├── .github └── workflows │ ├── build.yml │ └── deploy.yml ├── .gitignore ├── CODE_OF_CONDUCT.rst ├── LICENSE ├── MANIFEST.in ├── README.rst ├── assets ├── private │ ├── liang_2015_fig1fig2.png │ ├── liang_2015_fig5.png │ └── pyDeltaRCM_logo.svg └── symbol.svg ├── docs ├── Makefile ├── make.bat └── source │ ├── .nojekyll │ ├── _resources │ ├── checkpoint.yaml │ ├── checkpoint │ │ └── checkpoint.npz │ └── joss │ │ ├── figures │ │ ├── figures.py │ │ ├── pyDeltaRCM_20210810-151130.log │ │ └── timeseries.png │ │ ├── paper.bib │ │ └── paper.md │ ├── _static │ └── style.css │ ├── _templates │ └── page.html │ ├── conf.py │ ├── examples │ ├── basic_runs.rst │ ├── custom_class_preprocessor.rst │ ├── custom_saving.rst │ ├── custom_yaml.rst │ ├── index.rst │ ├── modelzoo.rst │ ├── overwrite_topo_diffusion.rst │ ├── resume_from_checkpoint.rst │ ├── simple_example.ipynb │ ├── slight_slope.rst │ ├── subsidence_region.rst │ ├── updating_boundary_conditions.rst │ ├── variable_bedload.rst │ └── variable_velocity.rst │ ├── guides │ ├── 10min.rst │ ├── advanced_configuration_guide.inc │ ├── developer_guide.rst │ ├── getting_started.rst │ ├── subsidence_guide.inc │ └── user_guide.rst │ ├── index.rst │ ├── info │ ├── hydrodynamics.rst │ ├── index.rst │ ├── initialization.rst │ ├── modeltime.rst │ ├── morphodynamics.rst │ ├── outputfile.rst │ └── yamlparameters.rst │ ├── meta │ ├── citing.rst │ ├── conduct.rst │ ├── contributing.rst │ ├── installing.rst │ ├── license.rst │ └── usedby.rst │ ├── pyplots │ ├── debug_tools │ │ └── debug_demo.py │ ├── guides │ │ ├── 10min_demo.py │ │ ├── cover.py │ │ └── output_file.py │ ├── init_tools │ │ ├── domain_basin_inlet_depth.py │ │ ├── domain_inlet_geometry.py │ │ ├── domain_parameters.py │ │ └── domain_size_compare.py │ ├── modeltime │ │ ├── _base.py │ │ ├── four_year_condensed_plot.py │ │ ├── four_year_plot.py │ │ └── one_year_plot.py │ ├── sed_tools │ │ ├── _initial_bed_state.py │ │ ├── route_all_mud_parcels.py │ │ ├── route_all_sand_parcels.py │ │ ├── sediment_weights_examples.py │ │ └── topo_diffusion.py │ └── water_tools │ │ ├── _accumulate_free_surface_walks.py │ │ ├── _check_for_loops.py │ │ ├── _smooth_free_surface.py │ │ ├── compute_free_surface_inputs.py │ │ ├── compute_free_surface_outputs.py │ │ ├── flooding_correction.py │ │ ├── run_water_iteration.py │ │ └── water_weights_examples.py │ └── reference │ ├── debug_tools │ └── index.rst │ ├── hook_tools │ └── index.rst │ ├── index.rst │ ├── init_tools │ └── index.rst │ ├── iteration_tools │ └── index.rst │ ├── model │ ├── index.rst │ ├── model_hooks.rst │ └── yaml_defaults.rst │ ├── preprocessor │ └── index.rst │ ├── sed_tools │ └── index.rst │ ├── shared_tools │ └── index.rst │ └── water_tools │ └── index.rst ├── pyDeltaRCM ├── __init__.py ├── __main__.py ├── _version.py ├── debug_tools.py ├── default.yml ├── hook_tools.py ├── init_tools.py ├── iteration_tools.py ├── model.py ├── preprocessor.py ├── sed_tools.py ├── shared_tools.py └── water_tools.py ├── pyproject.toml ├── requirements-docs.txt ├── requirements-test.txt ├── requirements.txt ├── strat_preprocess.py └── tests ├── __init__.py ├── imgs_baseline ├── test_plot_domain_cell_type.png ├── test_plot_domain_cell_type_list_index.png ├── test_plot_domain_cell_type_list_mix_tuple_index.png ├── test_plot_domain_cell_type_list_tuple.png ├── test_plot_domain_cell_type_multiple_diff_args.png ├── test_plot_domain_cell_type_multiple_diff_kwargs.png ├── test_plot_domain_cell_type_multiple_index_calls.png ├── test_plot_domain_cell_type_no_grid.png ├── test_plot_domain_cell_type_single_index.png ├── test_plot_domain_cell_type_single_tuple.png ├── test_plot_domain_velocity.png ├── test_plot_domain_withlabel.png ├── test_plot_iwalk.png ├── test_plot_multiple_subplots.png ├── test_show_line_pts_Nx2_array.png └── test_show_line_set_points.png ├── integration ├── __init__.py ├── test_checkpointing.py ├── test_cli.py ├── test_consistent_outputs.py └── test_timing_triggers.py ├── 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