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feat: replace gh-aw flock-action with Copilot coding agent
The gh-aw sandbox cannot connect the GitHub MCP server to api.github.com, causing every run to fail with fetch errors. Switch to the Copilot coding agent approach (copilot-swe-agent) which has native GitHub access and proven successful runs in nsip-example. - Add flock-action.yml workflow that assigns copilot-swe-agent - Add flock-action.instructions.md with full action dispatch - Add nsip-mcp.instructions.md with tool reference and glossary - Update copilot-instructions.md with NSIP/flock-action references - Fix .mcp.json to use `nsip mcp` (binary built by setup steps) - Remove gh-aw flock-action.md source and compiled lock file
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‎.github/copilot-instructions.md‎

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## NSIP MCP Server
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The binary includes an MCP server (`nsip mcp`) for sheep genetic evaluation. Configure in `.vscode/mcp.json`. See `docs/MCP.md` for the full API reference and `docs/llm-guides/` for ready-to-use LLM instruction templates.
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The binary includes an MCP server (`nsip mcp`) for sheep genetic evaluation.
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Configure in `.mcp.json`. See `docs/MCP.md` for the full API reference and
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`docs/llm-guides/` for ready-to-use LLM instruction templates.
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Available tools: `search`, `details`, `lineage`, `progeny`, `profile`,
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`breed_groups`, `trait_ranges`, `compare`, `rank`, `inbreeding_check`,
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`mating_recommendations`, `flock_summary`, `database_status`.
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See `.github/instructions/nsip-mcp.instructions.md` for full tool reference,
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workflow recipes, and formatting rules.
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## Flock Actions
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Issues with the `flock-action` label request automated breeding analyses. Parse
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the issue form fields, call the appropriate MCP tools, and produce a report PR
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in `reports/`. See `.github/instructions/flock-action.instructions.md`.

‎.github/instructions/flock-action.instructions.md‎

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---
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applyTo: "reports/**"
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---
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# Flock Action Instructions
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When assigned a `flock-action` issue, follow this workflow to produce a
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structured breeding report.
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## 1. Parse the Issue
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Extract these fields from the issue body:
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| Field | Location | Required |
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|---|---|---|
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| Action | `action` dropdown | yes |
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| LPN IDs | `lpn_ids` textarea (one per line) | yes |
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| Trait Weights | `trait_weights` textarea (`TRAIT:weight` per line) | only for Rank |
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| Sort Trait | `sort_trait` input | only for Compare |
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| Notes | `notes` textarea | no |
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## 2. Call MCP Tools by Action
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### Mating Recommendations
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For each LPN ID (assumed to be ewes):
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1. Call `details` to get the animal's breed.
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2. Call `mating_recommendations` with the animal's LPN ID and breed ID.
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3. For each recommended mate, call `inbreeding_check`.
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### Evaluate Flock
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1. Call `details` for every LPN ID.
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2. Extract the breed ID from the first animal.
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3. Call `trait_ranges` for that breed.
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4. For each animal, calculate breed-relative position per trait.
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### Compare Animals
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1. Call `compare` with all LPN IDs.
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2. If a sort trait is provided, sort the results by that trait.
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3. Call `trait_ranges` to add breed context.
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### Rank Animals
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1. Parse trait weights from the issue (format: `TRAIT:weight`).
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2. Call `details` for each LPN ID.
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3. Compute a weighted score: `score = sum(trait_value * weight * accuracy / 100)`.
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4. Sort animals by score descending.
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5. Call `trait_ranges` for breed context.
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### Inbreeding Matrix
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1. For every unique pair of LPN IDs, call `inbreeding_check`.
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2. Build a matrix of COI values with traffic-light ratings.
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### Flock Profile
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1. Call `details` for each LPN ID.
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2. Compute aggregate statistics: count, gender split, trait averages.
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3. Call `trait_ranges` for breed context.
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4. Compare flock averages against breed midpoints.
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## 3. Produce Artifacts
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Create output in `reports/{YYYY-MM-DD}-{action-slug}/` where:
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- `{YYYY-MM-DD}` is today's date
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- `{action-slug}` is the action in kebab-case (e.g., `mating-recommendations`)
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### report.md
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Formatted markdown with:
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- Header linking back to the issue (`Closes #N`)
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- Summary of the action and animals analyzed
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- Data tables with EBV values, accuracies, and breed-relative context
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- Recommendations or analysis conclusions
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- Trait glossary footnote for non-obvious abbreviations
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### data.csv
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Machine-readable export with columns appropriate to the action:
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- **Mating Recommendations**: `ewe_lpn,recommended_sire_lpn,rank_score,coi,predicted_bwt,predicted_wwt,...`
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- **Evaluate Flock**: `lpn_id,breed,gender,bwt,bwt_acc,wwt,wwt_acc,...`
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- **Compare Animals**: `lpn_id,trait,value,accuracy`
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- **Rank Animals**: `lpn_id,score,trait1_contribution,trait2_contribution,...`
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- **Inbreeding Matrix**: `sire_lpn,dam_lpn,coi,rating`
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- **Flock Profile**: `metric,value`
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## 4. Open a Pull Request
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Create a PR with:
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- **Title**: `[Flock Action] {Action Name} — {N} animals`
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- **Body**:
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- Summary of findings
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- Link to the issue: `Closes #{issue_number}`
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- List of artifacts produced
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- **Branch**: `flock-action/{issue_number}-{action-slug}`
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## Formatting Rules
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- Use markdown tables for all EBV data — never dump raw JSON.
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- Show accuracy alongside every EBV: `+9.6 (68%)`.
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- Use traffic-light indicators for COI: Green, Yellow, Red.
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- Include breed ranges for context when presenting individual values.
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- Round EBV values to 2 decimal places.
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- Use the trait's natural units (lbs, mm, lambs, eggs/g).

‎.github/instructions/nsip-mcp.instructions.md‎

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---
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applyTo: "**/*-record.yml,**/BREEDING-EVENT-LOG*,reports/**"
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---
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# NSIP MCP Agent Instructions
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When working with breeding record issues, event logs, or livestock data queries, use
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the NSIP MCP tools described below. This document is the authoritative reference for
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agent-driven interactions with the NSIP Search API.
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---
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## What is the NSIP MCP Server?
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The NSIP MCP server wraps the [National Sheep Improvement Program](https://nsip.org/)
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Search API as a Model Context Protocol service. It gives AI agents direct access to:
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- **400,000+ sheep** with estimated breeding values (EBVs)
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- **Pedigree trees** spanning multiple generations
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- **Breed-level benchmarks** (trait ranges, averages)
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- **Breeding analytics** — inbreeding coefficients, trait ranking, mating recommendations
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**Transport**: stdio only — started with `nsip mcp`
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---
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## Tool Reference
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### search
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Find animals matching filter criteria. Returns paginated results.
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| Parameter | Type | Required | Default | Description |
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|---|---|---|---|---|
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| `breed_group_id` | integer | no | | Breed group ID |
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| `breed_id` | integer | no | | Breed ID |
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| `status` | string | no | | `"CURRENT"`, `"SOLD"`, or `"DEAD"` |
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| `gender` | string | no | | `"Male"`, `"Female"`, or `"Both"` |
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| `born_after` | string | no | | Animals born after this date (`YYYY-MM-DD`) |
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| `born_before` | string | no | | Animals born before this date (`YYYY-MM-DD`) |
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| `proven_only` | boolean | no | false | Only return proven animals |
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| `flock_id` | string | no | | Flock ID |
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| `sort_by` | string | no | | Trait abbreviation to sort by (e.g. `"WWT"`) |
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| `reverse` | boolean | no | false | Reverse the sort order |
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| `page` | integer | no | 0 | Page number (0-indexed) |
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| `page_size` | integer | no | 15 | Results per page (1-100) |
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---
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### details
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Fetch full EBV data, breed, contact info, and status for one animal.
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| Parameter | Type | Required | Description |
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|---|---|---|---|
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| `animal_id` | string | yes | LPN ID or registration number |
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---
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### lineage
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Retrieve the pedigree (ancestry) tree — parents, grandparents, and deeper ancestors.
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| Parameter | Type | Required | Description |
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|---|---|---|---|
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| `animal_id` | string | yes | LPN ID |
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---
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### progeny
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List offspring for an animal with pagination.
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| Parameter | Type | Required | Default | Description |
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|---|---|---|---|---|
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| `animal_id` | string | yes | | LPN ID |
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| `page` | integer | no | 0 | Page number (0-indexed) |
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| `page_size` | integer | no | 10 | Results per page |
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---
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### profile
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All-in-one call that combines `details`, `lineage`, and `progeny` in a single request.
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| Parameter | Type | Required | Description |
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|---|---|---|---|
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| `animal_id` | string | yes | LPN ID |
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---
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### breed_groups
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List all breed groups and individual breeds in the NSIP database. No parameters.
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---
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### trait_ranges
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Get the min/max EBV values across all animals within a breed.
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| Parameter | Type | Required | Description |
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|---|---|---|---|
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| `breed_id` | integer | yes | Breed ID |
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---
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### compare
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Side-by-side EBV comparison of 2-5 animals. Optionally filter to specific traits.
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| Parameter | Type | Required | Description |
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|---|---|---|---|
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| `animal_ids` | array of strings | yes | LPN IDs (2-5 items) |
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| `traits` | string | no | Comma-separated trait filter (e.g. `"BWT,WWT,YWT"`) |
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---
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### rank
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Rank animals within a breed by a weighted composite score.
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| Parameter | Type | Required | Default | Description |
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|---|---|---|---|---|
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| `breed_id` | integer | yes | | Breed ID to search |
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| `weights` | object | yes | | Trait-to-weight map, e.g. `{"BWT": -1.0, "WWT": 2.0}` |
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| `gender` | string | no | | `"Male"`, `"Female"`, or `"Both"` |
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| `status` | string | no | | `"CURRENT"`, `"SOLD"`, `"DEAD"` |
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| `top_n` | integer | no | 10 | Number of top results to return |
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---
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### inbreeding_check
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Calculate Wright's coefficient of inbreeding (COI) for a potential sire x dam mating.
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| Parameter | Type | Required | Description |
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|---|---|---|---|
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| `sire_id` | string | yes | LPN ID of the sire (father) |
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| `dam_id` | string | yes | LPN ID of the dam (mother) |
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**COI traffic-light thresholds:**
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| Rating | COI | Recommendation |
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|---|---|---|
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| Green | < 6.25% | Safe — proceed |
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| Yellow | 6.25-12.5% | Caution — consider alternatives |
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| Red | > 12.5% | Avoid — high inbreeding depression risk |
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---
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### mating_recommendations
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Find optimal mates for an animal.
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| Parameter | Type | Required | Default | Description |
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|---|---|---|---|---|
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| `animal_id` | string | yes | | LPN ID of the animal to find mates for |
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| `breed_id` | integer | yes | | Breed ID to search for candidates |
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| `target_traits` | string | no | WWT, BWT, NLB | Comma-separated traits to optimize |
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| `max_results` | integer | no | 5 | Number of recommendations |
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---
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### flock_summary
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Summarize a flock: animal count, gender breakdown, and average EBV traits.
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| Parameter | Type | Required | Description |
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|---|---|---|---|
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| `flock_id` | string | yes | Flock ID |
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| `breed_id` | integer | no | Filter to a specific breed within the flock |
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---
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### database_status
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Check when the NSIP database was last updated. No parameters.
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---
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## EBV Trait Glossary
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| Abbreviation | Full Name | Unit | Selection |
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|---|---|---|---|
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| BWT | Birth Weight | lbs | Lower preferred |
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| WWT | Weaning Weight | lbs | Higher preferred |
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| PWWT | Post-Weaning Weight | lbs | Higher preferred |
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| YWT | Yearling Weight | lbs | Higher preferred |
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| FAT | Fat Depth | mm | Moderate preferred |
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| EMD | Eye Muscle Depth | mm | Higher preferred |
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| NLB | Number of Lambs Born | lambs | Higher (with caution) |
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| NWT | Number of Lambs Weaned | lambs | Higher preferred |
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| PWT | Pounds Weaned | lbs | Higher preferred |
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| DAG | Dag Score | score | Lower preferred |
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| WEC | Worm Egg Count | eggs/g | Lower preferred |
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| FEC | Faecal Egg Count | eggs/g | Lower preferred |
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## Formatting Rules
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1. **Always use tables** for EBV data — never dump raw JSON.
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2. **Show accuracy** alongside every EBV value: `+9.6 (68%)`.
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3. **Use the traffic light** for COI results (Green/Yellow/Red).
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4. **Include breed context** whenever possible via `trait_ranges`.
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5. **Caveat low accuracy**: Note if a key trait has accuracy below 40%.
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6. **Use the trait's natural units**: lbs for weights, mm for depth/fat, lambs for NLB/NWT.

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