Upload scripts/run_phase1_pipeline.py with huggingface_hub

scripts/run_phase1_pipeline.py

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+"""Phase 1 pipeline runner — executes all Phase 1 scripts in sequence.
+
+This script runs the complete Phase 1 pipeline:
+  1. Electrochemical stability windows (Li/Na entries)
+  2. CAVD channel dimensionality (all Li/Na entries with structures)
+  3. SSE candidate score (all entries, 5-gate system)
+  4. Mechanical properties (all entries, geometric proxy)
+  5. Oxidation states (all entries, BVA + heuristic)
+  6. JARVIS EaH (internal convex hull)
+  7. Commercial-safe edition extraction
+  8. Garnet enrichment (structure-based reclassification)
+
+Usage:
+    python scripts/run_phase1_pipeline.py                        # full pipeline
+    python scripts/run_phase1_pipeline.py --steps 1,3,5          # specific steps only
+    python scripts/run_phase1_pipeline.py --dry-run              # stats only, no writes
+    python scripts/run_phase1_pipeline.py --skip-write           # compute but don't save
+"""
+import sys, time, argparse, subprocess
+from pathlib import Path
+
+SCRIPTS_DIR = Path(__file__).resolve().parent
+BASE_DIR = SCRIPTS_DIR.parent
+
+STEPS = {
+    1: ("Electrochemical Windows", "compute_electrochemical_windows.py", 
+        ["python", "scripts/compute_electrochemical_windows.py", "--subset", "full"]),
+    2: ("CAVD Channel Dimensionality", "compute_cavd_channel_dimensionality.py",
+        ["python", "scripts/compute_cavd_channel_dimensionality.py", "--subset", "full"]),
+    3: ("SSE Candidate Score", "compute_sse_candidate_score.py",
+        ["python", "scripts/compute_sse_candidate_score.py", "--subset", "full"]),
+    4: ("Mechanical Properties", "compute_mechanical_properties.py",
+        ["python", "scripts/compute_mechanical_properties.py"]),
+    5: ("Oxidation States", "compute_oxidation_states.py",
+        ["python", "scripts/compute_oxidation_states.py"]),
+    6: ("JARVIS EaH", "compute_jarvis_hull_energy.py",
+        ["python", "scripts/compute_jarvis_hull_energy.py"]),
+    7: ("Commercial-Safe Edition", "extract_commercial_safe_edition.py",
+        ["python", "scripts/extract_commercial_safe_edition.py"]),
+    8: ("Garnet Enrichment", "enrich_garnet_family.py",
+        ["python", "scripts/enrich_garnet_family.py"]),
+}
+
+STEP_ORDER = [1, 2, 3, 4, 5, 6, 7, 8]
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Phase 1 pipeline runner")
+    parser.add_argument("--steps", type=str, default=None,
+                        help="Comma-separated step numbers (e.g. 1,3,5)")
+    parser.add_argument("--dry-run", action="store_true",
+                        help="Add --dry-run to all scripts")
+    parser.add_argument("--skip-write", action="store_true",
+                        help="Add --dry-run to dataset-modifying scripts")
+    args = parser.parse_args()
+    
+    if args.steps:
+        selected_steps = [int(s.strip()) for s in args.steps.split(",")]
+    else:
+        selected_steps = STEP_ORDER
+    
+    print("=" * 60)
+    print("  PHASE 1 PIPELINE")
+    print("  8 steps to transform Scandium-Dataset into SSB screening resource")
+    print("=" * 60)
+    
+    total_start = time.time()
+    
+    for step_num in selected_steps:
+        if step_num not in STEPS:
+            print(f"\n  [SKIP] Step {step_num}: unknown")
+            continue
+        
+        name, script, base_cmd = STEPS[step_num]
+        
+        print(f"\n{'─' * 60}")
+        print(f"  Step {step_num}/8: {name}")
+        print(f"  Script: scripts/{script}")
+        print(f"{'─' * 60}")
+        
+        cmd = list(base_cmd)
+        if args.dry_run or args.skip_write:
+            cmd.append("--dry-run")
+        
+        step_start = time.time()
+        print(f"  Running: {' '.join(cmd)}")
+        print()
+        
+        result = subprocess.run(cmd, cwd=str(BASE_DIR), capture_output=True, text=True)
+        
+        # Print stdout
+        for line in result.stdout.split("\n"):
+            print(f"  {line}")
+        
+        if result.stderr.strip():
+            print(f"\n  stderr:")
+            for line in result.stderr.strip().split("\n"):
+                print(f"  ! {line}")
+        
+        if result.returncode != 0:
+            print(f"\n  [FAILED] exit code {result.returncode}")
+            if not args.dry_run:
+                print("  Aborting pipeline.")
+                sys.exit(1)
+        
+        elapsed = time.time() - step_start
+        print(f"\n  [{elapsed/60:.1f} min]")
+    
+    total_elapsed = time.time() - total_start
+    print(f"\n{'=' * 60}")
+    print(f"  Pipeline complete: {len(selected_steps)} steps in {total_elapsed/60:.1f} min")
+    print(f"{'=' * 60}")
+
+
+if __name__ == "__main__":
+    main()