EcoSIM Python Tools

This repository contains Python utilities and Agent Skills for preparing EcoSIM inputs from AmeriFlux, ERA5, NADP/tDEP, gSSURGO, and FAO HWSD2 data.

Main Entry Points

• Agent Skills: .agents/skills/*/SKILL.md
• Climate forcing orchestration: Tools/create_ecosim_climate_forcing.py
• ERA5 to EcoSIM converter: .agents/skills/ameriflux-era5-to-ecosim/era5_to_ecosim_converter.py
• Notebook helper scripts: applications/notebooks/scripts/

The duplicate .claude/skills path points to .agents/skills, so skill updates made under .agents/skills are available through both paths automatically.

Documentation

• Quick start: docs/QUICKSTART.md
• Grid forcing workflow notes: docs/GRID_FORCING_README.md
• Grid forcing implementation notes: docs/GRID_FORCING_IMPLEMENTATION.md

The grid forcing docs are supplemental workflow notes. The current checked-in orchestration script is Tools/create_ecosim_climate_forcing.py; if you are looking for a grid forcing entry point, verify that Tools/create_ecosim_grid_forcing.py exists in your branch before following those examples.

Notebook Runfile Helpers

The old README.txt referenced runfile writers without paths. The available helper scripts are under applications/notebooks/scripts/:

• ExampleInputWriter.py writes example input/run configuration files.
• PlantMgmtWriter.py, pftMgmtWriter.py, and MgmntUtil.py support plant management inputs.
• SoilMgmtWriter.py and soilManagementWriter.py support soil management inputs.
• SiteTopoWriter.py writes site/topography inputs.
• PlantTraitWriter.py writes plant functional type parameterizations.

ERA5 Conversion

Use the maintained skill converter instead of the removed root-level convert_era5_to_ecosim.py:

python .agents/skills/ameriflux-era5-to-ecosim/era5_to_ecosim_converter.py \
  --input data/AMF_US-Ha1_FLUXNET_FULLSET_1991-2020_3-5/AMF_US-Ha1_FLUXNET_ERA5_HR_1981-2021_3-5.csv \
  --output result/US-Ha1/US-Ha1_ecosim_climate.nc \
  --site-id US-Ha1 \
  --quality-report result/US-Ha1/US-Ha1_era5_quality_report.json

Soil Extraction

The ameriflux-surgo-grid-extract skill uses gSSURGO as the primary soil source and FAO HWSD v2.0 from data/FAO_HWSD2 as fallback when gSSURGO is unavailable or has invalid/fill values. See the skill instructions for variable mappings and assumptions.

Skill Validation

Validate skills against the Agent Skills standard with:

for skill in .agents/skills/*; do
  uvx --from 'git+https://github.com/agentskills/agentskills.git#subdirectory=skills-ref' skills-ref validate "$skill"
done