v4.5.0: drop peptide CPT registration; add PR Core dependency check (#15)
Drops PSA registration of peptide CPT + peptide_category taxonomy (PR Core >= 0.2.0 now owns them per 2026-04-22 consolidation). Adds hard dependency check on PR Core 0.2.0+ — PSA self-deactivates with an admin notice if PR Core is missing or below min version.
CI note: PHPUnit failures (PSA_AI_Content, PSA_Directory_API not found) and WPCS failure are pre-existing on main at HEAD 65f973f (verified: same 5 errors in run 24530495421). PHP Lint green on 7.4/8.1/8.3. No regressions introduced by this PR.
QA: qa-reviews/2026-04-22-2609c66.md PASS.
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peptiderepo
@@ -10,8 +10,8 @@ Peptide Search AI is a WordPress plugin that transforms sites into intelligent,
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```
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peptide-search-ai/
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├── peptide-search-ai.php Main plugin file; defines constants, hooks init/admin_init
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├── uninstall.php Cleans up all peptide posts, meta, options, transients
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├── peptide-search-ai.php Main plugin file; defines constants, hooks init/admin_init, gates CPT boot paths on PSA_Dependency_Check
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├── uninstall.php Cleans up PSA-owned options, transients, and the `wp_psa_api_logs` table (v4.5.0+ does NOT touch peptide posts/terms — owned by PR Core)
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├── readme.txt Plugin directory listing (WordPress.org metadata)
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├── composer.json PHP dependencies; PSR-4 autoloader for includes/
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├── .phpcs.xml.dist WordPress Coding Standards (WPCS) configuration
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@@ -20,7 +20,8 @@ peptide-search-ai/
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├── includes/
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│ ├── class-psa-config.php Configuration constants (rate limits, timeouts, tokens, TTL)
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│ ├── class-psa-encryption.php AES-256-CBC encryption for API keys at rest
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│ ├── class-psa-post-type.php CPT registration, peptide_category taxonomy, meta field definitions
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│ ├── class-psa-dependency-check.php PR Core >= 0.2.0 dependency gate + admin notice (v4.5.0)
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│ ├── class-psa-post-type.php Admin columns + `psa_*` meta key definitions on the `peptide` CPT owned by PR Core
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│ ├── class-psa-search.php AJAX search, REST API route, shortcode rendering, cache mgmt
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│ ├── class-psa-directory.php Browsable directory: [peptide_directory] shortcode + /v1/compounds REST endpoint
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│ ├── class-psa-ai-generator.php AI pipeline orchestrator (validation, generation, category assignment, meta save)
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@@ -214,6 +215,9 @@ graph TD
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### 1. Custom Post Type + Post Meta vs. Custom Tables
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**Decision:** Use CPT (`post_type='peptide'`) with post meta fields (`psa_*`).
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Registration moved from PSA to Peptide Repo Core (PR Core) in PSA v4.5.0 —
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see the "Post types" section above. The CPT-vs-custom-tables choice itself
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still holds; only ownership of the registration moved.
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**Rationale:**
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- **WordPress integration:** Leverage native post, user, revision, and permission systems.
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@@ -274,6 +278,23 @@ graph TD
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- PubChem cache: 7 days for hits, 12 hours for misses
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- Rate limit counters: 1 hour per request window
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## Post types
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PSA no longer registers any post type. The `peptide` CPT and `peptide_category`
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taxonomy are owned by Peptide Repo Core (PR Core). PSA depends on PR Core ≥ 0.2.0
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for these to be available.
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PSA still owns:
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- Meta boxes attached to the `peptide` CPT (psa_peptide_data, psa_extended_data)
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- The `psa_*` meta key namespace on peptide posts
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- Search index, directory widget, KB renderer, search REST endpoints
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Dependency is enforced at boot by `PSA_Dependency_Check::is_satisfied()` — when
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PR Core < 0.2.0 or is absent, PSA renders an admin notice and all CPT-bound
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surfaces (meta boxes, admin columns, directory, KB renderer, search, single-
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peptide template) skip registration. Non-CPT surfaces (settings page, upgrade
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driver) still boot so the admin can read the notice and configure the plugin.
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## Data Storage
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### Post Meta Fields (PSA_Post_Type::META_FIELDS)
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@@ -307,13 +328,19 @@ All stored on peptide posts as post meta:
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| `psa_cycle_parameters` | Cycle/protocol phase info | Text | AI (v4.3.0) |
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| `psa_amino_acid_count` | Number of amino acids | Integer | Derived from sequence (v4.3.0) |
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### Taxonomy: peptide_category (v4.3.0)
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### Taxonomy: peptide_category
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Hierarchical taxonomy registered on the `peptide` CPT. Pre-populated terms:
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Tissue Repair, Lipid Metabolism, Aging Research, Dermatological, Metabolic, Growth Hormone, Immunology, Endocrine.
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Hierarchical taxonomy on the `peptide` CPT. **Registered by PR Core** (>= 0.2.0)
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as of PSA v4.5.0 — PSA no longer calls `register_taxonomy( 'peptide_category', … )`.
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The 8 terms seeded by earlier PSA versions (Tissue Repair, Lipid Metabolism, Aging
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Research, Dermatological, Metabolic, Growth Hormone, Immunology, Endocrine) stay
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intact because `wp_term_taxonomy` is keyed on the taxonomy name, which is
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unchanged.
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Auto-assigned during AI generation via `PSA_AI_Generator::assign_category_term()`.
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Migration for existing peptides via admin "Migrate Existing Peptides to Categories" button.
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PSA continues to *read* and *write* term assignments on peptide posts — any
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plugin can operate on a public taxonomy. `PSA_AI_Generator::assign_category_term()`
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still auto-assigns during AI generation; the admin "Migrate Existing Peptides
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to Categories" button still runs.
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### Integration Hooks (v4.3.0)
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@@ -434,40 +461,4 @@ The plugin stores the schema version it last migrated to in a separate option, `
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## Performance Optimizations
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- **Post caching:** `_prime_post_caches()` and `update_meta_cache()` batch-load posts and meta (lines 458–459 in class-psa-search.php).
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- **Transient caching:** Search results cached 6 hours; invalidated on post save.
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- **Conditional asset loading:** CSS/JS only loaded on relevant pages.
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- **Lazy PubChem:** Optional, can be disabled via setting.
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- **Daily generation cap:** 50/day to limit API costs.
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- **Separate validation model:** Fast/cheap model for upfront validation to reduce full-generation calls.
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## Testing
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**CI Pipeline:** `.github/workflows/ci.yml`
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- PHPUnit tests across PHP 7.4, 8.1, 8.3
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- PHP syntax checks across PHP 7.4, 8.1, 8.3
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- WordPress Coding Standards (PHPCS) validation
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- JavaScript syntax checks (Node.js)
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**Post-Deploy:** `.github/workflows/deploy.yml`
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- HTTP health check verifies site returns 200
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- REST API smoke test verifies `/wp-json/peptides/v1/search?q=BPC-157` responds
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**Manual Testing Checklist:**
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- Search for existing peptide → results appear
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- Search for new peptide (valid) → "pending" message → check back → content generated
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- Search for invalid peptide → "not recognized" message
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- Test rate limits (10/hour AJAX, 20/hour REST API)
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- Verify PubChem data merges correctly
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- Test auto-publish on/off
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- Verify shortcode works multiple times on same page
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- Test on mobile (600px breakpoint)
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## Deployment
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See `.github/workflows/deploy.yml`:
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1. Push to main triggers CI tests.
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2. If tests pass, validate deployment readiness (required files, no sensitive data).
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3. Sync clean files to orphan `deploy` branch.
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4. SSH to Hostinger, git pull `deploy` branch into plugin directory.
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5. Verify deployment (check version, required files exist).
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- **Post caching:** `_prime_post_caches()` and `update_meta_cache()` batch-load posts and meta (lines 458–4
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