From 023deba3706bbc131bbf42d0779773d47ef985e4 Mon Sep 17 00:00:00 2001 From: integrated_methane_inversion Continuous Integration Date: Sat, 15 Jun 2024 23:52:17 +0000 Subject: [PATCH] Continuous Integration Manifest Generation --- src/components/shell_variable_manifest.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/components/shell_variable_manifest.md b/src/components/shell_variable_manifest.md index daadbc85..06650725 100644 --- a/src/components/shell_variable_manifest.md +++ b/src/components/shell_variable_manifest.md @@ -22,12 +22,12 @@ Note: This does not include variables defined in python scripts. | 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 | ['config.yml', 'run_imi.sh', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'run_imi.sh', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | | condaEnv | ['src/write_BCs/run_boundary_conditions.sh', 'src/write_BCs/config_boundary_conditions.yml'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | +| CondaEnv | ['config.yml', 'run_imi.sh', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'run_imi.sh', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | | CondaFile | ['config.yml', 'run_imi.sh', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | ['config.yml', 'run_imi.sh', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml'] | [] | [] | | config_path | ['src/components/preview_component/preview.sh'] | ['src/components/preview_component/preview.sh'] | ['run_preview'] | ['run_preview'] | -| configFile | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | ['send_error'] | | ConfigFile | ['run_imi.sh', 'src/components/inversion_component/inversion.sh', 'src/components/preview_component/preview.sh', 'src/utilities/cleanup_script.sh'] | ['run_imi.sh', 'src/utilities/cleanup_script.sh'] | [] | ['setup_inversion', 'run_preview'] | +| configFile | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | ['send_error'] | | ConfigPath | ['run_imi.sh', 'src/components/kalman_component/kalman.sh', 'src/components/statevector_component/statevector.sh', 'src/components/inversion_component/inversion.sh', 'src/components/preview_component/preview.sh', 'src/components/jacobian_component/jacobian.sh'] | ['run_imi.sh'] | [] | ['setup_kf', 'run_period', 'create_statevector', 'reduce_dimension', 'run_notebooks', 'run_preview', 'run_jacobian'] | | 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'] | @@ -61,8 +61,8 @@ Note: This does not include variables defined in python scripts. | ErrorBCs | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | ['send_error'] | | ErrorOH | ['src/inversion_scripts/run_inversion.sh'] | ['src/inversion_scripts/run_inversion.sh'] | [] | ['send_error'] | | 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/geoschem_run_scripts/run_prior_simulation.sh', 'src/geoschem_run_scripts/run_bkgd_simulation.sh', 'src/geoschem_run_scripts/run_jacobian_simulations.sh'] | ['src/geoschem_run_scripts/run_prior_simulation.sh', 'src/geoschem_run_scripts/run_bkgd_simulation.sh', 'src/geoschem_run_scripts/run_jacobian_simulations.sh'] | [] | [] | | file | ['src/utilities/crop_met.sh', 'src/utilities/find_corrupt_files.sh', 'src/utilities/common.sh', 'src/inversion_scripts/run_inversion.sh'] | ['src/utilities/common.sh', 'src/inversion_scripts/run_inversion.sh'] | ['imi_failed', 'send_error'] | ['print_stats', 'imi_failed', 'ncmax', 'ncmin', 'calculate_geoschem_domain', 'send_error'] | +| FILE | ['src/geoschem_run_scripts/run_prior_simulation.sh', 'src/geoschem_run_scripts/run_bkgd_simulation.sh', 'src/geoschem_run_scripts/run_jacobian_simulations.sh'] | ['src/geoschem_run_scripts/run_prior_simulation.sh', 'src/geoschem_run_scripts/run_bkgd_simulation.sh', 'src/geoschem_run_scripts/run_jacobian_simulations.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', 'send_error'] | @@ -206,8 +206,8 @@ Note: This does not include variables defined in python scripts. | RegionID | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/template_component/template.sh', 'src/components/statevector_component/statevector.sh', 'src/components/setup_component/setup.sh', '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'] | [] | ['setup_template', 'create_statevector', 'setup_imi'] | | RemoveGlobalMet | ['src/utilities/crop_met.sh'] | ['src/utilities/crop_met.sh'] | [] | [] | | RequestedTime | ['config.yml', 'run_imi.sh', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/statevector_component/statevector.sh', 'src/components/inversion_component/inversion.sh', 'src/components/preview_component/preview.sh', 'src/components/posterior_component/posterior.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/spinup_component/spinup.sh', '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'] | [] | ['reduce_dimension', 'run_inversion', 'run_preview', 'run_posterior', 'run_jacobian', 'run_spinup'] | -| Res | ['config.yml', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/template_component/template.sh', 'src/components/inversion_component/inversion.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.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'] | [] | ['setup_template', 'setup_inversion', 'run_posterior', 'setup_imi', 'send_error'] | | 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/template_component/template.sh', 'src/components/inversion_component/inversion.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.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'] | [] | ['setup_template', 'setup_inversion', 'run_posterior', 'setup_imi', 'send_error'] | | 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'] | @@ -221,9 +221,9 @@ Note: This does not include variables defined in python scripts. | retVal | ['src/geoschem_run_scripts/run_prior_simulation.sh', 'src/geoschem_run_scripts/run_bkgd_simulation.sh', 'src/geoschem_run_scripts/run_jacobian_simulations.sh'] | ['src/geoschem_run_scripts/run_prior_simulation.sh', 'src/geoschem_run_scripts/run_bkgd_simulation.sh', 'src/geoschem_run_scripts/run_jacobian_simulations.sh'] | [] | [] | | rm_command | ['src/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.sh'] | [] | [] | | ROOT | ['src/components/template_component/template.sh'] | [] | [] | ['setup_template'] | +| RunDir | ['src/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.sh'] | [] | [] | | RUNDIR | ['src/geoschem_run_scripts/run_prior_simulation.sh', 'src/geoschem_run_scripts/run_bkgd_simulation.sh', 'src/geoschem_run_scripts/run_jacobian_simulations.sh'] | ['src/geoschem_run_scripts/run_prior_simulation.sh', 'src/geoschem_run_scripts/run_bkgd_simulation.sh', 'src/geoschem_run_scripts/run_jacobian_simulations.sh'] | [] | [] | | runDir | ['src/components/template_component/template.sh', 'src/components/preview_component/preview.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/spinup_component/spinup.sh', 'src/write_BCs/run_boundary_conditions.sh'] | ['src/components/preview_component/preview.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/spinup_component/spinup.sh', 'src/write_BCs/run_boundary_conditions.sh'] | ['run_preview', 'setup_posterior', 'setup_imi', 'create_simulation_dir', 'setup_spinup'] | ['setup_template', 'run_preview', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value', 'setup_imi', 'activate_observations', 'setup_jacobian', 'create_simulation_dir', 'run_jacobian', 'generate_BC_perturb_values', 'setup_spinup', 'run_spinup'] | -| RunDir | ['src/utilities/cleanup_script.sh'] | ['src/utilities/cleanup_script.sh'] | [] | [] | | RunDirs | ['run_imi.sh', 'src/components/kalman_component/kalman.sh', 'src/components/template_component/template.sh', 'src/components/statevector_component/statevector.sh', 'src/components/inversion_component/inversion.sh', 'src/components/preview_component/preview.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/spinup_component/spinup.sh'] | ['run_imi.sh', 'src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_kf', 'run_kf', 'run_period', 'setup_template', 'create_statevector', 'reduce_dimension', 'setup_inversion', 'run_inversion', 'run_notebooks', 'run_preview', 'setup_posterior', 'run_posterior', 'setup_imi', 'activate_observations', 'setup_jacobian', 'create_simulation_dir', 'run_jacobian', 'setup_spinup', 'run_spinup'] | | RunFilesPath | ['src/components/setup_component/setup.sh'] | ['src/components/setup_component/setup.sh'] | ['setup_imi'] | ['setup_imi', 'activate_observations'] | | RunName | ['config.yml', 'run_imi.sh', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/kalman_component/kalman.sh', 'src/components/inversion_component/inversion.sh', 'src/components/preview_component/preview.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/spinup_component/spinup.sh', 'src/utilities/cleanup_script.sh', 'src/utilities/common.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'] | [] | ['run_kf', 'run_period', 'setup_inversion', 'run_preview', 'setup_posterior', 'run_posterior', 'setup_imi', 'setup_jacobian', 'create_simulation_dir', 'run_jacobian', 'setup_spinup', 'run_spinup', 'imi_failed'] | @@ -258,8 +258,8 @@ Note: This does not include variables defined in python scripts. | 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 | ['src/write_BCs/run_boundary_conditions.sh', 'src/write_BCs/config_boundary_conditions.yml'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | | StartDate | ['config.yml', 'run_imi.sh', 'envs/Harvard-Cannon/config.harvard-cannon.global_inv.yml', 'envs/Harvard-Cannon/config.harvard-cannon.yml', 'src/components/kalman_component/kalman.sh', 'src/components/template_component/template.sh', 'src/components/preview_component/preview.sh', 'src/components/posterior_component/posterior.sh', 'src/components/setup_component/setup.sh', 'src/components/jacobian_component/jacobian.sh', 'src/components/spinup_component/spinup.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_kf', 'setup_template', 'run_preview', 'setup_posterior', 'run_posterior', 'setup_imi', 'create_simulation_dir', 'setup_spinup'] | +| startDate | ['src/write_BCs/run_boundary_conditions.sh', 'src/write_BCs/config_boundary_conditions.yml'] | ['src/write_BCs/config_boundary_conditions.yml'] | [] | [] | | StartDate_i | ['src/components/kalman_component/kalman.sh', 'src/components/inversion_component/inversion.sh', 'src/components/posterior_component/posterior.sh'] | ['src/components/kalman_component/kalman.sh', 'src/components/posterior_component/posterior.sh'] | ['run_period', 'run_posterior'] | ['setup_kf', 'run_kf', 'run_period', 'run_inversion', 'setup_posterior', 'run_posterior', 'generate_optimized_BC_values', 'generate_optimized_OH_value'] | | 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'] |