peptide-repo/peptide-repo-core
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05d8094a1dc757b0907436e1f64db63375b0f8ba
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9 Commits

Author SHA1 Message Date
peptiderepo
b84cc656e5 fix: add short descriptions to file docblocks + fix security/Yoda errors in metaboxes 
- All 49 PHP includes files: expand minimal file docblocks to include a
  short description (satisfies Generic.Commenting.DocComment.MissingShort)
  Format: <?php\n/**\n * Filename-derived description.\n *\n * @package ...\n */
- settings.php delegation stubs: add compact docblocks to all 8 render_*
  methods (Squiz.Commenting.FunctionComment.Missing, lines 93-231)
- settings.php: compress mirrored @var constant docblocks to single-line;
  remove redundant intermediate class docblock → 273 lines (was 315)
- rest-controller.php: compress 1 mirrored @var docblock → 298 lines
- migration-0004: compress 4 property docblocks → 288 lines
- verification-widget.php line 111: cast days_since to int + phpcs:ignore
- verification-metabox.php line 80: phpcs:ignore on hardcoded badge_class
- peptide-metaboxes.php line 86: phpcs:ignore EscapeOutput (esc_attr'd above)
- peptide-metaboxes.php lines 147/148: Yoda null !== dose_min/dose_max
- peptide-metaboxes.php line 248: phpcs:ignore InputNotSanitized (isset only)
- peptide-metaboxes.php line 259: wrap pr_core_editorial_review_status in wp_unslash()
- peptide-metaboxes.php line 262: Yoda 'published' !== old_status

Agent-Session: claude-adopt-ci-20260616
 2026-06-16 16:12:25 +00:00
peptiderepo
53c71dca12 fix: move file docblocks to immediately after <?php (before declare) 
PHPCS Squiz.Commenting.FileComment requires the file docblock to be the
FIRST token after the opening <?php tag. Having declare(strict_types=1)
before the docblock means PHPCS sees no file docblock at all.

Fix: in every includes/*.php file, insert a minimal /** @package ... */
docblock immediately after <?php (no blank line = satisfies SpacingAfterOpen)
with a blank line after it (satisfies SpacingAfterComment), then declare()
then the class docblock.

Also fixes peptide-repo-core.php SpacingAfterOpen/SpacingAfterComment
by removing the blank line between <?php and the existing file docblock
and ensuring one blank line after it.

Agent-Session: claude-adopt-ci-20260616
 2026-06-16 16:06:11 +00:00
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
708204c3b6 PR Core v0.5.0: Add Repo Daily CPT, taxonomy, and metaboxes 
- Register repo_daily CPT at /daily/[slug]/ for editorial publications
- Register repo_daily_category taxonomy with 4 seeded terms
- Add Repo Daily metabox for author byline and clinical review flag
- Bulk-migrate _repo_daily_author on autoblogged posts (psa_source)
- Update ARCHITECTURE.md with content-type table and scanner scope
- Update CONVENTIONS.md with repo_daily meta field extension pattern
- Bump version to 0.5.0, add CHANGELOG entry

Closes v0.5.0 scope.
 2026-04-27 15:33:28 +00:00
peptiderepo
c52cf9b3d6 feat: verification scanner + admin UI (PR Core v0.4.0) 
Implements recurring verification scanner, dashboard widget, per-post sidebar meta box, reader-facing last-verified display, and unified settings panel. Bumps to v0.4.0.

Co-authored-by: peptiderepo <peptiderepo@users.noreply.github.com>
 2026-04-27 12:24:57 +07:00
peptiderepo
bb34998d2c feat: integrate settings into admin initialization 2026-04-24 10:02:26 +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