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 resolve — Combine model + grids + cmor YAMLs into one resolved document for inspection

• 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

• Expects a self-contained CMOR YAML file

• Minimal Syntax: fremor yaml -y [yamlfile] [options]

• Required Options:

  • -y, --yamlfile TEXT — YAML file to parse

• Optional:

  • --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 cmor.yaml --dry_run

resolve

• Resolves a FRE model YAML plus referenced CMOR/grids YAML files into one combined YAML document

• Useful for inspecting how anchors and merge keys from the model and grids files expand into the CMOR section

• Minimal Syntax: fremor resolve -y [model_yaml] -e [experiment] [options]

• Required Options:

  • -y, --yamlfile TEXT — Model YAML file to resolve

  • -e, --experiment TEXT — Experiment name

• Optional:

  • -o, --output TEXT — Write the resolved YAML to a file instead of stdout

• Example: fremor resolve -y am5.yaml -e c96L65_am5f7b12r1_amip --output resolved.yaml

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