Added run-pipeline.py script.

README.md

@@ -18,6 +18,22 @@ End-to-end pipeline from selecting sites from the global [PhenoCam Network](http
 
 ## Quick start
 
+### Run pipeline wrapper (recommended)
+
+```bash
+uv sync
+uv run python run-pipeline.py --evaluation-year 2025
+```
+
+Runs all five steps in order. Steps 1 and 2 are skipped when their output already exists. Each site in steps 3–5 is skipped when `data/metrics/{year}/{site}/metrics.json` is present. Any failure stops the run immediately, so one can fix the issue and re-run; completed work is never repeated.
+
+```bash
+# single site (steps 1 and 2 still skip if already done)
+uv run python run-pipeline.py --evaluation-year 2025 --site ICOSFR-Fon1
+```
+
+### Step by step
+
 ```bash
 uv sync
 uv run python 1-phenocam.py --evaluation-year 2025

run-pipeline.py

@@ -0,0 +1,142 @@
+"""Pipeline wrapper: run steps 1 → 2 → 3 → 4 → 5.
+
+Steps 1 and 2 run once for the whole year (skipped when their output already
+exists).  Steps 3–5 run site-by-site for every PASS site from
+``data/phenocam_screening/{year}.json``; a site is skipped entirely when
+``data/metrics/{year}/{site}/metrics.json`` already exists.
+
+Any failure stops the run immediately.  Fix the issue and re-run — completed
+steps and sites are skipped automatically.
+
+CLI:
+
+- ``--evaluation-year`` (default 2025)
+- ``--site``            single site to run steps 3–5 for (default: all PASS sites)
+"""
+
+from __future__ import annotations
+
+import argparse
+import json
+import subprocess
+import sys
+from pathlib import Path
+from typing import Any
+
+DATA_DIR = Path("data")
+DEFAULT_YEAR = 2025
+
+# Steps 1 and 2 are global (once per year); steps 3–5 repeat per site.
+GLOBAL_STEPS: list[tuple[str, Path]] = [
+    # (script, skip-if-this-file-exists)
+    ("1-phenocam.py", Path("phenocam/{year}.json")),
+    ("2-phenocam-screening.py", Path("phenocam_screening/{year}.json")),
+]
+
+PER_SITE_STEPS = [
+    "3-sentinel-data.py",
+    "4-fusion.py",
+    "5-metrics.py",
+]
+
+
+def _load_pass_sites(year: int) -> list[str]:
+    path = DATA_DIR / "phenocam_screening" / f"{year}.json"
+    if not path.is_file():
+        raise SystemExit(f"Step-2 screening manifest not found: {path}")
+    payload: dict[str, Any] = json.loads(path.read_text(encoding="utf-8"))
+    sites = []
+    for row in payload.get("sites", []):
+        if row.get("calculations", {}).get("status") != "PASS":
+            continue
+        name = row.get("response", {}).get("camera", {}).get("Sitename")
+        if name:
+            sites.append(str(name))
+    return sorted(sites)
+
+
+def _is_site_complete(year: int, site: str) -> bool:
+    return (DATA_DIR / "metrics" / str(year) / site / "metrics.json").is_file()
+
+
+def _run_global_step(step: str, year: int) -> int:
+    result = subprocess.run(
+        [sys.executable, step, "--evaluation-year", str(year)],
+        check=False,
+    )
+    return result.returncode
+
+
+def _run_site_step(step: str, year: int, site: str) -> int:
+    result = subprocess.run(
+        [sys.executable, step, "--evaluation-year", str(year), "--site", site],
+        check=False,
+    )
+    return result.returncode
+
+
+def main(argv: list[str] | None = None) -> int:
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument("--evaluation-year", type=int, default=DEFAULT_YEAR)
+    parser.add_argument(
+        "--site",
+        type=str,
+        default=None,
+        help="Single sitename to process (default: all PASS sites)",
+    )
+    args = parser.parse_args(argv)
+    year = args.evaluation_year
+
+    # --- Global steps (steps 1 and 2) ---
+    for script, marker_template in GLOBAL_STEPS:
+        marker = DATA_DIR / str(marker_template).replace("{year}", str(year))
+        if marker.is_file():
+            print(f"[pipeline] {script} — skipping (output already exists)")
+        else:
+            print(f"[pipeline] Running {script}...")
+            rc = _run_global_step(script, year)
+            if rc != 0:
+                raise SystemExit(
+                    f"[pipeline] {script} failed (exit {rc}); cannot continue"
+                )
+
+    # --- Per-site steps (steps 3–5) ---
+    sites = _load_pass_sites(year)
+    if args.site:
+        if args.site not in sites:
+            raise SystemExit(
+                f"Site '{args.site}' not found in step-2 PASS sites for {year}"
+            )
+        sites = [args.site]
+
+    n_total = len(sites)
+    skipped: list[str] = []
+    succeeded: list[str] = []
+
+    print(f"[pipeline] {n_total} PASS site(s) for {year}")
+
+    for i, site in enumerate(sites, 1):
+        prefix = f"[pipeline] ({i}/{n_total}) {site}"
+
+        if _is_site_complete(year, site):
+            print(f"{prefix} — skipping (already complete)")
+            skipped.append(site)
+            continue
+
+        print(f"{prefix}")
+        for step in PER_SITE_STEPS:
+            rc = _run_site_step(step, year, site)
+            if rc != 0:
+                raise SystemExit(f"[pipeline] {step} failed for {site} (exit {rc})")
+
+        succeeded.append(site)
+
+    print(
+        f"\n[pipeline] Done: {len(skipped)} skipped, {len(succeeded)} succeeded"
+        f" (of {n_total} total)"
+    )
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())