Merge pull request 'docs: update README with COI direct-relation fix (v0.6.1)' (#48) from fix/coi-direct-relation into master

Reviewed-on: #48

README.md

@@ -28,10 +28,15 @@ A reactive, interactive dog breeding genealogy mapping system for professional k
 - **✅ Genetic Traits** - Inherited trait mapping
 - **✅ Settings Table** - Single-row kennel configuration with all contact/identity fields
 
-### Recently Added (March 9, 2026 — v0.6.0)
+### Recently Added (March 10, 2026 — v0.6.1)
+- **✅ COI Direct-Relation Fix** — `calculateCOI` now correctly computes inbreeding coefficient for parent×offspring pairings. Previously returned `0.00%` due to blanket exclusion of `sid` from `commonIds`; sire now correctly appears as a common ancestor in the dam's ancestry map when they are parent×offspring
+- **✅ pedigree.js Route Fix** — `commonIds` filter changed from `id !== sid && id !== did` → `id !== did` only; preserves parent×offspring COI path while still preventing reflexive dam self-loop
+- **Expected COI for parent×offspring pairing:** ~25.00% (Wright's path coefficient method)
+
+### Previously Added (March 9, 2026 — v0.6.0)
 - **✅ Champion Flag** — `is_champion INTEGER DEFAULT 0` on `dogs` table; safe `ALTER TABLE` migration guard for existing DBs
 - **✅ Champion Toggle in DogForm** — amber-gold highlighted checkbox row with `Award` icon; marks dog as titled champion
-- **✅ Champion ✪ in Parent Dropdowns** — sire/dam selects append `✪` to champion names for at-a-glance visibility
+- **✅ Champion ⭐ in Parent Dropdowns** — sire/dam selects append `⭐` to champion names for at-a-glance visibility
 - **✅ Champion Bloodline Badge** — offspring of champion parents display a badge on dog cards and detail pages
 - **✅ Kennel Settings API** — `GET/PUT /api/settings` with single-row column schema and ALLOWED_KEYS whitelist
 - **✅ Settings Table Migration** — all kennel fields added with safe `ALTER TABLE` guards on existing DBs; default seed row auto-created
@@ -147,18 +152,20 @@ For a **fresh install**, the database will automatically initialize with the cor
 # Install dependencies
 npm install
 
-# Run development server (frontend + backend)
+# Run development server (frontend + backend, nodemon auto-reload)
 npm run dev
 
 # Build for production
 npm run build
 ```
 
+> **Note:** `npm run dev` uses nodemon for auto-reload on the server. `npm start` (production) does **not** watch for changes — restart is required after pulling updates.
+
 ### Project Structure
 
 ```
 breedr/
-├── client/                # React frontend
+├── client/                 # React frontend
 │   ├── src/
 │   │   ├── pages/
 │   │   │   ├── BreedingCalendar.jsx  # Heat cycle calendar + whelping identifiers
@@ -175,19 +182,19 @@ breedr/
 │   │   │   └── useSettings.jsx       # SettingsProvider + useSettings context
 │   │   └── App.jsx
 │   └── package.json
-├── server/                # Node.js backend
+├── server/                 # Node.js backend
 │   ├── routes/
-│   │   ├── dogs.js        # is_champion in all queries
+│   │   ├── dogs.js         # is_champion in all queries
-│   │   ├── settings.js    # GET/PUT kennel settings (single-row schema)
+│   │   ├── settings.js     # GET/PUT kennel settings (single-row schema)
-│   │   ├── breeding.js    # Heat cycles, whelping, suggestions
+│   │   ├── breeding.js     # Heat cycles, whelping, suggestions
-│   │   ├── pedigree.js    # COI, trial pairing
+│   │   ├── pedigree.js     # COI, trial pairing (v0.6.1 direct-relation fix)
 │   │   ├── litters.js
 │   │   └── health.js
 │   ├── db/
-│   │   └── init.js        # Schema + ALTER TABLE migration guards
+│   │   └── init.js         # Schema + ALTER TABLE migration guards
 │   └── index.js
-├── static/                # Branding assets (br-logo.png, etc.)
+├── static/                 # Branding assets (br-logo.png, etc.)
-├── docs/                  # Documentation
+├── docs/                   # Documentation
 ├── ROADMAP.md
 ├── DATABASE.md
 ├── Dockerfile
@@ -210,6 +217,7 @@ breedr/
 ### Pedigree & Genetics
 - `GET /api/pedigree/:id` - Generate pedigree tree
 - `POST /api/pedigree/trial-pairing` - COI + common ancestors + risk recommendation
+- `GET /api/pedigree/relations/:sireId/:damId` - Direct relation detection (parent/grandparent check)
 
 ### Breeding & Heat Cycles
 - `GET /api/breeding/heat-cycles` - All heat cycles
@@ -230,6 +238,9 @@ breedr/
 
 ## Troubleshooting
 
+### COI shows 0.00% for parent×offspring pairings
+Ensure you are on v0.6.1+ (merge PR #47). The fix removes a blanket `id !== sid` exclusion in `calculateCOI` that was silently zeroing the inbreeding coefficient when the sire is a direct ancestor of the dam. After merging, restart the server.
+
 ### Server crashes with `SyntaxError: Unexpected end of input` on `settings.js`
 The settings route file may have been corrupted (double-encoded base64). Pull the latest code and rebuild.
 
@@ -272,6 +283,7 @@ A breeding date must be logged on the cycle for whelp window cells to appear. Us
 - [x] **Projected Whelping Calendar Identifier** (whelp window cells, due label, active card range, live modal preview, whelping banner)
 - [x] **Champion Bloodline Tracking** (is_champion flag, DogForm toggle, offspring badge)
 - [x] **Kennel Settings** (GET/PUT /api/settings, SettingsProvider, kennel name in navbar)
+- [x] **COI Direct-Relation Fix** (parent×offspring now correctly yields ~25% COI — v0.6.1)
 
 ### 🔜 In Progress / Up Next
 - [ ] Health Records System
@@ -287,10 +299,16 @@ A breeding date must be logged on the cycle for whelp window cells to appear. Us
 
 ## Recent Updates
 
+### March 10, 2026 - COI Direct-Relation Bug Fix (v0.6.1)
+- **Fixed:** `calculateCOI` in `server/routes/pedigree.js` — removed `id !== sid` from `commonIds` filter
+- **Root cause:** `getAncestorMap` includes each dog at `gen 0`; the sire (`sid`) correctly appears in the dam's ancestor map at `gen 1` for parent×offspring pairings, but `id !== sid` was filtering it out and returning `0.00%`
+- **Result:** Parent×offspring pairings now correctly return ~25.00% COI; all other pairings unaffected
+- **PR:** [#47](https://git.alwisp.com/jason/breedr/pulls/47)
+
 ### March 9, 2026 - Champion Bloodline, Settings, Build Fixes (v0.6.0)
 - **Added:** `is_champion` column to `dogs` table with safe `ALTER TABLE` migration guard
 - **Added:** Champion toggle checkbox in DogForm with amber-gold highlight and `Award` icon
-- **Added:** `✪` suffix on champion sire/dam in parent dropdowns
+- **Added:** `⭐` suffix on champion sire/dam in parent dropdowns
 - **Added:** Champion Bloodline badge on offspring cards/detail pages
 - **Added:** `GET/PUT /api/settings` route — single-row column schema with `ALLOWED_KEYS` whitelist
 - **Added:** Full kennel settings columns in `settings` table with migration guards