ecosim-pftpar-extractor

name	ecosim-pftpar-extractor
description	Extract one EcoSIM PFT parameter record from a PFT-parameter NetCDF file into a standalone NetCDF. Use when Codex needs to isolate all parameters for a given EcoSIM six-character PFT code such as ndlf34, or a four-character pfts_short value plus Koppen climate code, while preserving all non-PFT-specific variables such as pfts_short, pfts_long, and Koppen metadata.

EcoSIM PFT Parameter Extractor

Use this skill to create a single-PFT parameter NetCDF from an EcoSIM ecosim_pftpar_*.nc file.

Workflow

1. Identify the source PFT parameter NetCDF from the user request. If omitted, search under data/, then under the repo, then ask for the file.

2. Identify the target PFT:

   • Prefer an exact six-character pfts code such as ndlf34.
   • If only a four-character pfts_short code such as ndlf is supplied, require a two-digit --koppen-code unless exactly one matching pfts record exists.

3. Run the bundled extractor with the repo NetCDF-capable Python environment:

   .venv-cmip6/bin/python .agents/skills/ecosim-pftpar-extractor/scripts/extract_pftpar_record.py \
     --input /path/to/ecosim_pftpar_YYYYMMDD.nc \
     --pft ndlf34 \
     --output result/pftpar_extracts/ndlf34.nc
   

4. Verify the output summary reports npfts=1, the selected pfts code, and preserved non-PFT metadata dimensions such as npft and nkopenclms.

Extraction Contract

• Slice every variable with dimension npfts to the selected record only.
• Preserve all variables without npfts unchanged, including pfts_short, pfts_long, koppen_clim_no, koppen_clim_short, and koppen_clim_long.
• Preserve variable attributes, global attributes, fill values, and dimension names. Keep the output npfts dimension length at one record.
• Write the default output basename as <selected-pft>.nc; for example, ndlf34 becomes ndlf34.nc.

Notes

• Do not use regex or text parsing for NetCDF extraction when netCDF4 is available; preserve numeric dtypes and metadata directly.
• If .venv-cmip6/bin/python is unavailable, use any Python environment with netCDF4 installed. The base desktop Python may not include NetCDF support.
• If the requested PFT is missing, list exact available codes with the same four-character prefix and do not create an output file.