Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261015T072909Z-disease-width-readiness/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/disease_width_comparison_20261015/READINESS_SNAPSHOT.json

@@ -0,0 +1,108 @@
+{
+  "state": "waiting_results",
+  "matched_draws": 0,
+  "total_draws": 15,
+  "units": [
+    {
+      "cohort": "ye2026_sepsis",
+      "draw": 0,
+      "state": "x1_ready_waiting_x4_core_score"
+    },
+    {
+      "cohort": "ye2026_sepsis",
+      "draw": 1,
+      "state": "x1_ready_waiting_x4_core_score"
+    },
+    {
+      "cohort": "ye2026_sepsis",
+      "draw": 2,
+      "state": "x1_ready_waiting_x4_core_score"
+    },
+    {
+      "cohort": "ye2026_sepsis",
+      "draw": 3,
+      "state": "x1_ready_waiting_x4_core_score"
+    },
+    {
+      "cohort": "ye2026_sepsis",
+      "draw": 4,
+      "state": "x1_ready_waiting_x4_core_score"
+    },
+    {
+      "cohort": "imperial_eskd",
+      "draw": 0,
+      "state": "x1_ready_waiting_x4_core_score"
+    },
+    {
+      "cohort": "imperial_eskd",
+      "draw": 1,
+      "state": "x1_ready_waiting_x4_core_score"
+    },
+    {
+      "cohort": "imperial_eskd",
+      "draw": 2,
+      "state": "x1_ready_waiting_x4_core_score"
+    },
+    {
+      "cohort": "imperial_eskd",
+      "draw": 3,
+      "state": "x1_ready_waiting_x4_core_score"
+    },
+    {
+      "cohort": "imperial_eskd",
+      "draw": 4,
+      "state": "x1_ready_waiting_x4_core_score"
+    },
+    {
+      "cohort": "ji2025_chili",
+      "draw": 0,
+      "state": "x1_ready_waiting_x4_core_score"
+    },
+    {
+      "cohort": "ji2025_chili",
+      "draw": 1,
+      "state": "x1_ready_waiting_x4_core_score"
+    },
+    {
+      "cohort": "ji2025_chili",
+      "draw": 2,
+      "state": "waiting_x1_output_import"
+    },
+    {
+      "cohort": "ji2025_chili",
+      "draw": 3,
+      "state": "waiting_x1_output_import"
+    },
+    {
+      "cohort": "ji2025_chili",
+      "draw": 4,
+      "state": "waiting_x1_output_import"
+    }
+  ],
+  "gpu_operations": 0,
+  "observed_at": "2026-10-15T16:28:28.195228+09:00",
+  "x4_queue": {
+    "DOWNSTREAM_server_1.json": {
+      "phase": "paired",
+      "host": "server_1",
+      "at": "2026-10-15T07:12:17.816675+00:00",
+      "job": "strict/immicro/healthy/fold1/n5",
+      "index": 12,
+      "total": 105
+    },
+    "DOWNSTREAM_server_2.json": {
+      "phase": "paired",
+      "host": "server_2",
+      "at": "2026-10-15T06:51:49.148189+00:00",
+      "job": "strict/immicro/healthy/fold2/n10",
+      "index": 13,
+      "total": 105
+    }
+  },
+  "baseline_counts": {
+    "reused_summaries": 9,
+    "new_cpu_only_summaries": 3,
+    "prepared_x1_draws": 12,
+    "pending_x1_draws": 3
+  }
+}

paper-releases/pbisc-diffusion/updates/20261015T072909Z-disease-width-readiness/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/disease_width_comparison_20261015/TESTS.json

@@ -0,0 +1,5 @@
+{
+  "same_contract_pass": true,
+  "reference_mismatch_rejected": true,
+  "gpu_operations": 0
+}

paper-releases/pbisc-diffusion/updates/20261015T072909Z-disease-width-readiness/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/disease_width_comparison_20261015/archive_when_complete.py

@@ -0,0 +1,22 @@
+from pathlib import Path
+import json,time,subprocess,datetime,csv,statistics,hashlib
+R=Path(__file__).resolve().parent;S=R.parents[1];M=S.parents[1];release=M.parents[1]/'paper-release-20260928'
+while True:
+ if (R/'ERROR.json').exists():raise SystemExit('Comparison stopped; preserve error and inspect')
+ f=R/'STATUS.json'
+ if f.exists() and json.loads(f.read_text())['state']=='complete':break
+ time.sleep(120)
+rows=list(csv.DictReader((R/'COMPARISON.csv').open()));means={}
+for c in sorted({r['cohort'] for r in rows}):
+ means[c]={}
+ for method in ['x1_LoRA','x4_LoRA']:
+  q=[r for r in rows if r['cohort']==c and r['method']==method];assert len(q)==5
+  means[c][method]={k:statistics.mean(float(r[k]) for r in q) for k in ['composition_l1','coverage','expression_r','logfc_r','partial_r','deg_overlap']}
+(R/'RESULT.json').write_text(json.dumps({'means':means,'draws_per_cohort':5,'gpu_operations':0,'inference':'Descriptive means of overlapping support draws, no independent-replicate significance claim.'},indent=2)+'\n')
+assets=[{'host':'server_1','source':str(p),'kind':'code' if p.suffix=='.py' else 'table' if p.suffix=='.csv' else 'report','state':'completed'} for p in R.rglob('*') if p.is_file() and p.suffix in ['.json','.csv','.md','.py'] and '__pycache__' not in str(p) and 'ARCHIVE_REQUEST' not in p.name]
+request={'project_id':'pbisc-diffusion','summary':'CPU-only exact-support comparison of x1 and x4 LoRA for Sepsis, Imperial and CHILI,5 draws each. Existing generations reused.','assets':assets,'inference_locations':[]}
+p=R/'FINAL_ARCHIVE_REQUEST.json';p.write_text(json.dumps(request,indent=2)+'\n');ident=datetime.datetime.now(datetime.timezone.utc).strftime('%Y%m%dT%H%M%SZ')+'-disease-width-results'
+with (R/'final_archive.log').open('x') as log:
+ for args in [['prepare','--request',str(p),'--id',ident],['publish',ident,'--execute']]:subprocess.run(['/home/sj_server_1/miniforge3/bin/python',str(release/'maintenance/update.py'),*args],stdout=log,stderr=subprocess.STDOUT,check=True)
+f=release/'maintenance/updates'/ident/'UPDATE_VERIFIED.json';assert json.loads(f.read_text())['status']=='PASS'
+(R/'ARCHIVE_VERIFIED.json').write_text(json.dumps({'id':ident,'receipt':str(f),'sha256':hashlib.sha256(f.read_bytes()).hexdigest()},indent=2)+'\n')

paper-releases/pbisc-diffusion/updates/20261015T072909Z-disease-width-readiness/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/disease_width_comparison_20261015/test_comparison.py

@@ -0,0 +1,14 @@
+from pathlib import Path
+import tempfile,json
+import compare_ready as C
+base=C.S/'recoveries/giroux_width_comparison_20261015/draw0/score/summary.json';bound={'summary':str(base),'summary_sha256':C.sha256(base)};original=C.R
+with tempfile.TemporaryDirectory() as d:
+ C.R=Path(d)
+ C.compare('giroux2022',0,bound)
+ assert json.loads((C.R/'giroux2022/draw0/MATCHED.json').read_text())['same_contract']
+ bad=json.loads(base.read_text());bad['reference']['reference_sha256']='0'*64;f=C.R/'bad.json';f.write_text(json.dumps(bad))
+ try:C.compare('giroux2022',0,{'summary':str(f),'summary_sha256':C.sha256(f)})
+ except AssertionError:pass
+ else:raise AssertionError('Mismatched reference accepted')
+(original/'TESTS.json').write_text(json.dumps({'same_contract_pass':True,'reference_mismatch_rejected':True,'gpu_operations':0},indent=2)+'\n')
+print('Positive matched-contract and negative reference-mismatch checks PASS')