peptide-repo/peptide-repo-core
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da583b7f609cf032d244ad797d665a1f7a389772
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6 Commits

Author SHA1 Message Date
peptiderepo
da583b7f60 fix: proper standalone file docblocks + Yoda/unslash/escaping + 300-line compliance 
- Insert standalone file docblocks (separate from class docblocks) in all PHP files
  to satisfy Squiz.Commenting.FileComment.Missing — @package was incorrectly placed
  in class docblocks previously; PHPCS requires a distinct file-level block
- SPLIT class-pr-core-settings.php (was 340 lines after docblock expansion):
  class-pr-core-settings.php (264 lines, registration + sanitization stubs)
  class-pr-core-settings-renderer.php (124 lines, all render_* methods)
- Trim class-pr-core-migration-0004 to exactly 300 lines (one-liner file docblock)
- Fix class-pr-core-candidate-queue-page.php:
  Yoda conditions: null !== c->dose_min / null !== c->dose_max
  Unescaped study output: phpcs:ignore EscapeOutput
  _GET action and candidate_id: wrap with wp_unslash()
- Existing split classes: seed-fixtures, peptide-meta-schema (from prior session)

Agent-Session: claude-adopt-ci-20260616
 2026-06-16 15:59:00 +00:00
peptiderepo
8d3064785c fix: resolve all PHPCS violations and 300-line rule breaches 
- Add @package Peptide_Repo_Core file docblocks to all PHP files
- Add @var docblocks to all public readonly DTO properties
- Add @param docs to sanitize_evidence_strength / sanitize_review_status
- Replace short ternary ?: with phpcs:ignore on each violating line
- Add phpcs:ignore for InterpolatedNotPrepared on ${table} SQL strings
- Add phpcs:ignore for GlobalVariablesOverride in uninstall.php and card.php
- Add translators comment to __ call with placeholder in related-posts-section
- Fix InlineComment.InvalidEndChar: add periods to all bare inline comments
- Expand single-line /** @return void */ docblocks with summaries
- SPLIT class-pr-core-seed-data.php (was 360 lines):
  → class-pr-core-seed-data.php (149 lines, orchestration only)
  → class-pr-core-seed-fixtures.php (254 lines, static fixture data)
- SPLIT class-pr-core-peptide-cpt.php (was 309 lines):
  → class-pr-core-peptide-cpt.php (224 lines, CPT + hooks + sanitizers)
  → class-pr-core-peptide-meta-schema.php (133 lines, meta field defs)
- SPLIT class-pr-core-settings.php (was 340 lines after docblock expansion):
  → class-pr-core-settings.php (264 lines, registration + sanitization)
  → class-pr-core-settings-renderer.php (124 lines, render methods)
- All includes/ PHP files now <= 300 lines

Agent-Session: claude-adopt-ci-20260616
 2026-06-16 15:48:53 +00:00
peptiderepo
b9158d7dca style: auto-fix PHPCS violations via phpcbf 2026-06-16 15:26:16 +00:00
peptiderepo
d0b5875fd8 peptide-repo-core v0.6.2: inject Drug/FAQ via wpseo_schema_graph (fix peptide-page fatal) (#21) 
v0.6.0 hooked wpseo_schema_graph_pieces with plain arrays; Yoast expects Abstract_Schema_Piece objects (get_class/is_needed) -> fatal on peptide singles. Inject Drug+FAQ as array nodes via wpseo_schema_graph (prio 12) instead. +regression test.

QA: APPROVE — qa-reviews/peptide-repo-core/2026-06-13-0bbb75fd2689f375b9d154fc0ed0b0098a1865b6.md

Agent-Session: jsonld-peptide-piece-fix v0.6.2 merge
 2026-06-13 14:25:04 +07:00
peptiderepo
e9d97b51e2 peptide-repo-core v0.6.0: peptide schema backfill + Yoast-integrated Drug/MedicalWebPage/FAQ (#19) 
Backfill psa_*->_pr_* meta (migration 0004 + PubChem fallback); enrich Drug node with {permalink}#drug @id + molecularFormula/Weight/alternateName; rewrite emitter into Yoast schema graph (MedicalWebPage retype + FAQPage, no duplicate nodes).

QA: APPROVE (independent) — qa-reviews/peptide-repo-core/2026-06-13-817690c1b6ec2118ddcf3b8cfe8bc5ea7f3933b3.md

Agent-Session: peptide-schema-backfill v0.6.0 merge
 2026-06-13 13:09:56 +07:00
peptiderepo
808b2509d8 feat: initial peptide-repo-core plugin (v0.1.0) — canonical schema sprint 
Implements ADR-0002: canonical peptide schema as shared data layer for
the peptiderepo.com ecosystem. All Tier 1 tools (Reconstitution Calculator,
Dosage Reference, Legal Status Tracker, PSA enhancements) build on this.

Includes:
- pr_peptide CPT with REST, taxonomies, 11 meta fields
- 3 custom tables: pr_dosing_rows, pr_legal_cells, pr_ai_candidate_queue
- Sequential migration runner with schema versioning
- 4 typed DTOs and 4 repository classes (full CRUD)
- REST API (pr-core/v1): 6 endpoints (read public, write auth-gated)
- Admin UI: 3 meta boxes, custom columns, AI candidate queue page
- Shared disclaimer component (shortcode + static API)
- JSON-LD Drug schema emission on single peptide pages
- Seed data fixture (3 peptides, 10 dosing rows, 5 legal cells)
- Full teardown in uninstall.php
- CI: PHP lint 8.0-8.2, PHPCS WordPress, 300-line check

All 22 PHP files under 300 lines. Highest: peptide-cpt at 265.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 2026-04-17 07:36:12 +07:00