diff --git a/src/components/shell_variable_manifest.md b/src/components/shell_variable_manifest.md index 656f9cc7..8123fa62 100644 --- a/src/components/shell_variable_manifest.md +++ b/src/components/shell_variable_manifest.md @@ -3,266 +3,274 @@ This file is intended to automatically list shell script variables for greater t Note: This does not include variables defined in python scripts. -| ShellVariable | SourceScripts | DefinedIn | DefinedInFunction | UsedInFunction | -|:------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| aggregation_file | ['src/components/statevector_component/statevector.sh'] | ['src/components/statevector_component/statevector.sh'] | ['reduce_dimension'] | ['create_statevector', 'reduce_dimension'] | -| AIRS | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['activate_observations'] | -| archive_sv | ['src/components/statevector_component/statevector.sh'] | ['src/components/statevector_component/statevector.sh'] | ['reduce_dimension'] | ['create_statevector', 'reduce_dimension'] | -| array | ['src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations'] | -| bc_offset | ['src/utilities/common.sh'] | ['src/utilities/common.sh'] | ['ncmax'] | ['print_stats', 'imi_failed', 'ncmax', 'ncmin'] | -| bc_perturb | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['generate_BC_perturb_values'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values'] | -| BCdryrun | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | -| BCpath | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | -| bcThreshold | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['setup_jacobian', 'generate_BC_perturb_values'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values'] | -| BCversion | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | -| blendedDir | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | -| BlendedTROPOMI | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_posterior'] | -| BufferDeg | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | -| buildJacobian | ['src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values'] | -| c | ['src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/run_boundary_conditions.sh'] | [] | [] | -| channels | ['envs/Harvard-Cannon/imi_env.yml'] | ['envs/Harvard-Cannon/imi_env.yml'] | [] | [] | -| ClusteringMethod | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | -| cmd | ['src/components/template_component/template.sh'] | ['src/components/template_component/template.sh'] | ['setup_template'] | ['setup_template'] | -| CondaEnv | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh', 'src/components/inversion_component/inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi', 'run_inversion'] | -| condaEnv | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | -| CondaFile | ['config.yml', 'src/components/setup_component/setup.sh'] | ['config.yml'] | [] | ['setup_imi'] | -| config_path | ['src/components/statevector_component/statevector.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh'] | ['src/components/statevector_component/statevector.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh'] | ['create_statevector', 'reduce_dimension', 'run_preview', 'run_notebooks'] | ['create_statevector', 'reduce_dimension', 'run_preview', 'setup_inversion', 'run_inversion', 'run_notebooks'] | -| configFile | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | [] | -| ConfigFile | ['run_imi.sh', 'src/utilities/cleanup_script.sh', 'src/components/statevector_component/statevector.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh', 'src/components/kalman_component/kalman.sh'] | ['run_imi.sh', 'src/utilities/cleanup_script.sh'] | [] | ['create_statevector', 'reduce_dimension', 'run_preview', 'setup_inversion', 'run_notebooks', 'setup_kf', 'run_period'] | -| ConfigPath | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_period'] | ['setup_kf', 'run_kf', 'run_period'] | -| constYr | ['src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['create_statevector', 'setup_imi', 'activate_observations'] | -| copydir | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_period'] | ['setup_kf', 'run_kf', 'run_period'] | -| corrupt | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | ['report'] | ['download_aws_files', 'report'] | -| cpu_count | ['src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations'] | -| cpu_str | ['src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations'] | -| CreateAutomaticRectilinearStateVectorFile | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | -| cwd | ['src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/run_boundary_conditions.sh'] | [] | [] | -| DataPath | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/statevector_component/statevector.sh', 'src/components/template_component/template.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['create_statevector', 'setup_template'] | -| DataPathTROPOMI | ['run_imi.sh', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | -| debug | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | -| dependencies | ['envs/Harvard-Cannon/imi_env.yml'] | ['envs/Harvard-Cannon/imi_env.yml'] | [] | [] | -| DEST | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | [] | ['download_aws_files', 'report'] | -| dir | ['src/utilities/cleanup_script.sh'] | [] | [] | [] | -| DOFSThreshold | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | -| DoInversion | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_kf'] | -| DoJacobian | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/kalman_component/kalman.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_kf'] | -| DoPosterior | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/kalman_component/kalman.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_kf'] | -| DoPreview | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | -| DoSpinup | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_jacobian', 'setup_posterior', 'setup_imi'] | -| DownloadGlobalMet | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | -| DynamicKFClustering | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/statevector_component/statevector.sh', 'src/components/kalman_component/kalman.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['reduce_dimension', 'run_period'] | -| element | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['generate_BC_perturb_values'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values'] | -| end_time | ['run_imi.sh'] | ['run_imi.sh'] | [] | [] | -| endDate | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | -| EndDate | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/kalman_component/kalman.sh', 'src/components/template_component/template.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_posterior', 'setup_imi', 'setup_spinup', 'run_preview', 'setup_kf', 'setup_template'] | -| EndDate_i | ['src/components/posterior_component/posterior.sh', 'src/components/inversion_component/inversion.sh', 'src/components/kalman_component/kalman.sh'] | ['src/components/posterior_component/posterior.sh', 'src/components/kalman_component/kalman.sh'] | ['run_posterior', 'run_period'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'run_inversion', 'setup_kf', 'run_kf', 'run_period'] | -| EndMonth | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | -| FetchTROPOMI | ['src/components/posterior_component/posterior.sh'] | ['src/components/posterior_component/posterior.sh'] | ['run_posterior'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values'] | -| file | ['src/utilities/common.sh', 'src/utilities/find_corrupt_files.sh', 'src/utilities/crop_met.sh'] | ['src/utilities/common.sh'] | ['imi_failed'] | ['print_stats', 'imi_failed', 'ncmax', 'ncmin'] | -| FILE | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh'] | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh'] | [] | [] | -| FILE_LIST | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | [] | ['download_aws_files', 'report'] | -| FirstPeriod | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_kf'] | ['setup_kf', 'run_kf', 'run_period'] | -| FirstSimSwitch | ['src/components/inversion_component/inversion.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/inversion_component/inversion.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_inversion'] | ['setup_inversion', 'run_inversion', 'run_notebooks'] | -| ForcedNativeResolutionElements | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | -| fOut | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | -| fs | ['src/utilities/parse_yaml.sh'] | [] | [] | ['parse_yaml'] | -| fullBCpath | ['src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations', 'setup_template'] | -| Gamma | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | -| GCClassicPath | ['src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations', 'setup_template'] | -| GCDir | ['src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values'] | -| gcEndDate | ['src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/run_boundary_conditions.sh'] | [] | [] | -| GCsourcepth | ['src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values'] | -| gcStartDate | ['src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/run_boundary_conditions.sh'] | [] | [] | -| geosChemDataPath | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | -| GEOSChemEnv | ['envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/template_component/template.sh'] | ['envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_jacobian', 'run_posterior', 'setup_imi', 'run_spinup', 'run_preview', 'setup_template'] | -| geosChemEnv | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | -| GlobalDir | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | -| GOSAT | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['activate_observations'] | -| GriddedPosterior | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | [] | -| gridDir | ['src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['create_statevector', 'setup_imi', 'activate_observations'] | -| gridRes | ['src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['create_statevector', 'setup_imi', 'activate_observations'] | -| gridResLong | ['src/components/setup_component/setup.sh', 'src/components/inversion_component/inversion.sh', 'src/components/template_component/template.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations', 'setup_inversion', 'setup_template'] | -| HemcoDiagFile | ['src/components/statevector_component/statevector.sh'] | ['src/components/statevector_component/statevector.sh'] | ['create_statevector'] | ['create_statevector', 'reduce_dimension'] | -| HOME | ['src/components/template_component/template.sh'] | [] | [] | ['setup_template'] | -| HourlyCH4 | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/spinup_component/spinup.sh', 'src/components/template_component/template.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_jacobian', 'setup_posterior', 'setup_spinup', 'setup_template'] | -| indent | ['src/utilities/parse_yaml.sh'] | ['src/utilities/parse_yaml.sh'] | ['parse_yaml'] | ['parse_yaml'] | -| InPath | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | -| inv_result_path | ['src/components/posterior_component/posterior.sh'] | ['src/components/posterior_component/posterior.sh'] | ['run_posterior'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values'] | -| inversion_end | ['src/utilities/common.sh', 'src/components/inversion_component/inversion.sh'] | ['src/components/inversion_component/inversion.sh'] | ['run_inversion'] | ['print_stats', 'setup_inversion', 'run_inversion', 'run_notebooks'] | -| inversion_sensi_dir | ['src/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.sh'] | [] | [] | -| inversion_start | ['src/utilities/common.sh', 'src/components/inversion_component/inversion.sh'] | ['src/components/inversion_component/inversion.sh'] | ['run_inversion'] | ['print_stats', 'setup_inversion', 'run_inversion', 'run_notebooks'] | -| InversionDir | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_kf'] | ['setup_kf', 'run_kf', 'run_period'] | -| InversionPath | ['run_imi.sh', 'src/utilities/common.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh', 'src/components/kalman_component/kalman.sh', 'src/components/template_component/template.sh'] | ['run_imi.sh'] | [] | ['imi_failed', 'setup_jacobian', 'run_jacobian', 'run_posterior', 'create_statevector', 'reduce_dimension', 'setup_imi', 'run_preview', 'setup_inversion', 'run_notebooks', 'setup_kf', 'run_period', 'setup_template'] | -| invPath | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | [] | -| InvPeriodLength | ['src/components/template_component/template.sh'] | ['src/components/template_component/template.sh'] | ['setup_template'] | ['setup_template'] | -| isAWS | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh', 'src/components/template_component/template.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_jacobian', 'run_posterior', 'create_statevector', 'setup_imi', 'run_spinup', 'run_preview', 'run_inversion', 'setup_template'] | -| isPost | ['src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values'] | -| ithDates | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_period'] | ['setup_kf', 'run_kf', 'run_period'] | -| ithLine | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_period'] | ['setup_kf', 'run_kf', 'run_period'] | -| jacobian_dir | ['src/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.sh'] | [] | [] | -| jacobian_dirs_array | ['src/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.sh'] | [] | [] | -| jacobian_end | ['src/utilities/common.sh', 'src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['run_jacobian'] | ['print_stats', 'setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values'] | -| jacobian_sf | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | [] | -| jacobian_start | ['src/utilities/common.sh', 'src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['run_jacobian'] | ['print_stats', 'setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values'] | -| JacobianCPUs | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/geoschem_run_scripts/submit_jacobian_simulations_array.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | -| JacobianDir | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | [] | -| JacobianMemory | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/geoschem_run_scripts/submit_jacobian_simulations_array.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | -| JacobianRunsDir | ['src/components/jacobian_component/jacobian.sh', 'src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_kf'] | ['run_jacobian', 'setup_kf', 'run_kf', 'run_period'] | -| KalmanMode | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh', 'src/components/template_component/template.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_jacobian', 'run_posterior', 'reduce_dimension', 'setup_spinup', 'run_preview', 'setup_inversion', 'run_inversion', 'run_notebooks', 'setup_template'] | -| kf_inversion_dirs | ['src/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.sh'] | [] | [] | -| LandCoverFile | ['src/components/statevector_component/statevector.sh'] | ['src/components/statevector_component/statevector.sh'] | ['create_statevector'] | ['create_statevector', 'reduce_dimension'] | -| LandCoverFileExtension | ['src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['create_statevector', 'setup_imi', 'activate_observations'] | -| LandThreshold | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | -| LatMax | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/crop_met.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/crop_met.sh'] | [] | [] | -| LatMaxInvDomain | ['src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/inversion_component/inversion.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior', 'setup_imi'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'setup_imi', 'activate_observations', 'setup_inversion'] | -| LatMin | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/crop_met.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/crop_met.sh'] | [] | [] | -| LatMinInvDomain | ['src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/inversion_component/inversion.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior', 'setup_imi'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'setup_imi', 'activate_observations', 'setup_inversion'] | -| Lats | ['src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations', 'setup_template'] | -| LINENO | ['run_imi.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh'] | [] | [] | ['run_jacobian', 'run_posterior', 'run_spinup', 'run_preview', 'run_inversion'] | -| LonMax | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/crop_met.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/crop_met.sh'] | [] | [] | -| LonMaxInvDomain | ['src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/inversion_component/inversion.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior', 'setup_imi'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'setup_imi', 'activate_observations', 'setup_inversion'] | -| LonMin | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/crop_met.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/crop_met.sh'] | [] | [] | -| LonMinInvDomain | ['src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/inversion_component/inversion.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior', 'setup_imi'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'setup_imi', 'activate_observations', 'setup_inversion'] | -| Lons | ['src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations', 'setup_template'] | -| MET | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | [] | ['download_aws_files', 'report'] | -| Met | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | -| metDir | ['src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['create_statevector', 'setup_imi', 'activate_observations', 'setup_template'] | -| metUC | ['src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['create_statevector', 'setup_imi', 'activate_observations', 'setup_template'] | -| mm | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | -| Month | ['src/utilities/crop_met.sh'] | [] | [] | [] | -| name | ['envs/Harvard-Cannon/imi_env.yml', 'src/components/jacobian_component/jacobian.sh'] | ['envs/Harvard-Cannon/imi_env.yml', 'src/components/jacobian_component/jacobian.sh'] | ['setup_jacobian'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values'] | -| native | ['src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations', 'setup_template'] | -| native_state_vector_path | ['src/components/statevector_component/statevector.sh'] | ['src/components/statevector_component/statevector.sh'] | ['reduce_dimension'] | ['create_statevector', 'reduce_dimension'] | -| nBufferClusters | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | -| nElements | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', 'src/components/inversion_component/inversion.sh', 'src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', 'src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior', 'reduce_dimension', 'setup_imi', 'setup_kf'] | ['setup_jacobian', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'create_statevector', 'reduce_dimension', 'setup_imi', 'activate_observations', 'setup_inversion', 'setup_kf', 'run_kf', 'run_period'] | -| NestedGrid | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/template_component/template.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_template'] | -| NestedRegion | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/crop_met.sh', 'src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/crop_met.sh'] | [] | ['create_statevector', 'setup_imi', 'setup_template'] | -| NEW | ['src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['activate_observations', 'setup_template'] | ['setup_imi', 'activate_observations', 'setup_template'] | -| nPeriods | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_kf'] | ['setup_kf', 'run_kf', 'run_period'] | -| NudgeFactor | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/kalman_component/kalman.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_period'] | -| NumberOfElements | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | -| ObsError | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | -| OffshoreEmisThreshold | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | -| OLD | ['src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['activate_observations', 'setup_template'] | ['setup_imi', 'activate_observations', 'setup_template'] | -| OptimizeBCs | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', 'src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_jacobian', 'run_posterior', 'reduce_dimension', 'setup_imi', 'setup_kf'] | -| output | ['src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations'] | -| output_log_file | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh'] | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh'] | [] | [] | -| OutputPath | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/common.sh', 'src/utilities/cleanup_script.sh', 'src/components/setup_component/setup.sh', 'src/components/inversion_component/inversion.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/cleanup_script.sh', 'src/inversion_scripts/run_inversion.sh'] | [] | ['imi_failed', 'setup_imi', 'setup_inversion'] | -| partition | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | -| period_i | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/inversion_component/inversion.sh', 'src/components/kalman_component/kalman.sh'] | [] | [] | ['run_jacobian', 'run_posterior', 'reduce_dimension', 'run_inversion', 'run_notebooks', 'run_period'] | -| PeriodsFile | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_kf'] | ['setup_kf', 'run_kf', 'run_period'] | -| pert_index | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['generate_BC_perturb_values'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values'] | -| PerturbBCValues | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh'] | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh'] | ['setup_jacobian', 'run_posterior'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values'] | -| PerturbValue | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_jacobian'] | -| PerturbValueBCs | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_jacobian'] | -| PLANEFLIGHT | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['activate_observations'] | -| PointSourceDatasets | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | -| posterior_end | ['src/utilities/common.sh', 'src/components/posterior_component/posterior.sh'] | ['src/components/posterior_component/posterior.sh'] | ['run_posterior'] | ['print_stats', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values'] | -| posterior_start | ['src/utilities/common.sh', 'src/components/posterior_component/posterior.sh'] | ['src/components/posterior_component/posterior.sh'] | ['run_posterior'] | ['print_stats', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values'] | -| PosteriorDryRun | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/posterior_component/posterior.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_posterior'] | -| PosteriorName | ['src/components/posterior_component/posterior.sh'] | ['src/components/posterior_component/posterior.sh'] | ['setup_posterior'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values'] | -| PosteriorRunDir | ['src/components/posterior_component/posterior.sh', 'src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior', 'run_kf'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'setup_kf', 'run_kf', 'run_period'] | -| posteriorSF | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | [] | -| PrecomputedJacobian | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_jacobian'] | -| precomputedJacobianCache | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['run_jacobian'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values'] | -| prefix | ['src/utilities/parse_yaml.sh'] | [] | [] | ['parse_yaml'] | -| PrevDir | ['src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values'] | -| preview_dir | ['src/components/statevector_component/statevector.sh', 'src/components/preview_component/preview.sh'] | ['src/components/statevector_component/statevector.sh', 'src/components/preview_component/preview.sh'] | ['reduce_dimension', 'run_preview'] | ['create_statevector', 'reduce_dimension', 'run_preview'] | -| preview_end | ['src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations'] | -| preview_file | ['src/components/preview_component/preview.sh'] | ['src/components/preview_component/preview.sh'] | ['run_preview'] | ['run_preview'] | -| preview_start | ['src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations'] | -| PreviewDryRun | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/preview_component/preview.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_preview'] | -| PreviewEnd | ['src/components/preview_component/preview.sh'] | ['src/components/preview_component/preview.sh'] | ['run_preview'] | ['run_preview'] | -| PreviewName | ['src/components/preview_component/preview.sh'] | ['src/components/preview_component/preview.sh'] | ['run_preview'] | ['run_preview'] | -| PriorError | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | -| PriorErrorBCs | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | -| PriorRunDir | ['src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_kf'] | ['setup_kf', 'run_kf', 'run_period'] | -| ProcessConstantFields | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | -| ProductionDryRun | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_jacobian'] | -| PWD | ['src/utilities/cleanup_script.sh'] | [] | [] | [] | -| python_args | ['src/components/statevector_component/statevector.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/statevector_component/statevector.sh', 'src/inversion_scripts/run_inversion.sh'] | ['reduce_dimension'] | ['create_statevector', 'reduce_dimension'] | -| PYTHONPATH | ['run_imi.sh', 'src/components/kalman_component/kalman.sh'] | [] | [] | ['run_period'] | -| ReducedDimensionStateVector | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh', 'src/components/kalman_component/kalman.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi', 'run_period'] | -| ReferenceRunDir | ['src/components/jacobian_component/jacobian.sh'] | [] | [] | ['run_jacobian'] | -| RegionalDir | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | -| RemoveGlobalMet | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | -| RequestedTime | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/geoschem_run_scripts/submit_jacobian_simulations_array.sh', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_posterior', 'reduce_dimension', 'run_spinup', 'run_preview', 'run_inversion'] | -| RES | ['src/components/template_component/template.sh'] | [] | [] | ['setup_template'] | -| Res | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/inversion_scripts/run_inversion.sh'] | [] | ['setup_imi'] | -| RESOLUTION | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | [] | ['download_aws_files', 'report'] | -| response | ['src/utilities/cleanup_script.sh'] | [] | [] | [] | -| RestartDownload | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | -| RestartFile | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh'] | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh'] | ['setup_jacobian', 'setup_posterior', 'setup_imi', 'setup_spinup'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'setup_imi', 'activate_observations', 'setup_spinup', 'run_spinup'] | -| restartFileDate | ['src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/run_boundary_conditions.sh'] | [] | [] | -| RestartFileFromSpinup | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh'] | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh'] | ['setup_jacobian', 'setup_posterior'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values'] | -| restartFilePath | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | -| RestartFilePrefix | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_jacobian', 'setup_posterior', 'setup_imi', 'setup_spinup'] | -| RestartFilePreview | ['src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh'] | ['src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh'] | ['setup_imi', 'run_preview'] | ['setup_imi', 'activate_observations', 'run_preview'] | -| RestartFilePreviewPrefix | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi', 'run_preview'] | -| retVal | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh'] | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh'] | [] | [] | -| rm_command | ['src/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.sh'] | [] | [] | -| ROOT | ['src/components/template_component/template.sh'] | [] | [] | ['setup_template'] | -| runDir | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/template_component/template.sh', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/write_BCs/run_boundary_conditions.sh'] | ['setup_jacobian', 'setup_posterior', 'setup_imi', 'setup_spinup', 'run_preview'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'setup_imi', 'activate_observations', 'setup_spinup', 'run_spinup', 'run_preview', 'setup_template'] | -| RunDir | ['src/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.sh'] | [] | [] | -| RUNDIR | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh'] | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh'] | [] | [] | -| RunDirs | ['run_imi.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh', 'src/components/kalman_component/kalman.sh', 'src/components/template_component/template.sh'] | ['run_imi.sh', 'src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_jacobian', 'run_jacobian', 'setup_posterior', 'run_posterior', 'create_statevector', 'reduce_dimension', 'setup_imi', 'activate_observations', 'setup_spinup', 'run_spinup', 'run_preview', 'setup_inversion', 'run_inversion', 'run_notebooks', 'setup_kf', 'run_kf', 'run_period', 'setup_template'] | -| RunFilesPath | ['src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations'] | -| RunName | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/common.sh', 'src/utilities/cleanup_script.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh', 'src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/cleanup_script.sh'] | [] | ['imi_failed', 'setup_jacobian', 'setup_posterior', 'run_posterior', 'setup_imi', 'setup_spinup', 'run_spinup', 'run_preview', 'setup_inversion', 'run_kf', 'run_period'] | -| RunSetup | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | -| RunTemplate | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/template_component/template.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_jacobian', 'setup_posterior', 'setup_imi', 'activate_observations', 'setup_spinup', 'run_preview', 'setup_template'] | -| s | ['src/utilities/parse_yaml.sh'] | [] | [] | ['parse_yaml'] | -| S3_BUCKET | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | [] | ['download_aws_files', 'report'] | -| s3_hd_path | ['src/components/statevector_component/statevector.sh'] | ['src/components/statevector_component/statevector.sh'] | ['create_statevector'] | ['create_statevector', 'reduce_dimension'] | -| s3_lc_path | ['src/components/statevector_component/statevector.sh'] | ['src/components/statevector_component/statevector.sh'] | ['create_statevector'] | ['create_statevector', 'reduce_dimension'] | -| S3_PATH | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | [] | ['download_aws_files', 'report'] | -| S3Upload | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | -| SafeMode | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | -| SchedulerPartition | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/geoschem_run_scripts/submit_jacobian_simulations_array.sh', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_posterior', 'reduce_dimension', 'run_spinup', 'run_preview', 'run_inversion'] | -| sensiCache | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | [] | -| setup_end | ['run_imi.sh', 'src/utilities/common.sh'] | ['run_imi.sh'] | [] | ['print_stats'] | -| setup_start | ['run_imi.sh', 'src/utilities/common.sh'] | ['run_imi.sh'] | [] | ['print_stats'] | -| SetupInversion | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | -| SetupJacobianRuns | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | -| SetupPosteriorRun | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | -| SetupSpinupRun | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | -| SetupTemplateRundir | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | -| ShapeFile | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | -| SimulationCPUs | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_posterior', 'reduce_dimension', 'run_spinup', 'run_preview', 'run_inversion'] | -| SimulationMemory | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_posterior', 'reduce_dimension', 'run_spinup', 'run_preview', 'run_inversion'] | -| SLURM_ARRAY_TASK_ID | ['src/geoschem_run_scripts/run_jacobian_simulations.sh'] | [] | [] | [] | -| spinup_end | ['src/utilities/common.sh', 'src/components/spinup_component/spinup.sh'] | ['src/components/spinup_component/spinup.sh'] | ['run_spinup'] | ['print_stats', 'setup_spinup', 'run_spinup'] | -| spinup_start | ['src/utilities/common.sh', 'src/components/spinup_component/spinup.sh'] | ['src/components/spinup_component/spinup.sh'] | ['run_spinup'] | ['print_stats', 'setup_spinup', 'run_spinup'] | -| SpinupDir | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | [] | -| SpinupDryrun | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/spinup_component/spinup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_spinup'] | -| SpinupEnd | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_jacobian', 'setup_posterior', 'setup_imi', 'activate_observations', 'setup_spinup'] | -| SpinupMonths | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | -| SpinupName | ['src/components/spinup_component/spinup.sh'] | ['src/components/spinup_component/spinup.sh'] | ['setup_spinup'] | ['setup_spinup', 'run_spinup'] | -| SpinupStart | ['src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations', 'setup_spinup'] | -| START | ['src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations'] | -| start_time | ['run_imi.sh'] | ['run_imi.sh'] | [] | [] | -| StartDate | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/kalman_component/kalman.sh', 'src/components/template_component/template.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_jacobian', 'setup_posterior', 'run_posterior', 'setup_imi', 'setup_spinup', 'run_preview', 'setup_kf', 'setup_template'] | -| startDate | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | -| StartDate_i | ['src/components/posterior_component/posterior.sh', 'src/components/inversion_component/inversion.sh', 'src/components/kalman_component/kalman.sh'] | ['src/components/posterior_component/posterior.sh', 'src/components/kalman_component/kalman.sh'] | ['run_posterior', 'run_period'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'run_inversion', 'setup_kf', 'run_kf', 'run_period'] | -| StartMonth | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | -| state_vector_path | ['src/components/statevector_component/statevector.sh', 'src/components/preview_component/preview.sh'] | ['src/components/statevector_component/statevector.sh', 'src/components/preview_component/preview.sh'] | ['reduce_dimension', 'run_preview'] | ['create_statevector', 'reduce_dimension', 'run_preview'] | -| StateVectorFile | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh', 'src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['setup_kf'] | ['setup_imi', 'setup_kf', 'run_kf', 'run_period'] | -| StateVectorFName | ['src/components/statevector_component/statevector.sh'] | ['src/components/statevector_component/statevector.sh'] | ['create_statevector'] | ['create_statevector', 'reduce_dimension'] | -| stdout | ['run_imi.sh'] | ['run_imi.sh'] | [] | [] | -| TCCON | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['activate_observations'] | -| tropomi_cache | ['src/components/statevector_component/statevector.sh', 'src/components/preview_component/preview.sh'] | ['src/components/statevector_component/statevector.sh', 'src/components/preview_component/preview.sh'] | ['reduce_dimension', 'run_preview'] | ['create_statevector', 'reduce_dimension', 'run_preview'] | -| tropomiCache | ['run_imi.sh', 'src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_imi.sh', 'src/inversion_scripts/run_inversion.sh'] | [] | ['run_posterior'] | -| tropomiDir | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | -| UpdateFreqDays | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/kalman_component/kalman.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_kf'] | -| UseBCsForRestart | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_jacobian', 'setup_posterior', 'setup_imi', 'activate_observations', 'setup_spinup', 'run_preview'] | -| UseEmisSF | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/template_component/template.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_template'] | -| UseOHSF | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/template_component/template.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_template'] | -| UseSlurm | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['reduce_dimension', 'setup_imi', 'run_preview'] | -| vn | ['src/utilities/parse_yaml.sh'] | ['src/utilities/parse_yaml.sh'] | ['parse_yaml'] | ['parse_yaml'] | -| w | ['src/utilities/parse_yaml.sh'] | [] | [] | ['parse_yaml'] | -| workDir | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | -| x | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/kalman_component/kalman.sh'] | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/components/jacobian_component/jacobian.sh'] | ['setup_jacobian'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values', 'run_period'] | -| xhat | ['src/components/posterior_component/posterior.sh'] | ['src/components/posterior_component/posterior.sh'] | ['generate_optimized_BC_values'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values'] | -| xstr | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/kalman_component/kalman.sh'] | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/kalman_component/kalman.sh'] | ['setup_jacobian', 'run_period'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values', 'setup_kf', 'run_kf', 'run_period'] | -| xUSE | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['setup_jacobian'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values'] | -| Year | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | -| YEAR | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | [] | ['download_aws_files', 'report'] | \ No newline at end of file +| ShellVariable | SourceScripts | DefinedIn | DefinedInFunction | UsedInFunction | +|:------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| aggregation_file | ['src/components/statevector_component/statevector.sh'] | ['src/components/statevector_component/statevector.sh'] | ['reduce_dimension'] | ['create_statevector', 'reduce_dimension'] | +| AIRS | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['activate_observations'] | +| archive_sv | ['src/components/statevector_component/statevector.sh'] | ['src/components/statevector_component/statevector.sh'] | ['reduce_dimension'] | ['create_statevector', 'reduce_dimension'] | +| array | ['src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations'] | +| bc_perturb | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['generate_BC_perturb_values'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values'] | +| BCdryrun | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | +| BCpath | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | +| bcThreshold | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['setup_jacobian', 'generate_BC_perturb_values'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values'] | +| BCversion | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | +| blendedDir | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | +| BlendedTROPOMI | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_posterior'] | +| BufferDeg | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | +| buildJacobian | ['src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | +| c | ['src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/run_boundary_conditions.sh'] | [] | [] | +| channels | ['envs/Harvard-Cannon/imi_env.yml'] | ['envs/Harvard-Cannon/imi_env.yml'] | [] | [] | +| ClusteringMethod | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | +| cmd | ['src/components/template_component/template.sh'] | ['src/components/template_component/template.sh'] | ['setup_template'] | ['setup_template'] | +| condaEnv | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | +| CondaEnv | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh', 'src/components/inversion_component/inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi', 'run_inversion'] | +| CondaFile | ['config.yml', 'src/components/setup_component/setup.sh'] | ['config.yml'] | [] | ['setup_imi'] | +| config_path | ['src/components/statevector_component/statevector.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh'] | ['src/components/statevector_component/statevector.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh'] | ['create_statevector', 'reduce_dimension', 'run_preview', 'run_notebooks'] | ['create_statevector', 'reduce_dimension', 'run_preview', 'setup_inversion', 'run_inversion', 'run_notebooks'] | +| ConfigFile | ['run_imi.sh', 'src/utilities/cleanup_script.sh', 'src/components/statevector_component/statevector.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh', 'src/components/kalman_component/kalman.sh'] | ['run_imi.sh', 'src/utilities/cleanup_script.sh'] | [] | ['create_statevector', 'reduce_dimension', 'run_preview', 'setup_inversion', 'run_notebooks', 'setup_kf', 'run_period'] | +| configFile | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | [] | +| ConfigPath | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_period'] | ['setup_kf', 'run_kf', 'run_period'] | +| constYr | ['src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['create_statevector', 'setup_imi', 'activate_observations'] | +| copydir | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_period'] | ['setup_kf', 'run_kf', 'run_period'] | +| corrupt | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | ['report'] | ['download_aws_files', 'report'] | +| cpu_count | ['src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations'] | +| cpu_str | ['src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations'] | +| CreateAutomaticRectilinearStateVectorFile | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | +| cwd | ['src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/run_boundary_conditions.sh'] | [] | [] | +| DataPath | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/statevector_component/statevector.sh', 'src/components/template_component/template.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['create_statevector', 'setup_template'] | +| DataPathTROPOMI | ['run_imi.sh', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | +| debug | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | +| dependencies | ['envs/Harvard-Cannon/imi_env.yml'] | ['envs/Harvard-Cannon/imi_env.yml'] | [] | [] | +| DEST | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | [] | ['download_aws_files', 'report'] | +| dir | ['src/utilities/cleanup_script.sh'] | [] | [] | [] | +| DOFSThreshold | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | +| DoInversion | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_kf'] | +| DoJacobian | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/kalman_component/kalman.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_kf'] | +| DoPosterior | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/kalman_component/kalman.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_kf'] | +| DoPreview | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | +| DoSpinup | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_jacobian', 'setup_posterior', 'setup_imi'] | +| DownloadGlobalMet | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | +| DynamicKFClustering | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/statevector_component/statevector.sh', 'src/components/kalman_component/kalman.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['reduce_dimension', 'run_period'] | +| element | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['generate_BC_perturb_values'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values'] | +| end_time | ['run_imi.sh'] | ['run_imi.sh'] | [] | [] | +| endDate | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | +| EndDate | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/kalman_component/kalman.sh', 'src/components/template_component/template.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_posterior', 'setup_imi', 'setup_spinup', 'run_preview', 'setup_kf', 'setup_template'] | +| EndDate_i | ['src/components/posterior_component/posterior.sh', 'src/components/inversion_component/inversion.sh', 'src/components/kalman_component/kalman.sh'] | ['src/components/posterior_component/posterior.sh', 'src/components/kalman_component/kalman.sh'] | ['run_posterior', 'run_period'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value', 'run_inversion', 'setup_kf', 'run_kf', 'run_period'] | +| EndMonth | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | +| ErrorBCs | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | [] | +| ErrorOH | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | [] | +| FetchTROPOMI | ['src/components/posterior_component/posterior.sh'] | ['src/components/posterior_component/posterior.sh'] | ['run_posterior'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | +| file | ['src/utilities/common.sh', 'src/utilities/find_corrupt_files.sh', 'src/utilities/crop_met.sh'] | ['src/utilities/common.sh'] | ['imi_failed'] | ['print_stats', 'imi_failed', 'ncmax', 'ncmin'] | +| FILE | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh'] | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh'] | [] | [] | +| FILE_LIST | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | [] | ['download_aws_files', 'report'] | +| FirstPeriod | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_kf'] | ['setup_kf', 'run_kf', 'run_period'] | +| FirstSimSwitch | ['src/components/inversion_component/inversion.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/inversion_component/inversion.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_inversion'] | ['setup_inversion', 'run_inversion', 'run_notebooks'] | +| ForcedNativeResolutionElements | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | +| fOut | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | +| fs | ['src/utilities/parse_yaml.sh'] | [] | [] | ['parse_yaml'] | +| fullBCpath | ['src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations', 'setup_template'] | +| Gamma | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | +| GCClassicPath | ['src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations', 'setup_template'] | +| GCDir | ['src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | +| gcEndDate | ['src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/run_boundary_conditions.sh'] | [] | [] | +| GCsourcepth | ['src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | +| gcStartDate | ['src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/run_boundary_conditions.sh'] | [] | [] | +| geosChemDataPath | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | +| GEOSChemEnv | ['run_imi.sh', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh'] | ['envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_jacobian', 'run_posterior'] | +| geosChemEnv | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | +| GlobalDir | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | +| GOSAT | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['activate_observations'] | +| GriddedPosterior | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | [] | +| gridDir | ['src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['create_statevector', 'setup_imi', 'activate_observations'] | +| gridFile | ['src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['create_statevector', 'setup_imi', 'activate_observations'] | +| HemcoDiagFile | ['src/components/statevector_component/statevector.sh'] | ['src/components/statevector_component/statevector.sh'] | ['create_statevector'] | ['create_statevector', 'reduce_dimension'] | +| HOME | ['src/components/template_component/template.sh'] | [] | [] | ['setup_template'] | +| HourlyCH4 | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/spinup_component/spinup.sh', 'src/components/template_component/template.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_jacobian', 'setup_posterior', 'setup_spinup', 'setup_template'] | +| indent | ['src/utilities/parse_yaml.sh'] | ['src/utilities/parse_yaml.sh'] | ['parse_yaml'] | ['parse_yaml'] | +| InPath | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | +| inv_result_path | ['src/components/posterior_component/posterior.sh'] | ['src/components/posterior_component/posterior.sh'] | ['run_posterior'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | +| inversion_end | ['src/utilities/common.sh', 'src/components/inversion_component/inversion.sh'] | ['src/components/inversion_component/inversion.sh'] | ['run_inversion'] | ['print_stats', 'setup_inversion', 'run_inversion', 'run_notebooks'] | +| inversion_sensi_dir | ['src/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.sh'] | [] | [] | +| inversion_start | ['src/utilities/common.sh', 'src/components/inversion_component/inversion.sh'] | ['src/components/inversion_component/inversion.sh'] | ['run_inversion'] | ['print_stats', 'setup_inversion', 'run_inversion', 'run_notebooks'] | +| InversionDir | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_kf'] | ['setup_kf', 'run_kf', 'run_period'] | +| InversionPath | ['run_imi.sh', 'src/utilities/common.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh', 'src/components/kalman_component/kalman.sh', 'src/components/template_component/template.sh'] | ['run_imi.sh'] | [] | ['imi_failed', 'setup_jacobian', 'run_jacobian', 'run_posterior', 'create_statevector', 'reduce_dimension', 'setup_imi', 'run_preview', 'setup_inversion', 'run_notebooks', 'setup_kf', 'run_period', 'setup_template'] | +| invPath | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | [] | +| InvPeriodLength | ['src/components/template_component/template.sh'] | ['src/components/template_component/template.sh'] | ['setup_template'] | ['setup_template'] | +| isAWS | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', 'src/components/inversion_component/inversion.sh', 'src/components/template_component/template.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_jacobian', 'run_posterior', 'create_statevector', 'setup_imi', 'run_inversion', 'setup_template'] | +| isPost | ['src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | +| isRegional | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['create_statevector', 'setup_imi', 'setup_template'] | +| ithDates | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_period'] | ['setup_kf', 'run_kf', 'run_period'] | +| ithLine | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_period'] | ['setup_kf', 'run_kf', 'run_period'] | +| jacobian_dir | ['src/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.sh'] | [] | [] | +| jacobian_dirs_array | ['src/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.sh'] | [] | [] | +| jacobian_end | ['src/utilities/common.sh', 'src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['run_jacobian'] | ['print_stats', 'setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values'] | +| jacobian_sf | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | [] | +| jacobian_start | ['src/utilities/common.sh', 'src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['run_jacobian'] | ['print_stats', 'setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values'] | +| JacobianCPUs | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/geoschem_run_scripts/submit_jacobian_simulations_array.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | +| JacobianDir | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | [] | +| JacobianMemory | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/geoschem_run_scripts/submit_jacobian_simulations_array.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | +| JacobianRunsDir | ['src/components/jacobian_component/jacobian.sh', 'src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_kf'] | ['run_jacobian', 'setup_kf', 'run_kf', 'run_period'] | +| KalmanMode | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh', 'src/components/template_component/template.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_jacobian', 'run_posterior', 'reduce_dimension', 'setup_spinup', 'run_preview', 'setup_inversion', 'run_inversion', 'run_notebooks', 'setup_template'] | +| kf_inversion_dirs | ['src/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.sh'] | [] | [] | +| LandCoverFile | ['src/components/statevector_component/statevector.sh'] | ['src/components/statevector_component/statevector.sh'] | ['create_statevector'] | ['create_statevector', 'reduce_dimension'] | +| LandCoverFileExtension | ['src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['create_statevector', 'setup_imi', 'activate_observations'] | +| LandThreshold | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | +| LatMax | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/crop_met.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/crop_met.sh'] | [] | [] | +| LatMaxInvDomain | ['src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/inversion_component/inversion.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior', 'setup_imi'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value', 'setup_imi', 'activate_observations', 'setup_inversion'] | +| LatMin | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/crop_met.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/crop_met.sh'] | [] | [] | +| LatMinInvDomain | ['src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/inversion_component/inversion.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior', 'setup_imi'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value', 'setup_imi', 'activate_observations', 'setup_inversion'] | +| Lats | ['src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations', 'setup_template'] | +| LINENO | ['run_imi.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh'] | [] | [] | ['run_jacobian', 'run_posterior', 'run_spinup', 'run_preview', 'run_inversion'] | +| LonMax | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/crop_met.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/crop_met.sh'] | [] | [] | +| LonMaxInvDomain | ['src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/inversion_component/inversion.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior', 'setup_imi'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value', 'setup_imi', 'activate_observations', 'setup_inversion'] | +| LonMin | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/crop_met.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/crop_met.sh'] | [] | [] | +| LonMinInvDomain | ['src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/inversion_component/inversion.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior', 'setup_imi'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value', 'setup_imi', 'activate_observations', 'setup_inversion'] | +| Lons | ['src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations', 'setup_template'] | +| MaxSimultaneousRuns | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_jacobian'] | +| Met | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['create_statevector', 'setup_imi', 'setup_template'] | +| MET | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | [] | ['download_aws_files', 'report'] | +| metDir | ['src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['create_statevector', 'setup_imi', 'activate_observations'] | +| metNum | ['src/components/template_component/template.sh'] | ['src/components/template_component/template.sh'] | ['setup_template'] | ['setup_template'] | +| mm | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | +| Month | ['src/utilities/crop_met.sh'] | [] | [] | [] | +| name | ['envs/Harvard-Cannon/imi_env.yml', 'src/components/jacobian_component/jacobian.sh'] | ['envs/Harvard-Cannon/imi_env.yml', 'src/components/jacobian_component/jacobian.sh'] | ['setup_jacobian'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values'] | +| native | ['src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations'] | +| native_state_vector_path | ['src/components/statevector_component/statevector.sh'] | ['src/components/statevector_component/statevector.sh'] | ['reduce_dimension'] | ['create_statevector', 'reduce_dimension'] | +| nBufferClusters | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | +| nElements | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', 'src/components/inversion_component/inversion.sh', 'src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', 'src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior', 'reduce_dimension', 'setup_imi', 'setup_kf'] | ['setup_jacobian', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value', 'create_statevector', 'reduce_dimension', 'setup_imi', 'activate_observations', 'setup_inversion', 'setup_kf', 'run_kf', 'run_period'] | +| NEW | ['src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['activate_observations', 'setup_template'] | ['setup_imi', 'activate_observations', 'setup_template'] | +| nPeriods | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_kf'] | ['setup_kf', 'run_kf', 'run_period'] | +| NudgeFactor | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/kalman_component/kalman.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_period'] | +| NumberOfElements | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | +| ObsError | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | +| OffshoreEmisThreshold | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | +| OHthreshold | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['setup_jacobian'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values'] | +| OLD | ['src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['activate_observations', 'setup_template'] | ['setup_imi', 'activate_observations', 'setup_template'] | +| OptimizeBCs | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', 'src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_jacobian', 'run_posterior', 'reduce_dimension', 'setup_imi', 'setup_kf'] | +| OptimizeOH | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', 'src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_jacobian', 'run_posterior', 'generate_optimized_BC_values', 'reduce_dimension', 'setup_imi', 'setup_kf'] | +| output | ['src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations'] | +| output_log_file | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh'] | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh'] | [] | [] | +| OutputPath | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/common.sh', 'src/utilities/cleanup_script.sh', 'src/components/setup_component/setup.sh', 'src/components/inversion_component/inversion.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/cleanup_script.sh', 'src/inversion_scripts/run_inversion.sh'] | [] | ['imi_failed', 'setup_imi', 'setup_inversion'] | +| partition | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | +| period_i | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/inversion_component/inversion.sh', 'src/components/kalman_component/kalman.sh'] | [] | [] | ['run_jacobian', 'run_posterior', 'reduce_dimension', 'run_inversion', 'run_notebooks', 'run_period'] | +| PeriodsFile | ['src/components/kalman_component/kalman.sh'] | ['src/components/kalman_component/kalman.sh'] | ['run_kf'] | ['setup_kf', 'run_kf', 'run_period'] | +| pert_index | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['generate_BC_perturb_values'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values'] | +| pertBCs | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | [] | +| pertOH | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | [] | +| PerturbBCValues | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh'] | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh'] | ['setup_jacobian', 'run_posterior'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | +| PerturbOHValue | ['src/components/posterior_component/posterior.sh'] | ['src/components/posterior_component/posterior.sh'] | ['run_posterior'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | +| PerturbValue | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_jacobian'] | +| PerturbValueBCs | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_jacobian'] | +| PerturbValueOH | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_jacobian'] | +| PLANEFLIGHT | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['activate_observations'] | +| PointSourceDatasets | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | +| posterior_end | ['src/utilities/common.sh', 'src/components/posterior_component/posterior.sh'] | ['src/components/posterior_component/posterior.sh'] | ['run_posterior'] | ['print_stats', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | +| posterior_start | ['src/utilities/common.sh', 'src/components/posterior_component/posterior.sh'] | ['src/components/posterior_component/posterior.sh'] | ['run_posterior'] | ['print_stats', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | +| PosteriorDryRun | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/posterior_component/posterior.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_posterior'] | +| PosteriorName | ['src/components/posterior_component/posterior.sh'] | ['src/components/posterior_component/posterior.sh'] | ['setup_posterior'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | +| PosteriorRunDir | ['src/components/posterior_component/posterior.sh', 'src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior', 'run_kf'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value', 'setup_kf', 'run_kf', 'run_period'] | +| posteriorSF | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | [] | +| PrecomputedJacobian | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_jacobian'] | +| precomputedJacobianCache | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['run_jacobian'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values'] | +| prefix | ['src/utilities/parse_yaml.sh'] | [] | [] | ['parse_yaml'] | +| PrevDir | ['src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_posterior'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | +| preview_dir | ['src/components/statevector_component/statevector.sh', 'src/components/preview_component/preview.sh'] | ['src/components/statevector_component/statevector.sh', 'src/components/preview_component/preview.sh'] | ['reduce_dimension', 'run_preview'] | ['create_statevector', 'reduce_dimension', 'run_preview'] | +| preview_end | ['src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations'] | +| preview_file | ['src/components/preview_component/preview.sh'] | ['src/components/preview_component/preview.sh'] | ['run_preview'] | ['run_preview'] | +| preview_start | ['src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations'] | +| PreviewDryRun | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/preview_component/preview.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_preview'] | +| PreviewEnd | ['src/components/preview_component/preview.sh'] | ['src/components/preview_component/preview.sh'] | ['run_preview'] | ['run_preview'] | +| PreviewName | ['src/components/preview_component/preview.sh'] | ['src/components/preview_component/preview.sh'] | ['run_preview'] | ['run_preview'] | +| PriorError | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | +| PriorErrorBCs | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | +| PriorErrorOH | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | +| PriorRunDir | ['src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_kf'] | ['setup_kf', 'run_kf', 'run_period'] | +| ProcessConstantFields | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | +| ProductionDryRun | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_jacobian'] | +| PWD | ['src/utilities/cleanup_script.sh'] | [] | [] | [] | +| python_args | ['src/components/statevector_component/statevector.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/components/statevector_component/statevector.sh', 'src/inversion_scripts/run_inversion.sh'] | ['reduce_dimension'] | ['create_statevector', 'reduce_dimension'] | +| PYTHONPATH | ['run_imi.sh', 'src/components/kalman_component/kalman.sh'] | [] | [] | ['run_period'] | +| ReducedDimensionStateVector | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh', 'src/components/kalman_component/kalman.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi', 'run_period'] | +| ReferenceRunDir | ['src/components/jacobian_component/jacobian.sh'] | [] | [] | ['run_jacobian'] | +| RegionalDir | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | +| RegionID | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/crop_met.sh', 'src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', 'src/components/template_component/template.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/crop_met.sh'] | [] | ['create_statevector', 'setup_imi', 'setup_template'] | +| RemoveGlobalMet | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | +| RequestedTime | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/geoschem_run_scripts/submit_jacobian_simulations_array.sh', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_posterior', 'reduce_dimension', 'run_spinup', 'run_preview', 'run_inversion'] | +| RES | ['src/components/template_component/template.sh'] | [] | [] | ['setup_template'] | +| Res | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/inversion_component/inversion.sh', 'src/components/template_component/template.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/inversion_scripts/run_inversion.sh'] | [] | ['run_posterior', 'setup_imi', 'setup_inversion', 'setup_template'] | +| RESOLUTION | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | [] | ['download_aws_files', 'report'] | +| response | ['src/utilities/cleanup_script.sh'] | [] | [] | [] | +| RestartDownload | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | +| RestartFile | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh'] | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh'] | ['setup_jacobian', 'setup_posterior', 'setup_imi', 'setup_spinup'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value', 'setup_imi', 'activate_observations', 'setup_spinup', 'run_spinup'] | +| restartFileDate | ['src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/run_boundary_conditions.sh'] | [] | [] | +| RestartFileFromSpinup | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh'] | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh'] | ['setup_jacobian', 'setup_posterior'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | +| restartFilePath | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | +| RestartFilePrefix | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_jacobian', 'setup_posterior', 'setup_imi', 'setup_spinup'] | +| RestartFilePreview | ['src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh'] | ['src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh'] | ['setup_imi', 'run_preview'] | ['setup_imi', 'activate_observations', 'run_preview'] | +| RestartFilePreviewPrefix | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi', 'run_preview'] | +| retVal | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh'] | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh'] | [] | [] | +| rm_command | ['src/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.sh'] | [] | [] | +| ROOT | ['src/components/template_component/template.sh'] | [] | [] | ['setup_template'] | +| runDir | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/template_component/template.sh', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/write_BCs/run_boundary_conditions.sh'] | ['setup_jacobian', 'setup_posterior', 'setup_imi', 'setup_spinup', 'run_preview'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value', 'setup_imi', 'activate_observations', 'setup_spinup', 'run_spinup', 'run_preview', 'setup_template'] | +| RUNDIR | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh'] | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh'] | [] | [] | +| RunDir | ['src/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.sh'] | [] | [] | +| RunDirs | ['run_imi.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh', 'src/components/kalman_component/kalman.sh', 'src/components/template_component/template.sh'] | ['run_imi.sh', 'src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_jacobian', 'run_jacobian', 'setup_posterior', 'run_posterior', 'create_statevector', 'reduce_dimension', 'setup_imi', 'activate_observations', 'setup_spinup', 'run_spinup', 'run_preview', 'setup_inversion', 'run_inversion', 'run_notebooks', 'setup_kf', 'run_kf', 'run_period', 'setup_template'] | +| RunFilesPath | ['src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations'] | +| RunName | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/common.sh', 'src/utilities/cleanup_script.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh', 'src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/utilities/cleanup_script.sh'] | [] | ['imi_failed', 'setup_jacobian', 'setup_posterior', 'run_posterior', 'setup_imi', 'setup_spinup', 'run_spinup', 'run_preview', 'setup_inversion', 'run_kf', 'run_period'] | +| RunSetup | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | +| RunTemplate | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/template_component/template.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_jacobian', 'setup_posterior', 'setup_imi', 'activate_observations', 'setup_spinup', 'run_preview', 'setup_template'] | +| s | ['src/utilities/parse_yaml.sh'] | [] | [] | ['parse_yaml'] | +| S3_BUCKET | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | [] | ['download_aws_files', 'report'] | +| s3_hd_path | ['src/components/statevector_component/statevector.sh'] | ['src/components/statevector_component/statevector.sh'] | ['create_statevector'] | ['create_statevector', 'reduce_dimension'] | +| s3_lc_path | ['src/components/statevector_component/statevector.sh'] | ['src/components/statevector_component/statevector.sh'] | ['create_statevector'] | ['create_statevector', 'reduce_dimension'] | +| S3_PATH | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | [] | ['download_aws_files', 'report'] | +| S3Upload | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | +| SafeMode | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | +| SchedulerPartition | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/geoschem_run_scripts/submit_jacobian_simulations_array.sh', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_posterior', 'reduce_dimension', 'run_spinup', 'run_preview', 'run_inversion'] | +| sensiCache | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | [] | +| setup_end | ['run_imi.sh', 'src/utilities/common.sh'] | ['run_imi.sh'] | [] | ['print_stats'] | +| setup_start | ['run_imi.sh', 'src/utilities/common.sh'] | ['run_imi.sh'] | [] | ['print_stats'] | +| SetupInversion | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | +| SetupJacobianRuns | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | +| SetupPosteriorRun | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | +| SetupSpinupRun | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | +| SetupTemplateRundir | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | +| ShapeFile | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | +| SimulationCPUs | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_posterior', 'reduce_dimension', 'run_spinup', 'run_preview', 'run_inversion'] | +| SimulationMemory | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/posterior_component/posterior.sh', 'src/components/statevector_component/statevector.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/inversion_component/inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['run_posterior', 'reduce_dimension', 'run_spinup', 'run_preview', 'run_inversion'] | +| SLURM_ARRAY_TASK_ID | ['src/geoschem_run_scripts/run_jacobian_simulations.sh'] | [] | [] | [] | +| spinup_end | ['src/utilities/common.sh', 'src/components/spinup_component/spinup.sh'] | ['src/components/spinup_component/spinup.sh'] | ['run_spinup'] | ['print_stats', 'setup_spinup', 'run_spinup'] | +| spinup_start | ['src/utilities/common.sh', 'src/components/spinup_component/spinup.sh'] | ['src/components/spinup_component/spinup.sh'] | ['run_spinup'] | ['print_stats', 'setup_spinup', 'run_spinup'] | +| SpinupDir | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | [] | +| SpinupDryrun | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/spinup_component/spinup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_spinup'] | +| SpinupEnd | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_jacobian', 'setup_posterior', 'setup_imi', 'activate_observations', 'setup_spinup'] | +| SpinupMonths | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_imi'] | +| SpinupName | ['src/components/spinup_component/spinup.sh'] | ['src/components/spinup_component/spinup.sh'] | ['setup_spinup'] | ['setup_spinup', 'run_spinup'] | +| SpinupStart | ['src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations', 'setup_spinup'] | +| START | ['src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations'] | +| start_time | ['run_imi.sh'] | ['run_imi.sh'] | [] | [] | +| StartDate | ['run_imi.sh', 'config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh', 'src/components/kalman_component/kalman.sh', 'src/components/template_component/template.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_jacobian', 'setup_posterior', 'run_posterior', 'setup_imi', 'setup_spinup', 'run_preview', 'setup_kf', 'setup_template'] | +| startDate | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | +| StartDate_i | ['src/components/posterior_component/posterior.sh', 'src/components/inversion_component/inversion.sh', 'src/components/kalman_component/kalman.sh'] | ['src/components/posterior_component/posterior.sh', 'src/components/kalman_component/kalman.sh'] | ['run_posterior', 'run_period'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value', 'run_inversion', 'setup_kf', 'run_kf', 'run_period'] | +| StartMonth | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | +| state_vector_path | ['src/components/statevector_component/statevector.sh', 'src/components/preview_component/preview.sh'] | ['src/components/statevector_component/statevector.sh', 'src/components/preview_component/preview.sh'] | ['reduce_dimension', 'run_preview'] | ['create_statevector', 'reduce_dimension', 'run_preview'] | +| StateVectorFile | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh', 'src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/kalman_component/kalman.sh', 'src/inversion_scripts/run_inversion.sh'] | ['setup_kf'] | ['setup_imi', 'setup_kf', 'run_kf', 'run_period'] | +| StateVectorFName | ['src/components/statevector_component/statevector.sh'] | ['src/components/statevector_component/statevector.sh'] | ['create_statevector'] | ['create_statevector', 'reduce_dimension'] | +| stdout | ['run_imi.sh'] | ['run_imi.sh'] | [] | [] | +| TCCON | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/setup_component/setup.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['activate_observations'] | +| tropomi_cache | ['src/components/statevector_component/statevector.sh', 'src/components/preview_component/preview.sh'] | ['src/components/statevector_component/statevector.sh', 'src/components/preview_component/preview.sh'] | ['reduce_dimension', 'run_preview'] | ['create_statevector', 'reduce_dimension', 'run_preview'] | +| tropomiCache | ['run_imi.sh', 'src/components/posterior_component/posterior.sh', 'src/inversion_scripts/run_inversion.sh'] | ['run_imi.sh', 'src/inversion_scripts/run_inversion.sh'] | [] | ['run_posterior'] | +| tropomiDir | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | +| UpdateFreqDays | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/kalman_component/kalman.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_kf'] | +| UseBCsForRestart | ['src/components/jacobian_component/jacobian.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/spinup_component/spinup.sh', 'src/components/preview_component/preview.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_jacobian', 'setup_posterior', 'setup_imi', 'activate_observations', 'setup_spinup', 'run_preview'] | +| UseEmisSF | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/template_component/template.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_template'] | +| UseOHSF | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/template_component/template.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['setup_template'] | +| UseSlurm | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', 'src/components/preview_component/preview.sh'] | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | ['reduce_dimension', 'setup_imi', 'run_preview'] | +| vn | ['src/utilities/parse_yaml.sh'] | ['src/utilities/parse_yaml.sh'] | ['parse_yaml'] | ['parse_yaml'] | +| w | ['src/utilities/parse_yaml.sh'] | [] | [] | ['parse_yaml'] | +| workDir | ['src/write_BCs/config_boundary_conditions.yml', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | +| x | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/kalman_component/kalman.sh'] | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/components/jacobian_component/jacobian.sh'] | ['setup_jacobian'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values', 'run_period'] | +| xhat | ['src/components/posterior_component/posterior.sh'] | ['src/components/posterior_component/posterior.sh'] | ['generate_optimized_BC_values', 'generate_optimized_OH_value'] | ['setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | +| xstr | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/kalman_component/kalman.sh'] | ['src/geoschem_run_scripts/run_jacobian_simulations.sh', 'src/geoschem_run_scripts/run_prior_simulation.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/kalman_component/kalman.sh'] | ['setup_jacobian', 'run_period'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values', 'setup_kf', 'run_kf', 'run_period'] | +| xUSE | ['src/components/jacobian_component/jacobian.sh'] | ['src/components/jacobian_component/jacobian.sh'] | ['setup_jacobian'] | ['setup_jacobian', 'run_jacobian', 'generate_BC_perturb_values'] | +| Year | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | +| YEAR | ['src/utilities/find_corrupt_files.sh'] | ['src/utilities/find_corrupt_files.sh'] | [] | ['download_aws_files', 'report'] | \ No newline at end of file