Workflow files for CCMMF deliverables

This repo contains the magic-ensemble CLI and the scripts it orchestrates for running SIPNET carbon flux ensemble analyses.

Structure

workflows/
├── magic-ensemble               CLI entry point
├── workflow/                    Canonical, data-agnostic workflow scripts
│   ├── workflow_manifest.yaml   Fixed step definitions, paths, dispatch config
│   ├── 00_fetch_s3_and_prepare_run_dir.sh
│   ├── 00_stage_external_inputs.sh
│   ├── 01_ERA5_nc_to_clim.R
│   ├── 02_ic_build.R
│   ├── 03_xml_build.R
│   ├── 04_run_model.R
│   └── template.xml
├── examples/                    Example analyses (phase-specific data prep)
│   ├── 1a_single_site/
│   ├── 1b_statewide_woody/
│   ├── 2a_grass/
│   └── 3_rowcrop/
└── tools/                       Shared utility scripts

The workflow/ directory holds the canonical implementation. The examples/ directories contain phase-specific preparation scripts (steps 01–03) and their own template.xml and site_info.csv. Step 04 (run_model) is shared — all workflows dispatch through workflow/04_run_model.R.

See magic-ensemble-README.md for usage and magic-ensemble-DEVELOPERS.md for architecture details.