes (psa_peptide_data, psa_extended_data) and all psa_* meta keys on peptide posts.
• Directory shortcode [peptide_directory] and its /wp-json/peptide-search-ai/v1/compounds REST endpoint.
• Single-peptide template (PSA_Template) and KB article renderer (PSA_KB_Builder).
• Search widget, /wp-json/peptides/v1/search REST endpoint, and AJAX search handler.
• Cost tracker, API logs table schema, and the psa_db_version option.

Migration notes

• No data migration required. The existing peptide posts and all peptide_category term assignments remain intact and functional — PR Core registers the same post-type name (peptide) and taxonomy name (peptide_category), so wp_posts.post_type and wp_term_taxonomy.taxonomy continue to resolve.
• After upgrading, ensure PR Core is at 0.2.0 or later — otherwise PSA surfaces an admin notice and degrades the peptide-dependent features until PR Core is updated.
• Deploy order (coordinated release): PR Core v0.2.0 ships first and restores the peptide detail pages on its own (PSA v4.4.3's existing post_type_exists( 'peptide' ) guard no-ops its registration once PR Core claims the CPT). PSA v4.5.0 ships second as cleanup — no user-visible change at that point.

[4.4.3] - 2026-04-14

Fixed

• Cost tracker $0.00 bug: DeepSeek models on OpenRouter omit the usage object from API responses, causing all token counts and costs to log as zero. Added character-based token estimation fallback (~3.75 chars/token for scientific English) so spend is always tracked.

Added

• token_source column in psa_api_logs table distinguishing measured (api) vs. estimated (estimated) token counts. Migrated via dbDelta on plugin activation.
• DeepSeek and Qwen model pricing in PSA_Cost_Tracker::estimate_cost(): deepseek/deepseek-v3.2, deepseek/deepseek-chat, deepseek/deepseek-r1, qwen/qwen3.6-plus:free.
• PSA_Cost_Tracker::get_monthly_estimated_count() method for querying how many API calls used estimates in a given month.
• Admin UI indicators for estimated data: amber warning icon on monthly summary ("includes estimates"), ~ prefix on estimated token/cost values in the log table, and tooltips explaining the estimation method.
• Diagnostic logging of raw usage field from OpenRouter for models that report zero tokens (temporary — remove after confirming).

Changed

• PSA_OpenRouter::send_request_once() now passes token_source to cost tracker alongside token counts.
• Version bump to 4.4.3.

[4.3.0] - Unreleased

Added

• Browsable Peptide Directory: [peptide_directory] shortcode renders a card-based grid with category filtering, search, pagination, and detail modal.
• Category Taxonomy: peptide_category taxonomy on the peptide CPT with 8 pre-populated terms (Tissue Repair, Lipid Metabolism, Aging Research, Dermatological, Metabolic, Growth Hormone, Immunology, Endocrine).
• 9 Extended Meta Fields: half-life, stability, solubility, vial size, storage (lyophilized/reconstituted), typical dose, cycle parameters, amino acid count.
• REST API Endpoint: GET /wp-json/peptide-search-ai/v1/compounds with search, category, pagination, and basic/full field sets for cross-plugin data access.
• Detail Modal: Accessible overlay triggered from directory cards showing full compound data, copyable sequence, PubChem link, and "View Full Page" link.
• Integration Hooks: psa_after_peptide_detail action, psa_directory_card_extras and psa_rest_compound_data filters for Peptide Community plugin.
• Category Auto-Assignment: AI generator now assigns peptide_category taxonomy terms during content generation.
• Admin Data Tools: "Migrate Existing Peptides to Categories" button and "Re-enrich Existing Peptides" button with background job queuing.
• Dark Mode Support: Directory styles work with data-theme="dark" via CSS custom properties.
• Category Badge Colors: Exported as CSS custom properties (--psa-cat-*) for reuse by other plugins.
• New file: includes/class-psa-directory.php — directory REST endpoint and shortcode.
• New file: assets/js/psa-directory.js — directory grid, filters, modal (vanilla JS).
• New file: assets/css/psa-directory.css — directory styles with responsive breakpoints.
• PHPUnit tests for PostType and Directory classes.

Changed

• Updated AI generation prompt to request extended fields (half-life, stability, storage, etc.).
• class-psa-post-type.php now includes taxonomy registration and EXTENDED_META_FIELDS constant.
• class-psa-template.php refactored into smaller private methods; shows extended research data on single peptide pages.
• class-psa-admin.php includes Data Tools section with migration and re-enrichment actions.
• peptide-search-ai.php registers new directory class, taxonomy, and conditional asset loading.
• Version bump to 4.3.0.

[4.2.0] - Unreleased

Added

• PHPUnit test execution in CI pipeline across PHP 7.4, 8.1, 8.3.
• HTTP health check and REST API smoke test after deployment.
• declare(strict_types=1) and typed parameters/return types on all class files.
• Consistent 3-question preamble docblocks on all classes (what / who calls / dependencies).
• @see cross-references at top of related class files.
• New PSA_OpenRouter class — extracted API communication layer from PSA_AI_Generator.
• New PSA_KB_Builder class — extracted KB article builder from PSA_AI_Generator.
• Internationalization (i18n) for all frontend JS strings via wp_localize_script.
• This CHANGELOG file.

Changed

• PSA_AI_Generator now delegates to PSA_OpenRouter and PSA_KB_Builder (reduced from 827 to ~470 lines).
• Updated test suite to call PSA_OpenRouter::parse_response() instead of removed private method.
• Updated