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skill: add Step 4.5 graph-health gate + anchor caches on the scan root

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Two integrity improvements to the core skill runbook (rendered via skillgen):

1. Graph-health gate (new Step 4.5): runs diagnostics.diagnose_extraction
   read-only after build, before labeling, and surfaces dangling/missing/
   self-loop and same-endpoint-collapsed edges — the silent-corruption modes of
   incremental updates and AST/LLM id mismatches. Never aborts.
2. Anchor the AST and semantic caches on the scan root (root/cache_root=
   'INPUT_PATH') instead of the cwd, matching the CLI extract path
   (ast cache_root=out_root, check/save_semantic_cache(root=out_root)) and
   build_from_json/save_manifest (#1361 parity). Without this, running from a
   cwd != scan root cold-misses the cache and can split AST vs semantic caches.

Source edited in tools/skillgen/fragments/core/core.md; artifacts + expected/
regenerated via 'python -m tools.skillgen' (+ --bless). Full suite green
(2229 passed); skillgen + cache suites green (80 passed).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
This commit is contained in:
Mamadou Bah
2026-06-23 12:47:02 +01:00
committed by safishamsi
co-authored by Claude Opus 4.8
parent 53edd27e6a
commit e7ba16bfa3
27 changed files with 783 additions and 81 deletions
Download Patch File Download Diff File Expand all files Collapse all files
graphify/skill-amp.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -308,7 +308,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -442,6 +442,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
graphify/skill-claw.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -311,7 +311,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -445,6 +445,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
graphify/skill-codex.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -308,7 +308,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -442,6 +442,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
graphify/skill-copilot.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -311,7 +311,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -445,6 +445,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
graphify/skill-droid.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -308,7 +308,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -442,6 +442,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
graphify/skill-kilo.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -311,7 +311,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -445,6 +445,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
graphify/skill-kiro.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -311,7 +311,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -445,6 +445,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
graphify/skill-opencode.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -303,7 +303,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -437,6 +437,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
graphify/skill-pi.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -311,7 +311,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -445,6 +445,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
graphify/skill-trae.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -309,7 +309,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -443,6 +443,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
graphify/skill-vscode.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -307,7 +307,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -441,6 +441,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
graphify/skill-windows.md
+29 -3
View File
@@ -201,7 +201,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -246,7 +246,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -333,7 +333,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -467,6 +467,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
graphify/skill.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -311,7 +311,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -445,6 +445,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
tools/skillgen/expected/graphify__skill-amp.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -308,7 +308,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -442,6 +442,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
tools/skillgen/expected/graphify__skill-claw.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -311,7 +311,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -445,6 +445,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
tools/skillgen/expected/graphify__skill-codex.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -308,7 +308,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -442,6 +442,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
tools/skillgen/expected/graphify__skill-copilot.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -311,7 +311,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -445,6 +445,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
tools/skillgen/expected/graphify__skill-droid.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -308,7 +308,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -442,6 +442,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
tools/skillgen/expected/graphify__skill-kilo.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -311,7 +311,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -445,6 +445,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
tools/skillgen/expected/graphify__skill-kiro.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -311,7 +311,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -445,6 +445,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
tools/skillgen/expected/graphify__skill-opencode.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -303,7 +303,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -437,6 +437,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
tools/skillgen/expected/graphify__skill-pi.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -311,7 +311,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -445,6 +445,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
tools/skillgen/expected/graphify__skill-trae.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -309,7 +309,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -443,6 +443,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
tools/skillgen/expected/graphify__skill-vscode.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -307,7 +307,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -441,6 +441,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
tools/skillgen/expected/graphify__skill-windows.md
+29 -3
View File
@@ -201,7 +201,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -246,7 +246,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -333,7 +333,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -467,6 +467,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
tools/skillgen/expected/graphify__skill.md
+29 -3
View File
@@ -179,7 +179,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -224,7 +224,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -311,7 +311,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -445,6 +445,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").
tools/skillgen/fragments/core/core.md
+29 -3
View File
@@ -138,7 +138,7 @@ for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
if code_files:
result = extract(code_files, cache_root=Path('.'))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
@@ -183,7 +183,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files)
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH')
# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
@@ -246,7 +246,7 @@ from graphify.cache import save_semantic_cache
from pathlib import Path
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []))
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH')
print(f'Cached {saved} files')
"
```
@@ -380,6 +380,32 @@ If this step prints `ERROR: Graph is empty`, stop and tell the user what happene
Replace INPUT_PATH with the actual path.
### Step 4.5 - Graph health check (read-only integrity gate)
A non-destructive diagnostic on the extraction, before labeling. It surfaces edge collapse, dangling/missing endpoints, and self-loops — the silent-corruption modes of incremental updates and AST/LLM id mismatches. Read-only; never aborts.
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report
extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
('missing_endpoint_edges', 'missing-endpoint edges'),
('self_loop_edges', 'self-loop edges'),
('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"
```
Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
### Step 5 - Label communities
Read `graphify-out/.graphify_analysis.json`. For each community key, look at its node labels and write a 2-5 word plain-language name (e.g. "Attention Mechanism", "Training Pipeline", "Data Loading").