033 — Science validation

This tutorial runs the four ecophysiology validation tests (light response, Q10, WUE, inter-chamber agreement) against literature bounds. It depends on the cycles output from notebook 030.

The bundled synthetic sample is intentionally minimal — it lacks the H2O slope and Global_Radiation columns that real LIBZ data has — so this notebook will report “skipped (insufficient input columns)” at the end. That’s expected. Run against real LIBZ data to see the actual validation scorecard.

import json
from palmwtc.config import DataPaths
from palmwtc.pipeline import run_step

paths = DataPaths.resolve()
print(paths.describe())

DataPaths (source=sample (bundled synthetic), site=libz):
  raw_dir       = /home/runner/work/palmwtc/palmwtc/src/palmwtc/data/sample/synthetic
  processed_dir = /home/runner/work/palmwtc/palmwtc/src/palmwtc/data/sample/Data/Integrated_QC_Data
  exports_dir   = /home/runner/work/palmwtc/palmwtc/src/palmwtc/data/sample/exports
  config_dir    = /home/runner/work/palmwtc/palmwtc/src/palmwtc/data/sample/config
  extras        = <none>

Run the validation step

run_step("validation") reads the cycles CSV produced by notebook 030, checks for the required columns, and either runs the four tests or gracefully reports which columns are missing.

result = run_step("validation", paths)
print(f"Status:    {'OK' if result.ok else 'FAILED'}")
print(f"Elapsed:   {result.elapsed_seconds:.1f}s")
print(f"Rows in:   {result.rows_in}")
print(f"Metrics:")
print(json.dumps(result.metrics, indent=2, default=str))

Status:    OK
Elapsed:   0.0s
Rows in:   3
Metrics:
{
  "skipped": true,
  "missing_columns": [
    "h2o_slope",
    "Global_Radiation"
  ],
  "note": "validation needs full H2O flux + weather merge; not available on bundled synthetic sample. Real LIBZ data exercises this step."
}

What the validation tests check

When run against full LIBZ data (with h2o_slope + Global_Radiation columns), run_science_validation produces a JSON report with four scorecards:

Test	Literature bound	Pass criterion
light_response	A_max 15-35 µmol/m² ground/s (Lamade & Bouillet 2005)	Per-chamber A_max within range
q10	1.4-2.5 (tropical canopy)	Q10 fit value within range
wue	Medlyn g₁ formulation	Slope coefficient within published bounds
inter_chamber	< 30% relative difference	Cross-chamber means agree

The full report writes to exports/digital_twin/033_science_validation_summary.json.

Next

• CLI shortcut — palmwtc run --only validation re-runs just this step.

• For real data: see the palmwtc run end-to-end output for a full pipeline summary.