landice

Landice()

The collection of all test case for the MALI core

Utilities

calculate_decomp_core_pair(config, ...)

Get a pair of decomposition task counts based on available cores.

ISMIP7 framework

ice_sheet_params.get_params(config)	Get ice-sheet-specific parameters from the config.
archive.ForcingSource(directory, files, ...)	A resolved collection of ISMIP7 forcing files.
archive.resolve_atmosphere_source(config, ...)	Resolve one atmosphere variable from the native archive hierarchy.
archive.resolve_ocean_source(config[, choice])	Resolve ocean thermal forcing from the native archive hierarchy.
archive.resolve_fracture_source(config, ...)	Resolve one fracture product, keeping all pathways on one version.
archive.resolve_version_directory(base_path)	Resolve an explicit version or the numerically latest version directory.
archive.mapping_file_name(config, component, ...)	Build a mapping filename that identifies the selected source grid.
mapping.build_mapping_file(config, logger, ...)	Build a mapping file for regridding from an ISMIP7 polar stereographic grid to the MALI unstructured mesh.
remap.netcdf_file_is_valid(path[, varname, ...])	Return True if path exists, opens cleanly, contains varname and (optionally) a time coordinate, and its last time record can actually be read.
remap.extrapolate_source(input_file, ...)	Extrapolate fill/missing values on the source polar stereographic grid using nearest-neighbor via distance_transform_edt.
remap.open_rename_and_trim(remapped_file, ...)	Open a remapped file, rename dimensions/variables to MALI conventions, and restrict to the requested year range.
remap.add_xtime_and_write(ds, years, output_file)	Add an xtime variable (January 1st of each year), drop auxiliary remapping variables, and write the dataset.

Test Groups

antarctica

Antarctica(mpas_core)	A test group for Antarctica test cases
mesh_gen.MeshGen(test_group)	The default test case for the Antarctica test group simply creates the mesh and initial condition.
mesh.Mesh(test_case)	A step for creating a mesh and initial condition for Antarctica test cases
mesh.Mesh.run()	Run this step of the test case

calving_dt_convergence

CalvingDtConvergence(mpas_core)	A test group for a series of test cases for assessing timestep convergence related to calving.
dt_convergence_test.DtConvergenceTest(...)	A test case for running the same configuration with a series of values for config_adaptive_timestep_calvingCFL_fraction to check for convergence
dt_convergence_test.DtConvergenceTest.validate()	Test cases can override this method to perform validation of variables and timers
run_model.RunModel(test_case, name, mesh, ...)	A step for performing forward MALI runs as part of calving dt convergence test cases.
run_model.RunModel.run()	Run this step of the test case

circular_shelf

CircularShelf(mpas_core)	A test group for circular shelf test cases
decomposition_test.DecompositionTest(...)	A test case for performing two MALI runs of a circular shelf setup, one with one core and one with four.
decomposition_test.DecompositionTest.run()	This method is deprecated.
run_model.RunModel(test_case[, name, ...])	A step for performing forward MALI runs as part of circular_shelf test cases.
run_model.RunModel.run()	Run this step of the test case
setup_mesh.SetupMesh(test_case)	A step for creating a mesh and initial condition for circular_shelf test cases
setup_mesh.SetupMesh.run()	Run this step of the test case
visualize.Visualize(test_case[, name, ...])	A step for visualizing the output from a circular_shelf test case
visualize.Visualize.run()	Run this step of the test case
visualize.visualize_circular_shelf(config, ...)	Plot the output from a circular_shelf test case

crane

Crane(mpas_core)	A test group for Crane Glacier test cases.
mesh_gen.MeshGen(test_group)	The high resolution test case for the crane test group simply creates the mesh and initial condition.
mesh_gen.MeshGen.run()	This method is deprecated.
mesh.Mesh(test_case)	A step for creating a mesh and initial condition for thwaites test cases
mesh.Mesh.run()	Run this step of the test case

dome

Dome(mpas_core)	A test group for dome test cases
decomposition_test.DecompositionTest(...)	A test case for performing two MALI runs of a dome setup, one with one core and one with four.
decomposition_test.DecompositionTest.run()	This method is deprecated.
restart_test.RestartTest(test_group, ...)	A test case for performing two MALI runs of a dome setup, one full run and one run broken into two segments with a restart.
restart_test.RestartTest.run()	This method is deprecated.
smoke_test.SmokeTest(test_group, ...)	The default test case for the dome test group simply creates the mesh and initial condition, then performs a short forward run on 4 cores.
smoke_test.SmokeTest.run()	This method is deprecated.
run_model.RunModel(test_case, velo_solver, ...)	A step for performing forward MALI runs as part of dome test cases.
run_model.RunModel.setup()	Set up the test case in the work directory, including downloading any dependencies.
run_model.RunModel.run()	Run this step of the test case
setup_mesh.SetupMesh(test_case, mesh_type)	A step for creating a mesh and initial condition for dome test cases
setup_mesh.SetupMesh.run()	Run this step of the test case
visualize.Visualize(test_case, mesh_type[, ...])	A step for visualizing the output from a dome test case
visualize.Visualize.run()	Run this step of the test case
visualize.visualize_dome(config, logger, ...)	Plot the output from a dome test case

enthalpy_benchmark

EnthalpyBenchmark(mpas_core)	A test group for enthalpy benchmark test cases
A.A(test_group)	The Kleiner enthalpy benchmark test case A
A.A.configure()	Modify the configuration options for this test case
A.A.run()	This method is deprecated.
A.visualize.Visualize(test_case)	A step for visualizing the output from a dome test case
A.visualize.Visualize.run()	Run this step of the test case
B.B(test_group)	The Kleiner enthalpy benchmark test case B
B.B.configure()	Modify the configuration options for this test case
B.B.run()	This method is deprecated.
B.visualize.Visualize(test_case)	A step for visualizing the output from a dome test case
B.visualize.Visualize.run()	Run this step of the test case
run_model.RunModel(test_case, name[, ...])	A step for performing forward MALI runs as part of dome test cases.
run_model.RunModel.setup()	Set up the test case in the work directory, including downloading any dependencies.
run_model.RunModel.run()	Run this step of the test case
setup_mesh.SetupMesh(test_case)	A step for creating a mesh and initial condition for enthalpy benchmark test cases
setup_mesh.SetupMesh.run()	Run this step of the test case

eismint2

Eismint2(mpas_core)	A test group for eismint2 test cases
decomposition_test.DecompositionTest(...)	A test case for performing two MALI runs of a EISMINT2 setup, one with one core and one with four.
decomposition_test.DecompositionTest.run()	This method is deprecated.
restart_test.RestartTest(test_group, ...)	A test case for performing two MALI runs of an EISMINT2 setup, one full run and one run broken into two segments with a restart.
restart_test.RestartTest.run()	This method is deprecated.
standard_experiments.StandardExperiments(...)	A test case for performing the standard EISMINT2 experiments.
standard_experiments.StandardExperiments.run()	This method is deprecated.
standard_experiments.visualize.Visualize(...)	A step for visualizing the output from a EISMINT2 test case
standard_experiments.visualize.Visualize.run()	Run this step of the test case
standard_experiments.visualize.visualize_eismint2(...)	Plot the output from an EISMINT2 experiment
run_experiment.RunExperiment(test_case, ...)	A step for performing forward MALI runs as part of eismint2 test cases.
run_experiment.RunExperiment.setup()	Set up the test case in the work directory, including downloading any dependencies.
run_experiment.RunExperiment.run()	Run this step of the test case
setup_mesh.SetupMesh(test_case)	A step for creating a mesh and initial condition for EISMINT2 test cases
setup_mesh.SetupMesh.run()	Run this step of the test case

ensemble_generator

EnsembleGenerator(mpas_core)	A test group for generating ensembles of MALI simulations for uncertainty quantification or parameter sensitivity tests.
ensemble_manager.EnsembleManager(test_case)	A step for an ensemble manager.
ensemble_manager.EnsembleManager.setup()	Sets up the ensemble manager
ensemble_manager.EnsembleManager.run()	Use the ensemble manager to manage and launch jobs for each run Each ensemble member is a step of the test case.
ensemble_member.EnsembleMember(test_case, ...)	A step for setting up a single ensemble member
ensemble_member.EnsembleMember.setup()	Set up this run by setting up a baseline run configuration and then modifying parameters for this ensemble member based on an externally provided unit parameter vector
ensemble_member.EnsembleMember.run()	Run this member of the ensemble.
ensemble_template.get_ensemble_template_name(config)	Get the configured ensemble template name.
ensemble_template.get_spinup_template_package(config)	Get the package containing spinup ensemble template resources.
ensemble_template.get_branch_template_package(config)	Get the package containing branch ensemble template resources.
spinup_ensemble.SpinupEnsemble(test_group)	A test case for performing an ensemble of simulations for uncertainty quantification studies.
spinup_ensemble.SpinupEnsemble.configure()	Configure a parameter ensemble of MALI simulations.
branch_ensemble.BranchEnsemble(test_group)	A test case for performing an ensemble of simulations for uncertainty quantification studies.
branch_ensemble.BranchEnsemble.configure()	Configure a parameter ensemble of MALI simulations.

greenland

Greenland(mpas_core)	A test group for Greenland test cases
decomposition_test.DecompositionTest(...)	A test case for performing two MALI runs of the Greenland Ice Sheet setup with different decompositions.
decomposition_test.DecompositionTest.configure()	Choose decomposition sizes from framework-detected resources and add run steps.
decomposition_test.DecompositionTest.run()	This method is deprecated.
restart_test.RestartTest(test_group, velo_solver)	A test case for performing two MALI runs of the Greenland Ice Sheet setup, one full run and one run broken into two segments with a restart.
restart_test.RestartTest.run()	This method is deprecated.
smoke_test.SmokeTest(test_group, velo_solver)	The default test case for the Greenland test group simply downloads the mesh and initial condition, then performs a short forward run on 36 cores.
smoke_test.SmokeTest.run()	This method is deprecated.
run_model.RunModel(test_case, velo_solver[, ...])	A step for performing forward MALI runs as part of low-res 20km Greenland test cases.
run_model.RunModel.setup()	Set up the test case in the work directory, including downloading any dependencies.
run_model.RunModel.run()	Run this step of the test case
mesh.Mesh(test_case)	A step for creating a mesh and initial condition for greenland test cases
mesh.Mesh.setup()	Add the configured geojson cull-mask file as an input.
mesh.Mesh.run()	Run this step of the test case
mesh_gen.MeshGen(test_group)	The high resolution test case for the greenland test group simply creates the mesh and initial condition.
mesh_gen.MeshGen.run()	This method is deprecated.

humboldt

Humboldt(mpas_core)	A test group for humboldt test cases
mesh_gen.MeshGen(test_group)	The MeshGen test case for the humboldt test group simply creates the mesh and initial condition.
mesh_gen.MeshGen.run()	This method is deprecated.
mesh.Mesh(test_case)	A step for creating a mesh and initial condition for humboldt test cases
mesh.Mesh.run()	Run this step of the test case
run_model.RunModel(test_case, velo_solver, ...)	A step for performing forward MALI runs as part of Humboldt test cases.
run_model.RunModel.run()	Run this step of the test case
decomposition_test.DecompositionTest(...[, ...])	A test case for performing two MALI runs of a Humboldt setup with different decompositions.
decomposition_test.DecompositionTest.configure()	Choose decomposition sizes from framework-detected resources and add run steps.
decomposition_test.DecompositionTest.validate()	Test cases can override this method to perform validation of variables and timers
restart_test.RestartTest(test_group, ...[, ...])	A test case for performing two MALI runs of a Humboldt setup, one full run and one run broken into two segments with a restart.
restart_test.RestartTest.configure()	Set restart-test task counts from framework-detected resources.
restart_test.RestartTest.validate()	Test cases can override this method to perform validation of variables and timers

hydro_radial

HydroRadial(mpas_core)	A test group for radially symmetric hydrology test cases
decomposition_test.DecompositionTest(test_group)	A test case for performing two MALI runs of a radially symmetric hydrological setup, one with one core and one with three.
decomposition_test.DecompositionTest.run()	This method is deprecated.
restart_test.RestartTest(test_group)	A test case for performing two MALI runs of a radially symmetric hydrological setup, one full run and one run broken into two segments with a restart.
restart_test.RestartTest.run()	This method is deprecated.
spinup_test.SpinupTest(test_group)	A spin-up test case for the radially symmetric hydrological test group that creates the mesh and initial condition, then performs a long short forward run on 4 cores until a quasi-steady state is reached.
spinup_test.SpinupTest.run()	This method is deprecated.
steady_state_drift_test.SteadyStateDriftTest(...)	This test case assesses the drift of the model away from an initial condition that is a quasi-exact solution.
steady_state_drift_test.SteadyStateDriftTest.run()	This method is deprecated.
run_model.RunModel(test_case[, name, ...])	A step for performing forward MALI runs as part of radially symmetric
run_model.RunModel.setup()	Set up the test case in the work directory, including downloading any dependencies.
run_model.RunModel.run()	Run this step of the test case
setup_mesh.SetupMesh(test_case, ...)	A step for creating a mesh and initial condition for dome test cases
setup_mesh.SetupMesh.run()	Run this step of the test case
visualize.Visualize(test_case[, name, ...])	A step for visualizing the output from a dome test case
visualize.Visualize.run()	Run this step of the test case
visualize.visualize_hydro_radial(config, logger)	Plot the output from a hydro_radial test case

ismip6_forcing

Ismip6Forcing(mpas_core)	A test group for processing the ISMIP6 atmosphere, ocean and shelf-collapse forcing data
configure.configure(config, check_model_options)	A shared function for configuring options for all ismip6 forcing test cases
create_mapfile.build_mapping_file(config, ...)	Build a mapping file if it does not exist.
create_mapfile.create_scrip_from_latlon(...)	Create a scripfile based on the lat/lon coordinates of a source dataset.
atmosphere.Atmosphere(test_group)	A test case for processing the ISMIP6 atmosphere forcing data.
atmosphere.Atmosphere.configure()	Configures test case
atmosphere.process_smb.ProcessSMB(test_case)	A step for processing the ISMIP6 surface mass balance data
atmosphere.process_smb.ProcessSMB.setup()	Set up this step of the test case
atmosphere.process_smb.ProcessSMB.run()	Run this step of the test case
atmosphere.process_smb.ProcessSMB.remap_ismip6_smb_to_mali(...)	Remap the input ismip6 smb forcing data onto mali mesh
atmosphere.process_smb.ProcessSMB.rename_ismip6_smb_to_mali_vars(...)	Rename variables in the remapped source input data to the ones that MALI uses.
atmosphere.process_smb.ProcessSMB.correct_smb_anomaly_for_climatology(...)	Apply the MALI base SMB to the ismip6 SMB anomaly field
atmosphere.process_smb_racmo.ProcessSmbRacmo(...)	A step for processing the regional RACMO surface mass balance data
atmosphere.process_smb_racmo.ProcessSmbRacmo.setup()	Set up this step of the test case
atmosphere.process_smb_racmo.ProcessSmbRacmo.run()	Run this step of the test case
atmosphere.process_smb_racmo.ProcessSmbRacmo.remap_source_smb_to_mali(...)	Remap the input ismip6 smb forcing data onto mali mesh
atmosphere.process_smb_racmo.ProcessSmbRacmo.rename_source_smb_to_mali_vars(...)	Rename variables in the remapped source input data to the ones that MALI uses.
atmosphere.process_smb_racmo.ProcessSmbRacmo.correct_smb_anomaly_for_base_smb(...)	Apply the MALI base SMB to the ismip6 SMB anomaly field
ocean_basal.OceanBasal(test_group)	A test case for processing the ISMIP6 ocean basalmelt param.
ocean_basal.OceanBasal.configure()	Configures test case
ocean_basal.process_basal_melt.ProcessBasalMelt(...)	A step for processing (combine, remap and rename) the ISMIP6 basalmelt data
ocean_basal.process_basal_melt.ProcessBasalMelt.setup()	Set up this step of the test case
ocean_basal.process_basal_melt.ProcessBasalMelt.run()	Run this step of the test case
ocean_basal.process_basal_melt.ProcessBasalMelt.combine_ismip6_inputfiles(...)	Combine ismip6 input files before regridding onto mali mesh
ocean_basal.process_basal_melt.ProcessBasalMelt.remap_ismip6_basal_melt_to_mali_vars(...)	Remap the input ismip6 basal melt data onto mali mesh
ocean_basal.process_basal_melt.ProcessBasalMelt.rename_ismip6_basal_melt_to_mali_vars(...)	Rename variables in the remapped ismip6 input data to the ones that MALI uses.
ocean_thermal.OceanThermal(test_group, ...)	A test case for processing the ISMIP6 ocean thermal forcing data.
ocean_thermal.OceanThermal.configure()	Configures test case
ocean_thermal.process_thermal_forcing.ProcessThermalForcing(...)	A step for creating a mesh and initial condition for dome test cases
ocean_thermal.process_thermal_forcing.ProcessThermalForcing.setup()	Set up this step of the test case
ocean_thermal.process_thermal_forcing.ProcessThermalForcing.run()	Run this step of the test case
ocean_thermal.process_thermal_forcing.ProcessThermalForcing.remap_ismip6_thermal_forcing_to_mali_vars(...)	Remap the input ismip6 thermal forcing data onto mali mesh
ocean_thermal.process_thermal_forcing.ProcessThermalForcing.rename_ismip6_thermal_forcing_to_mali_vars(...)	Rename variables in the remapped ismip6 input data to the ones that MALI uses.
shelf_collapse.ShelfCollapse(test_group)	A test case for processing the ISMIP6 shelf-collapse mask data.
shelf_collapse.ShelfCollapse.configure()	Configures test case
shelf_collapse.process_shelf_collapse.ProcessShelfCollapse.setup()	Set up this step of the test case
shelf_collapse.process_shelf_collapse.ProcessShelfCollapse.run()	Run this step of the test case
shelf_collapse.process_shelf_collapse.ProcessShelfCollapse.remap_ismip6_shelf_mask_to_mali_vars(...)	Remap the input ismip6 ice shelf-collapse mask data onto mali mesh
shelf_collapse.process_shelf_collapse.ProcessShelfCollapse.rename_ismip6_shelf_mask_to_mali_vars(...)	Rename variables in the remapped ismip6 input data to the ones that MALI uses.

ismip6_run

Ismip6Run(mpas_core)	A test group for automated setup of a suite of standardized ISMIP6 simulations
ismip6_ais_proj2300.Ismip6AisProj2300(test_group)	A test case for automated setup of a suite of standardized simulations for ISMIP6-Projections2300-Antarctica See: https://www.climate-cryosphere.org/wiki/index.php?title=ISMIP6-Projections2300-Antarctica) # noqa
ismip6_ais_proj2300.Ismip6AisProj2300.configure()	Set up the desired ISMIP6 AIS 2300 experiments.
ismip6_ais_proj2300.Ismip6AisProj2300.run()	A dummy run method
ismip6_ais_proj2300.set_up_experiment.SetUpExperiment(...)	A step for setting up an ISMIP6 experiment
ismip6_ais_proj2300.set_up_experiment.SetUpExperiment.setup()	Set up the test case in the work directory, including downloading any dependencies.
ismip6_ais_proj2300.set_up_experiment.SetUpExperiment.run()	Run this step of the test case

ismip7_calibration

Ismip7Calibration(mpas_core)	A test group for calibrating MALI's sub-shelf melt parameterization against the ISMIP7 Antarctic ice-ocean protocol (Reese et al., Sect.
configure.check_options(config, options)	Check that user-supplied config options have been set.
configure.melt_forms(config)	The melt forms to calibrate.
configure.objective_options(config)	The sample size and random seed for the parameter selection.
configure.parameter_name(melt_form)	The name of the parameter a melt form calibrates.
configure.parameter_values(config, melt_form)	The grid of parameter values to select from, for one melt form.
configure.weighting(config)	Which summands of J3 and J4 carry non-zero weight.
datasets.climatology_files(base_path)	Paths to the Zhou et al. present-day climatology TF and salinity.
datasets.load_targets(base_path)	Load the observational targets for the four objective-function terms.
datasets.mask_files(base_path[, resolution_km])	Paths to the ISMIP7 mask datasets on the ISMIP polar stereographic grid.
datasets.missing_files(states)	The input files of states that are not present on disk.
datasets.ocean_states(base_path[, subset])	The ocean states to run the melt module for.
objective.build_toolbox_terms(units, ...[, ...])	Assemble the arguments calculate_objective_function expects.
objective.run_optimisation(terms, param_values)	Sample the objective function and return the parameter distribution.
objective.scale_to_ensemble(unit_aggregate, ...)	Turn a unit-parameter aggregate into the (p1, p2, ...) ensemble.
quadratic.angle_from_sin_slope(sin_slope)	The slope angle corresponding to a sine, in radians.
quadratic.draft_slope(draft, dx, dy[, ...])	Ice-draft slope angle on a structured grid, in radians.
quadratic.local_quadratic_melt(k, ...[, ...])	Melt rate from the quadratic local parameterisation, in kg m-2 yr-1.
quadratic.mean_slope(draft, floating, dx, dy)	Antarctic-mean ice-draft slope angle over floating ice, in radians.
quadratic.nonlocal_quadratic_melt(gamma0, ...)	Melt rate from the ISMIP6 non-local quadratic, in kg m-2 yr-1.
quadratic.u_factor(salinity)	The velocity-scale factor of Jenkins et al. (2018).
terms.average_by_group(melt, area, mask, ...)	Area-weighted mean melt rate over each group, in kg m-2 yr-1.
terms.calculate_term1(ensemble, area, mask, ...)	J1: basin-integrated present-day melt, in Gt yr-1.
terms.calculate_term2(ensemble, area, mask, ...)	J2: melt integrated over buttressing (BFRN) bins, in Gt yr-1.
terms.calculate_term3(cold_ensemble, ...[, var])	J3: warm-minus-cold basin-mean melt difference, in kg m-2 yr-1.
terms.calculate_term4(obs_ensemble, area, ...)	J4: PIG/Dotson integrated melt per observation year, in Gt yr-1.
terms.integrate_by_group(melt, area, mask, ...)	Integrate a melt rate over each group, in Gt yr-1.
terms.stack_cells(da, cell_dims)	Flatten the cell dimensions of da into a single dimension.
terms.uniform_area(template, resolution, ...)	Build a uniform cell-area array, for structured grids.
toolbox.check_integrity()	Verify that the vendored toolbox still matches the recorded upstream copy.
toolbox.file_sha256()	The SHA256 of the vendored toolbox source file, as it is on disk.
toolbox.toolbox_path()	The path to the vendored toolbox source file.
replication.Replication(test_group)	A test case that reproduces the published ISMIP7 quadratic calibration on the ISMIP 8 km grid, through compass's own code path.
replication.Replication.configure()	Check that the ISMIP7 dataset path has been supplied
replication.Replication.validate()	Check the percentiles against the published values, and against a baseline if one was provided
replication.replicate.Replicate(test_case)	A step that reproduces the published 8 km quadratic calibration.
replication.replicate.Replicate.setup()	Check that the ISMIP7 datasets this step needs are present
replication.replicate.Replicate.run()	Run this step of the test case
replication.replicate.check_published(...)	Check the replicated percentiles against the published values.
ais.Ais(test_group)	A test case that calibrates MALI's sub-shelf melt parameterization on an Antarctic MALI mesh, following the ISMIP7 protocol.
ais.Ais.configure()	Add a step per ocean state and melt form, once the config is known
ais.Ais.validate()	Compare the calibration against a baseline, if one was provided
ais.aggregate.Aggregate(test_case, ...)	A step that turns the MALI melt fields into unit-parameter aggregates of the four objective-function terms.
ais.aggregate.Aggregate.setup()	Set up this step of the test case
ais.aggregate.Aggregate.run()	Run this step of the test case
ais.aggregate.unit_aggregates(filename)	Read the unit aggregates written by this step.
ais.aggregate.basin_coordinate(units)	The ISMIP7 basin numbers present in an aggregate, as integers.
ais.calibrate.Calibrate(test_case, melt_forms)	A step that runs the ISMIP7 parameter selection on the MALI ensemble.
ais.calibrate.Calibrate.run()	Run this step of the test case
ais.fit_delta_t.FitDeltaT(test_case, melt_forms)	A step that fits the basin thermal-forcing correction dT_b.
ais.fit_delta_t.FitDeltaT.setup()	Set up this step of the test case
ais.fit_delta_t.FitDeltaT.run()	Run this step of the test case
ais.make_graph.MakeGraph(test_case)	A step that builds a graph partition file for the MALI mesh.
ais.make_graph.MakeGraph.setup()	Set up this step of the test case
ais.make_graph.MakeGraph.run()	Run this step of the test case
ais.melt_model.basin_mean_tf(tf_draft, area, ...)	Area-weighted mean thermal forcing per basin, mapped back onto cells.
ais.melt_model.initial_draft(mesh_file[, ...])	Reconstruct the ice draft from the mesh file, before the timestep.
ais.melt_model.integrate_by_basin(melt, ...)	Integrate a melt rate over each basin, in Gt yr-1.
ais.melt_model.interpolate_to_draft(...[, ...])	Interpolate a 3-D ocean field to the ice draft.
ais.melt_model.melt_from_tf(melt_form, ...)	Recompute the melt field from the thermal forcing at the draft.
ais.melt_model.read_run(filename, mesh_file)	Read the fields a melt diagnostic run writes.
ais.remap_forcing.RemapForcing(test_case)	A step that remaps the ISMIP7 calibration thermal forcing onto the MALI mesh, one file per ocean state.
ais.remap_forcing.RemapForcing.setup()	Set up this step of the test case
ais.remap_forcing.RemapForcing.run()	Run this step of the test case
ais.remap_masks.RemapMasks(test_case)	A step that remaps the ISMIP7 masks onto the MALI mesh.
ais.remap_masks.RemapMasks.setup()	Set up this step of the test case
ais.remap_masks.RemapMasks.run()	Run this step of the test case
ais.report.Report(test_case, melt_forms)	A step that plots and tabulates the calibration result.
ais.report.Report.run()	Run this step of the test case
ais.run_state.RunState(test_case, ...[, ...])	A step that runs MALI for a single timestep to diagnose the melt field for one ocean state, using one melt form.
ais.run_state.RunState.setup()	Set up this step of the test case
ais.run_state.RunState.runtime_setup()	Set the number of ocean layers from the forcing file
ais.run_state.RunState.run()	Run this step of the test case
ais.verify_melt.VerifyMelt(test_case, ...[, ...])	A step that checks MALI's melt field against an independent Python implementation of the same equations.
ais.verify_melt.VerifyMelt.setup()	Set up this step of the test case
ais.verify_melt.VerifyMelt.run()	Run this step of the test case

ismip7_forcing

Ismip7Forcing(mpas_core)	A test group for processing ISMIP7 forcing data for the Antarctic Ice Sheet
configure.configure(config)	A shared function for configuring options for all ismip7 forcing test cases
atmosphere.Atmosphere(test_group)	A test case for processing ISMIP7 atmosphere forcing data.
atmosphere.Atmosphere.configure()	Configures test case
atmosphere.build_mapping_file.BuildMappingFile(...)	Build weights from the selected atmosphere grid to the MALI mesh.
atmosphere.build_mapping_file.BuildMappingFile.setup()	Set up the test case in the work directory, including downloading any dependencies.
atmosphere.build_mapping_file.BuildMappingFile.run()	Run the step.
atmosphere.process_smb.ProcessSmb(test_case)	A step for processing ISMIP7 surface mass balance (acabf) data.
atmosphere.process_smb.ProcessSmb.setup()	Set up this step of the test case
atmosphere.process_smb.ProcessSmb.run()	Run this step of the test case
atmosphere.process_temperature.ProcessTemperature(...)	A step for processing ISMIP7 ice surface temperature (ts) data.
atmosphere.process_temperature.ProcessTemperature.setup()	Set up this step of the test case
atmosphere.process_temperature.ProcessTemperature.run()	Run this step of the test case
atmosphere.process_smb_gradient.ProcessSmbGradient(...)	A step for processing ISMIP7 SMB elevation gradient (dacabfdz) data.
atmosphere.process_smb_gradient.ProcessSmbGradient.setup()	Set up this step of the test case
atmosphere.process_smb_gradient.ProcessSmbGradient.run()	Run this step of the test case
atmosphere.process_temperature_gradient.ProcessTemperatureGradient(...)	A step for processing ISMIP7 temperature elevation gradient (dtsdz) data.
atmosphere.process_temperature_gradient.ProcessTemperatureGradient.setup()	Set up this step of the test case
atmosphere.process_temperature_gradient.ProcessTemperatureGradient.run()	Run this step of the test case
atmosphere.process_runoff.ProcessRunoff(...)	A step for processing ISMIP7 ice sheet runoff (mrro) data.
atmosphere.process_runoff.ProcessRunoff.setup()	Set up this step of the test case
atmosphere.process_runoff.ProcessRunoff.run()	Run this step of the test case
ocean_thermal.OceanThermal(test_group)	A test case for processing ISMIP7 ocean thermal forcing data.
ocean_thermal.OceanThermal.configure()	Configures test case
ocean_thermal.build_mapping_file.BuildMappingFile(...)	Build weights from selected ocean grids to the MALI mesh.
ocean_thermal.build_mapping_file.BuildMappingFile.setup()	Set up the test case in the work directory, including downloading any dependencies.
ocean_thermal.build_mapping_file.BuildMappingFile.run()	Run the step.
ocean_thermal.process_thermal_forcing.ProcessThermalForcing(...)	A step for processing ISMIP7 ocean thermal forcing (tf) data.
ocean_thermal.process_thermal_forcing.ProcessThermalForcing.setup()	Set up this step of the test case
ocean_thermal.process_thermal_forcing.ProcessThermalForcing.run()	Run this step of the test case
ocean_thermal.build_3d_thermal_forcing.BuildGreenland3dThermalForcing(...)	A step that builds regional 3-D Greenland ocean thermal forcing from the 2-D forcing produced by ProcessThermalForcing.
ocean_thermal.build_3d_thermal_forcing.BuildGreenland3dThermalForcing.run()	Run this step of the test case
ocean_thermal.greenland_3d.Config(mesh_file, ...)
ocean_thermal.greenland_3d.run(cfg, logger)
fracture.Fracture(test_group)	A test case for processing ISMIP7 fracture forcing data.
fracture.Fracture.configure()	Configures test case
fracture.build_mapping_file.BuildMappingFile(...)	Build weights from the fracture grid to the MALI mesh.
fracture.build_mapping_file.BuildMappingFile.setup()	Set up the test case in the work directory, including downloading any dependencies.
fracture.build_mapping_file.BuildMappingFile.run()	Run the step.
fracture.process_excess_melt.ProcessExcessMelt(...)	A step for processing the ISMIP7 excess meltwater field (Path A).
fracture.process_excess_melt.ProcessExcessMelt.setup()	Set up this step of the test case
fracture.process_excess_melt.ProcessExcessMelt.run()	Run this step of the test case
fracture.process_lake_properties.ProcessLakeProperties(...)	A step for processing the ISMIP7 supraglacial lake properties (Path B).
fracture.process_lake_properties.ProcessLakeProperties.setup()	Set up this step of the test case
fracture.process_lake_properties.ProcessLakeProperties.run()	Run this step of the test case
fracture.process_shelf_collapse.ProcessShelfCollapse(...)	A step for processing the ISMIP7 ice shelf collapse mask (Path C).
fracture.process_shelf_collapse.ProcessShelfCollapse.setup()	Set up this step of the test case
fracture.process_shelf_collapse.ProcessShelfCollapse.run()	Run this step of the test case

ismip7_run

Ismip7Run(mpas_core)	A test group for automated setup of a suite of standardized ISMIP7 simulations for both AIS and GrIS.
gia_options.parse_gia_model(config[, section])	Parse the gia_model config option into sea_level_model and fastisostasy flags.
ismip7_ais.Ismip7Ais(test_group)	A test case for automated setup of a suite of standardized ISMIP7 simulations for the Antarctic Ice Sheet.
ismip7_ais.Ismip7Ais.configure()	Set up the desired ISMIP7 AIS experiments.
ismip7_ais.Ismip7Ais.run()	A dummy run method
ismip7_ais.set_up_experiment.SetUpExperiment(...)	A step for setting up an ISMIP7 AIS experiment
ismip7_ais.set_up_experiment.SetUpExperiment.setup()	Set up the experiment directory with all needed files.
ismip7_ais.set_up_experiment.SetUpExperiment.run()	Run this step of the test case
ismip7_ais.create_slm_mapping_files.CreateSlmMappingFiles(...)	A step for creating mapping files for the Sea Level Model
ismip7_ais.create_slm_mapping_files.CreateSlmMappingFiles.setup()	Set up the test case in the work directory, including downloading any dependencies.
ismip7_ais.create_slm_mapping_files.CreateSlmMappingFiles.run()	Run this step of the test case
ismip7_ais.create_fastiso_mapping_files.CreateFastIsoMappingFiles(...)	A step for creating mapping files for FastIsostasy bedrock model
ismip7_ais.create_fastiso_mapping_files.CreateFastIsoMappingFiles.setup()	Set up the test case in the work directory, including downloading any dependencies.
ismip7_ais.create_fastiso_mapping_files.CreateFastIsoMappingFiles.run()	Run this step of the test case
ismip7_ais.create_fastiso_mapping_files.create_ismip7_grid_file(...)	Create a minimal ISMIP7 standard grid file containing only x and y projected coordinate variables (metres).
ismip7_gris.Ismip7Gris(test_group)	A test case for automated setup of a suite of standardized ISMIP7 simulations for the Greenland Ice Sheet.
ismip7_gris.Ismip7Gris.configure()	Set up the desired ISMIP7 GrIS experiments.
ismip7_gris.Ismip7Gris.run()	A dummy run method
ismip7_gris.set_up_experiment.SetUpExperiment(...)	A step for setting up an ISMIP7 GrIS experiment
ismip7_gris.set_up_experiment.SetUpExperiment.setup()	Set up the experiment directory with all needed files.
ismip7_gris.set_up_experiment.SetUpExperiment.run()	Run this step of the test case

isunnguata_sermia

IsunnguataSermia(mpas_core)	A test group for isunnguata_sermia test cases
mesh_gen.MeshGen(test_group)	The MeshGen test case for the isunnguata_sermia test group simply creates the mesh and initial condition.
mesh_gen.MeshGen.run()	This method is deprecated.
mesh.Mesh(test_case)	A step for creating a mesh and initial condition for isunnguata sermia test cases
mesh.Mesh.run()	Run this step of the test case

kangerlussuaq

Kangerlussuaq(mpas_core)	A test group for kangerlussuaq test cases
mesh_gen.MeshGen(test_group)	The default test case for the Kangerlussuaq test group simply creates the mesh and initial condition.
mesh_gen.MeshGen.run()	This method is deprecated.
mesh.Mesh(test_case)	A step for creating a mesh and initial condition for kangerlussuaq test cases
mesh.Mesh.run()	Run this step of the test case

koge_bugt_s

KogeBugtS(mpas_core)	A test group for koge_bugt_s test cases
mesh_gen.MeshGen(test_group)	The default test case for the Koge_Bugt_S test group simply creates the mesh and initial condition.
mesh_gen.MeshGen.run()	This method is deprecated.
mesh.Mesh(test_case)	A step for creating a mesh and initial condition for koge_bugt_s test cases
mesh.Mesh.run()	Run this step of the test case

mesh_convergence

MeshConvergence(mpas_core)	A test group for convergence tests with MALI
conv_test_case.ConvTestCase(test_group, name)	A test case for various convergence tests on in MALI with planar, doubly periodic meshes
conv_test_case.ConvTestCase.configure()	Set config options for the test case
conv_test_case.ConvTestCase.update_cores()	Update the number of cores and min_tasks for each forward step
conv_init.ConvInit(test_case, resolution)	A step for creating a mesh for a given resolution in a mesh convergence test case.
conv_init.ConvInit.run()	Run this step of the test case
conv_analysis.ConvAnalysis(test_case, ...)	A step for visualizing and/or analyzing the output from a convergence test case
forward.Forward(test_case, resolution)	A step for performing forward MALI runs as part of a mesh convergence test case
forward.Forward.setup()	Set namelist options based on config options
forward.Forward.constrain_resources(...)	Update resources at runtime from config options
forward.Forward.run()	Run this step of the testcase
forward.Forward.get_dt_duration()	Get the time step and run duration as namelist options from config options
halfar.Halfar(test_group)	A test case for testing mesh convergence with the Halfar analytic test
halfar.Halfar.create_init(resolution)	Child class must override this to return an instance of a ConvInit step
halfar.Halfar.create_analysis(resolutions)	Child class must override this to return an instance of a ConvergenceInit step
halfar.init.Init(test_case, resolution)	A step for creating an initial_condition for advection convergence test case
halfar.init.Init.run()	Run this step of the test case
halfar.analysis.Analysis(test_case, resolutions)	A step for visualizing the output from the advection convergence test case
halfar.analysis.Analysis.run()	Run this step of the test case
halfar.analysis.Analysis.rmse(resolution)	Compute the RMSE for a given resolution
horizontal_advection.HorizontalAdvection(...)	A test case for testing horizontal advection in MALI with planar, doubly periodic meshes
horizontal_advection.HorizontalAdvection.create_init(...)	Child class must override this to return an instance of a ConvInit step
horizontal_advection.HorizontalAdvection.create_analysis(...)	Child class must override this to return an instance of a ConvergenceInit step
horizontal_advection.init.Init(test_case, ...)	A step for creating an initial_condition for advection convergence test case
horizontal_advection.init.Init.run()	Run this step of the test case
horizontal_advection.analysis.Analysis(...)	A step for visualizing the output from the advection convergence test case
horizontal_advection.analysis.Analysis.run()	Run this step of the test case
horizontal_advection.analysis.Analysis.rmse(...)	Compute the RMSE for a given resolution
horizontal_advection_thickness.HorizontalAdvectionThickness(...)	A test case for testing horizontal advection of thickness in MALI with planar, doubly periodic meshes
horizontal_advection_thickness.HorizontalAdvectionThickness.create_init(...)	Child class must override this to return an instance of a ConvInit step
horizontal_advection_thickness.HorizontalAdvectionThickness.create_analysis(...)	Child class must override this to return an instance of a ConvergenceInit step
horizontal_advection_thickness.init.Init(...)	A step for creating an initial_condition for advection convergence test case
horizontal_advection_thickness.init.Init.run()	Run this step of the test case
horizontal_advection_thickness.analysis.Analysis(...)	A step for visualizing the output from the advection convergence test case
horizontal_advection_thickness.analysis.Analysis.run()	Run this step of the test case
horizontal_advection_thickness.analysis.Analysis.rmse(...)	Compute the RMSE for a given resolution

mesh_modifications

MeshModifications(mpas_core)	A test group for automating modifications to existing meshes
subdomain_extractor.SubdomainExtractor(...)	A class for a test case that extracts a subdomain from a larger domain
subdomain_extractor.extract_region.ExtractRegion(...)	A step for extracting a regional domain from a larger domain

mismipplus

MISMIPplus(mpas_core)	A test group for MISMIP+ test cases.
smoke_test.SmokeTest(test_group, resolution)	A test case for running a smoke test of the MISMIP+ configuration
smoke_test.SmokeTest.validate()	Test cases can override this method to perform validation of variables and timers
spin_up.SpinUp(test_group)	Test case for creating the MISMIP+ mesh, initial conditions, input files, and runs a short segment of the spin up experiments
spin_up.SpinUp.configure()	Set up the directory structure, based on the requested resolution.
setup_mesh.SetupMesh(test_case, name[, subdir])	A step for creating a mesh and initial condition for MISMIP+ test cases Experimental protocol described in: Asay-Davis, et al. 2016.
setup_mesh.SetupMesh.run()	Run this step of the test case
setup_mesh.calculate_mesh_params(...[, Lx, ...])	Calculate the appropriate parameters for use by make_planar_hex_mesh from the desired nominal resolution (e.g. 8e3, 4e3, 2e3, 1e3...).
setup_mesh.mark_cull_cells_for_MISMIP(ds_mesh)
setup_mesh.center_trough(ds_mesh)	Shift the origin so that the bed trough is centered about the Y-axis and the X-axis is shifted all the way to the left.
run_model.RunModel(test_case, name[, ...])	A step for performing forward MALI runs as part of MISMIP+ test cases.
run_model.RunModel.setup()	Set the number of MPI tasks based on a tentative scaling of a the ncells_at_1km_res heuristic from the config file based on the desired resolution.
run_model.RunModel.constrain_resources(...)	Update resources at runtime from config options
run_model.RunModel.process_inputs_and_outputs()	Process inputs/outputs and apply optional mesh updates during setup.
run_model.RunModel.run()	Run this step of the test case
tasks.get_ntasks_from_cell_count(config, ...)	Computes ntasks and min_tasks based on mesh size (i.e. cell_count).
tasks.exact_cell_count(mesh_filename)	Get the number of cells from an already generated mesh file.
tasks.approx_cell_count(resolution, ...)	Approximate the number of cells based on the resolution ratio squared times the number of cells at 1km resolution.

slm_circ_icesheet ~~~

SlmCircIcesheet(mpas_core)	This test group generates an idealized, circular ice sheet that has a prescribed thickness evolution for testing coupling between MALI and the Sea-Level Model.
mesh_convergence.MeshConvergenceTest(test_group)	This test uses the circular ice sheet test case to test the convergence of the coupled MALI-SLM system with respect to mesh resolution of both MALI and the SLM.
mesh_convergence.MeshConvergenceTest.configure()	Set up the desired mesh-resolution tests
smoke_test.SmokeTest(test_group)	A lightweight smoke test using the baseline circ_icesheet configuration.
run_model.RunModel(test_case, res, nglv[, ...])	A step for performing forward MALI runs as part of dome test cases.
run_model.RunModel.setup()	Set up the test case in the work directory, including downloading any dependencies.
run_model.RunModel.run()	Run this step of the test case
setup_mesh.SetupMesh(test_case, name, res, nglv)	A step for creating a mesh with initial conditions plus forcing file for circular icesheet test
setup_mesh.SetupMesh.run()	Run this step of the test case
visualize.Visualize(test_case[, name, ...])	A step for visualizing the output from a dome test case
visualize.Visualize.setup()
visualize.Visualize.run()	Run this step of the test case
visualize.visualize_slm_circsheet(config, ...)	Plot the output from a circular ice sheet test case

thwaites

Thwaites(mpas_core)	A test group for low-res 4-14km Thwaites test cases.
decomposition_test.DecompositionTest(test_group)	A test case for performing two MALI runs of the Thwaites setup with different decompositions.
decomposition_test.DecompositionTest.configure()	Choose decomposition sizes from framework-detected resources and add run steps.
decomposition_test.DecompositionTest.run()	This method is deprecated.
restart_test.RestartTest(test_group[, ...])	A test case for performing two MALI runs of the Thwaites setup, one full run and one run broken into two segments with a restart.
restart_test.RestartTest.run()	This method is deprecated.
run_model.RunModel(test_case[, name, ...])	A step for performing forward MALI runs as part of Thwaites test cases.
run_model.RunModel.setup()	Set up the test case in the work directory, including downloading any dependencies.
run_model.RunModel.run()	Run this step of the test case
mesh_gen.MeshGen(test_group)	The high resolution test case for the thwaites test group simply creates the mesh and initial condition.
mesh_gen.MeshGen.run()	This method is deprecated.
mesh.Mesh(test_case)	A step for creating a mesh and initial condition for thwaites test cases
mesh.Mesh.run()	Run this step of the test case

Landice Framework

ais_observations
extrapolate.extrapolate_variable(nc_file, ...)	Function to extrapolate variable values into undefined regions
iceshelf_melt.calc_mean_TF(geometry_file, ...)	Function to calculate mean thermal forcing across all floating ice in a domain.
mesh.add_bedmachine_thk_to_ais_gridded_data(...)	Copy BedMachine thickness to AIS reference gridded dataset.
mesh.add_grid_imask_from_dst_scrip_hull(...)	Create a new source SCRIP file with grid_imask set to 1 only for cells that fall within the boundary (plus buffer) of the destination SCRIP footprint.
mesh.build_dst_scrip_hull(dest_scrip, domain)	Build a buffered concave boundary from the footprint of a destination SCRIP file and return it as a matplotlib.path.Path.
mesh.clean_up_after_interp(fname)	Perform some final clean up steps after interpolation
mesh.clip_mesh_to_bounding_box(mask_ds, ...)	Set cells to culled if they lay outside the bounding box
mesh.plot_hull_diagnostic(hull_path, ...[, ...])	Save a diagnostic PNG (mesh_boundary.png) showing the masking geometry.
mesh.get_mesh_config_bounding_box(section[, ...])	Get bounding-box coordinates from a mesh config section.
mesh.get_optional_interp_datasets(section, ...)	Determine whether optional interpolation inputs are configured.
mesh.gridded_flood_fill(field[, iStart, jStart])	Uses a flood fill to fill disconnected regions.
mesh.interp_gridded2mali(self, source_file, ...)	Interpolate gridded dataset (e.g. MEASURES, BedMachine) onto a MALI mesh.
mesh.mpas_flood_fill(seed_mask, grow_mask, ...)	Flood-fill for mpas meshes using mpas cells.
mesh.preprocess_ais_data(self, ...)	Perform adjustments to gridded AIS datasets needed for rest of compass workflow to utilize them
mesh.run_optional_interpolation(self, ...[, ...])	Run optional interpolation from high-resolution BedMachine and MEaSUREs datasets and perform some necessary cleanup.
mesh.set_rectangular_geom_points_and_edges(...)	Set node and edge coordinates to pass to mpas_tools.mesh.creation.build_mesh.build_planar_mesh().
mesh.set_cell_width(self, section_name, thk, bed)	Set cell widths based on settings in config file to pass to mpas_tools.mesh.creation.build_mesh.build_planar_mesh().
mesh.subset_gridded_dataset_to_bounds(...)	Subset a gridded source dataset to a bounding box.
mesh.get_dist_to_edge_and_gl(self, thk, ...)	Calculate distance from each point to ice edge and grounding line, to be used in mesh density functions in compass.landice.mesh.set_cell_width().
mesh.build_cell_width(self, section_name, ...)	Determine MPAS mesh cell size based on user-defined density function.
mesh.build_mali_mesh(self, cell_width, x1, ...)	Create the MALI mesh based on final cell widths determined by compass.landice.mesh.build_cell_width(), using Jigsaw and MPAS-Tools functions.
mesh.make_region_masks(self, mesh_filename, ...)	Create masks for ice-sheet subregions based on data in MPAS-Dev/geometric_fatures.