feat: PR/Commit Links in Investigation Output (fn-38)

.flow/specs/fn-38.md

@@ -6,27 +6,52 @@
 
 ## Overview
 
-When an investigation identifies a code change as root cause, include direct links to the PR or commit in GitHub/GitLab/Bitbucket. Add PR metadata enrichment during git sync and URL template rendering per provider.
+When an investigation identifies a code change as root cause, include direct links to the PR or commit in GitHub/GitLab/Bitbucket. **Leverage bond-agent's existing git tools** (`githunter` and `github` toolsets) for PR metadata lookup rather than building custom API clients.
+
+## Architecture
+
+```
+bond-agent (external PyPI package)
+├── bond.tools.githunter
+│   ├── find_pr_discussion(repo_path, commit_hash) → PRDiscussion
+│   ├── blame_line(repo_path, file_path, line_no) → BlameResult
+│   └── get_file_experts(repo_path, file_path) → List[FileExpert]
+└── bond.tools.github
+    ├── github_get_pr(owner, repo, number) → PullRequest
+    ├── github_get_commits(owner, repo, path) → List[Commit]
+    └── ... (other tools)
+
+dataing (this repo)
+├── migrations/ (schema for PR metadata)
+├── adapters/git/url_templates.py (URL rendering)
+└── output formatting (CLI, notebook, markdown, API)
+```
 
 ## Scope
 
-- Extend `code_changes` table with `pr_number`, `pr_url`, `pr_title`
-- PR metadata lookup via GitHub/GitLab API during sync
-- URL templates per provider for commit and PR links
-- Links in CLI output, notebook output, markdown export, API response
+**Use from bond-agent (DO NOT rebuild):**
+- PR lookup from commit hash (`find_pr_discussion`)
+- PR metadata fetching (`github_get_pr`)
+- Commit history (`github_get_commits`)
+
+**Build in dataing:**
+- Database schema changes (`code_changes` table + PR columns)
+- URL template rendering for GitHub/GitLab/Bitbucket
+- Integration layer to call bond-agent tools during sync
+- Output formatting for CLI/notebook/markdown/API
 
 ## Key Files
 
 - `python-packages/dataing/migrations/` (alter code_changes table)
-- `python-packages/dataing/src/dataing/models/` (update model)
+- `python-packages/dataing/src/dataing/adapters/git/url_templates.py` (URL rendering)
+- `python-packages/dataing/src/dataing/adapters/git/pr_enrichment.py` (bond-agent integration)
 - `python-packages/dataing-cli/src/dataing_cli/display.py` (CLI output)
-- `python-packages/dataing-cli/src/dataing_cli/export.py` (export output)
-- `python-packages/dataing-notebook/src/dataing_notebook/rendering.py`
+- `python-packages/dataing-notebook/src/dataing_notebook/rendering.py` (notebook output)
 
 ## Quick Commands
 
 ```bash
-uv run pytest python-packages/dataing/tests/unit/ -v -k "git or export"
+uv run pytest python-packages/dataing/tests/unit/ -v -k "git or export or pr"
 ```
 
 ## Acceptance
@@ -36,7 +61,9 @@ uv run pytest python-packages/dataing/tests/unit/ -v -k "git or export"
 - Links formatted for web and CLI
 - Support for GitHub, GitLab, Bitbucket URL formats
 - Metadata includes PR number, title, author, merge date
+- Uses bond-agent tools for GitHub API calls (no custom API client)
 
 ## Dependencies
 
 - Blocked by fn-36 (Git Integration) and fn-37 (Agent Code Context)
+- Requires `bond-agent>=0.1.2` (already in pyproject.toml)

.flow/tasks/fn-38.1.json

@@ -1,14 +1,27 @@
 {
-  "assignee": null,
+  "assignee": "bordumbb@gmail.com",
   "claim_note": "",
-  "claimed_at": null,
+  "claimed_at": "2026-01-31T16:05:39.377826Z",
   "created_at": "2026-01-28T03:52:30.310569Z",
   "depends_on": [],
   "epic": "fn-38",
+  "evidence": {
+    "files_created": [
+      "python-packages/dataing/migrations/034_code_changes_pr_metadata.sql"
+    ],
+    "files_modified": [
+      "python-packages/dataing/src/dataing/models/code_change.py",
+      "python-packages/dataing/src/dataing/core/domain_types.py"
+    ],
+    "verification": {
+      "model_import": "OK",
+      "mypy": "passed"
+    }
+  },
   "id": "fn-38.1",
   "priority": 1,
   "spec_path": ".flow/tasks/fn-38.1.md",
-  "status": "todo",
+  "status": "done",
   "title": "Add migration to extend code_changes with PR metadata columns",
-  "updated_at": "2026-01-28T03:52:30.310795Z"
+  "updated_at": "2026-01-31T16:07:05.572932Z"
 }

.flow/tasks/fn-38.1.md

@@ -2,25 +2,25 @@
 
 ## Description
 
-Extend the `code_changes` table (created by fn-36) with columns to store pull request metadata. When investigations link an anomaly to a code change, PR information provides richer context (title, author, review status) and enables deep links to the PR in GitHub/GitLab/Bitbucket. This migration adds the columns; fn-38.2 populates them during sync.
+Extend the `code_changes` table (created by fn-36) with columns to store pull request metadata. When investigations link an anomaly to a code change, PR information provides richer context (title, author, review status) and enables deep links to the PR in GitHub/GitLab/Bitbucket. This migration adds the columns; fn-38.2 populates them using bond-agent tools.
 
 ### Implementation
 
-1. Create a new migration file `python-packages/dataing/migrations/032_code_changes_pr_metadata.sql`:
+1. Create a new migration file `python-packages/dataing/migrations/034_code_changes_pr_metadata.sql`:
    ```sql
    -- PR metadata for code changes
    -- Epic fn-38: PR/Commit Link in Investigation Output
 
    ALTER TABLE code_changes
-       ADD COLUMN pr_number INTEGER,
-       ADD COLUMN pr_url TEXT,
-       ADD COLUMN pr_title TEXT,
-       ADD COLUMN pr_author TEXT,
-       ADD COLUMN pr_merged_at TIMESTAMPTZ,
-       ADD COLUMN provider TEXT;  -- github, gitlab, bitbucket (denormalized from git_repositories)
+       ADD COLUMN IF NOT EXISTS pr_number INTEGER,
+       ADD COLUMN IF NOT EXISTS pr_url TEXT,
+       ADD COLUMN IF NOT EXISTS pr_title TEXT,
+       ADD COLUMN IF NOT EXISTS pr_author TEXT,
+       ADD COLUMN IF NOT EXISTS pr_merged_at TIMESTAMPTZ,
+       ADD COLUMN IF NOT EXISTS provider TEXT;  -- github, gitlab, bitbucket
 
    -- Index for PR lookups by commit
-   CREATE INDEX idx_code_changes_pr_number
+   CREATE INDEX IF NOT EXISTS idx_code_changes_pr_number
        ON code_changes(repo_id, pr_number)
        WHERE pr_number IS NOT NULL;
 
@@ -32,7 +32,7 @@ Extend the `code_changes` table (created by fn-36) with columns to store pull re
    COMMENT ON COLUMN code_changes.provider IS 'Git provider: github, gitlab, bitbucket';
    ```
 
-2. Update the SQLAlchemy model for `CodeChange` (created by fn-36) to include the new columns. The model file location depends on fn-36 but is expected at `python-packages/dataing/src/dataing/models/code_change.py`:
+2. Update the SQLAlchemy model for `CodeChange` to include the new columns:
    ```python
    pr_number: Mapped[int | None] = mapped_column(Integer, nullable=True)
    pr_url: Mapped[str | None] = mapped_column(Text, nullable=True)
@@ -42,7 +42,7 @@ Extend the `code_changes` table (created by fn-36) with columns to store pull re
    provider: Mapped[str | None] = mapped_column(String(20), nullable=True)
    ```
 
-3. Update the `CodeChange` domain type in `python-packages/dataing/src/dataing/core/domain_types.py` (added by fn-37.1) to include PR fields:
+3. Update the `CodeChange` domain type in `domain_types.py` to include PR fields:
    ```python
    class CodeChange(BaseModel):
        ...
@@ -55,31 +55,41 @@ Extend the `code_changes` table (created by fn-36) with columns to store pull re
    ```
 
 ### Key Files
-- **CREATE**: `python-packages/dataing/migrations/032_code_changes_pr_metadata.sql`
+- **CREATE**: `python-packages/dataing/migrations/034_code_changes_pr_metadata.sql`
 - **MODIFY**: `python-packages/dataing/src/dataing/models/code_change.py` (add PR columns)
 - **MODIFY**: `python-packages/dataing/src/dataing/core/domain_types.py` (extend CodeChange)
 
 ### Verification
 ```bash
-# Verify migration SQL is valid (syntax check)
-psql -f python-packages/dataing/migrations/032_code_changes_pr_metadata.sql --dry-run
-
 # Verify model compiles
 uv run python -c "from dataing.models.code_change import CodeChange; print('OK')"
 uv run mypy python-packages/dataing/src/dataing/models/code_change.py
 ```
 
 ## Acceptance
-- [ ] Migration adds pr_number, pr_url, pr_title, pr_author, pr_merged_at, provider columns to code_changes
-- [ ] All new columns are nullable (backward compatible with existing rows)
+- [ ] Migration adds pr_number, pr_url, pr_title, pr_author, pr_merged_at, provider columns
+- [ ] All new columns are nullable (backward compatible)
 - [ ] Index created on (repo_id, pr_number) for efficient PR lookups
 - [ ] SQLAlchemy model updated with matching mapped columns
 - [ ] CodeChange domain type includes PR fields with None defaults
-- [ ] Migration file follows existing naming convention (032_*.sql)
+- [ ] Migration file follows existing naming convention
 
 ## Done summary
-TBD
+# fn-38.1 Done Summary
+
+Added PR metadata columns to code_changes table for storing pull request information
+enriched during git sync.
+
+## Changes
+- Created migration `034_code_changes_pr_metadata.sql` adding columns:
+  - pr_number, pr_url, pr_title, pr_author, pr_merged_at, provider
+  - Index on (repo_id, pr_number) for efficient PR lookups
+- Updated SQLAlchemy CodeChange model with matching mapped columns
+- Updated RelevantCodeChange domain type with PR fields
 
+## Verification
+- Model compiles successfully
+- mypy passes with no errors
 ## Evidence
 - Commits:
 - Tests:

.flow/tasks/fn-38.2.json

@@ -1,16 +1,33 @@
 {
-  "assignee": null,
+  "assignee": "bordumbb@gmail.com",
   "claim_note": "",
-  "claimed_at": null,
+  "claimed_at": "2026-01-31T16:07:16.261572Z",
   "created_at": "2026-01-28T03:52:34.548035Z",
   "depends_on": [
     "fn-38.1"
   ],
   "epic": "fn-38",
+  "evidence": {
+    "files_created": [
+      "python-packages/dataing/src/dataing/adapters/git/pr_enrichment.py",
+      "python-packages/dataing/tests/unit/adapters/git/test_pr_enrichment.py"
+    ],
+    "files_modified": [
+      "python-packages/dataing/src/dataing/adapters/git/__init__.py",
+      "python-packages/dataing/src/dataing/adapters/db/code_changes.py"
+    ],
+    "tests": {
+      "failed": 0,
+      "passed": 9
+    },
+    "verification": {
+      "mypy": "passed"
+    }
+  },
   "id": "fn-38.2",
   "priority": 2,
   "spec_path": ".flow/tasks/fn-38.2.md",
-  "status": "todo",
+  "status": "done",
   "title": "Implement PR metadata lookup during git sync (GitHub API)",
-  "updated_at": "2026-01-28T03:52:34.548226Z"
+  "updated_at": "2026-01-31T16:10:35.710667Z"
 }