Skip to content

commands.rst

Latest commit

 

History

History
122 lines (107 loc) · 5.97 KB

commands.rst

File metadata and controls

122 lines (107 loc) · 5.97 KB

Subcommands Reference

fremor rewrites climate model output files with CMIP-compliant metadata. Both CMIP6 and CMIP7 workflows are supported. Available subcommands:

  • fremor init — Initialize CMOR resources: generate config templates and fetch MIP tables
  • fremor run — Rewrite individual directories of netCDF files
  • fremor yaml — Process multiple directories/tables using YAML configuration
  • fremor find — Search MIP tables for variable definitions
  • fremor varlist — Generate variable lists from netCDF files
  • fremor config — Generate a CMOR YAML configuration from a post-processing directory tree

init

  • Initializes CMOR resources by generating experiment configuration templates and/or fetching MIP tables
  • Fetches tables from trusted GitHub repositories (CMIP6: PCMDI/cmip6-cmor-tables, CMIP7: WCRP-CMIP/cmip7-cmor-tables)
  • Minimal Syntax: fremor init -m [mip_era] [options]
  • Required Options:
    • -m, --mip_era TEXT — MIP era: cmip6 or cmip7
  • Optional:
    • -e, --exp_config TEXT — Output path for experiment config JSON template
    • -t, --tables_dir TEXT — Directory to fetch MIP tables into
    • --tag TEXT — Specific git tag or release for MIP tables (e.g., 6.9.33)
    • --fast — Use curl to download tarball instead of git clone (faster)
  • Examples:
    • fremor init -m cmip6 -e exp_config.json -t cmip6-tables
    • fremor init -m cmip7 -e exp_config.json -t cmip7-tables --fast
    • fremor init -m cmip6 -t cmip6-tables --tag 6.9.33

run

  • Rewrites netCDF files in a directory to be CMIP-compliant
  • Requires MIP tables and controlled vocabulary configuration
  • Minimal Syntax: fremor run -d [indir] -l [varlist] -r [table_config] -p [exp_config] -o [outdir] [options]
  • Required Options:
    • -d, --indir TEXT — Input directory with netCDF files
    • -l, --varlist TEXT — Variable list dictionary mapping modeler variable names to MIP table variable names
    • -r, --table_config TEXT — MIP table JSON configuration
    • -p, --exp_config TEXT — Experiment/model metadata JSON
    • -o, --outdir TEXT — Output directory prefix
  • Optional:
    • -v, --opt_var_name TEXT — Target specific variable
    • --run_one — Process one file for testing
    • -g, --grid_label TEXT — Grid type (e.g. gn, gr)
    • --grid_desc TEXT — Grid description
    • --nom_res TEXT — Nominal resolution
    • --start TEXT — Minimum year (YYYY)
    • --stop TEXT — Maximum year (YYYY)
    • --calendar TEXT — Calendar type
  • Example: fremor run --run_one -g gr --nom_res "10000 km" -d input/ -l varlist.json -r CMIP6_Omon.json -p exp_config.json -o output/

yaml

  • Processes YAML configuration to CMORize multiple directories/tables
  • Requires FRE-flavored YAML files with experiment configuration
  • Minimal Syntax: fremor yaml -y [yamlfile] -e [experiment] -p [platform] -t [target] [options]
  • Required Options:
    • -y, --yamlfile TEXT — YAML file to parse
    • -e, --experiment TEXT — Experiment name
    • -p, --platform TEXT — Platform name
    • -t, --target TEXT — Target name
  • Optional:
    • -o, --output TEXT — Output file
    • --run_one — Process one file for testing
    • --dry_run — Print planned calls without executing
    • --print_cli_call/--no-print_cli_call — In dry-run mode, print the equivalent CLI invocation (default) or the Python cmor_run_subtool() call
    • --start TEXT — Minimum year (YYYY)
    • --stop TEXT — Maximum year (YYYY)
  • Example: fremor yaml -y am5.yaml -e c96L65_am5f7b12r1_amip -p ncrc5.intel -t prod-openmp --dry_run

find

  • Searches MIP tables for variable definitions
  • Minimal Syntax: fremor find -r [table_config_dir] [options]
  • Required Options:
    • -r, --table_config_dir TEXT — Directory with MIP tables
  • Optional:
    • -l, --varlist TEXT — Variable list file
    • -v, --opt_var_name TEXT — Specific variable to search
  • Example: fremor find -r cmip6-cmor-tables/Tables/ -v sos

varlist

  • Generates variable list from netCDF files in a directory
  • Minimal Syntax: fremor varlist -d [dir_targ] -o [output_file]
  • Required Options:
    • -d, --dir_targ TEXT — Target directory
    • -o, --output_variable_list TEXT — Output file path
  • Optional:
    • -t, --mip_table TEXT — MIP table JSON file to filter variables against
  • Example: fremor varlist -d ocean_data/ -o varlist.json

config

  • Generates a CMOR YAML configuration file by scanning a post-processing directory tree and cross-referencing against MIP tables
  • Creates per-component variable list JSON files and the structured YAML that fremor yaml consumes
  • Minimal Syntax: fremor config -p [pp_dir] -t [mip_tables_dir] -m [mip_era] -e [exp_config] -o [output_yaml] -d [output_dir] -l [varlist_dir]
  • Required Options:
    • -p, --pp_dir TEXT — Root post-processing directory
    • -t, --mip_tables_dir TEXT — Directory containing MIP table JSON files
    • -m, --mip_era TEXT — MIP era identifier (e.g. cmip6, cmip7)
    • -e, --exp_config TEXT — Path to experiment configuration JSON
    • -o, --output_yaml TEXT — Path for the output CMOR YAML file
    • -d, --output_dir TEXT — Root output directory for CMORized data
    • -l, --varlist_dir TEXT — Directory for per-component variable list files
  • Optional:
    • --freq TEXT — Temporal frequency (default: monthly)
    • --chunk TEXT — Time chunk string (default: 5yr)
    • --grid TEXT — Grid label anchor name (default: g99)
    • --overwrite — Overwrite existing variable list files
    • --calendar TEXT — Calendar type (default: noleap)
  • Example: fremor config -p /path/to/pp -t /path/to/tables -m cmip7 -e exp_config.json -o cmor.yaml -d /path/to/output -l /path/to/varlists