IMMM-SFA · crvernon · Dec 4, 2023 · Jan 5, 2023 · Jan 5, 2023 · Jan 5, 2023
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -96,9 +96,9 @@
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs. This file should be a Windows icon file (.ico), 16x16 or 32x32 pixels.
-html_favicon = '_static/favicon.ico'
+# html_favicon = '_static/favicon.ico'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named 'default.css' will overwrite the builtin 'default.css'.
-html_static_path = ['_static']
+# html_static_path = ['_static']
diff --git a/docs/source/examples/modify-inputs.rst b/docs/source/examples/modify-inputs.rst
diff --git a/docs/source/getting-started/quickstarter.rst b/docs/source/getting-started/quickstarter.rst
@@ -1,2 +1,55 @@
 Quickstarter
 ==============
+
+To demonstrate the functionality of **statemodify**, we have generated 5 notebooks that highlight how to use the functions in the package and show some very basic analyses that can be done with the output data. Each notebook demonstrates 1-2 **statemodify** functions for a specific West Slope basin in Colorado. The notebooks usually follow a specific form:
+
+1. Run a baseline simulation for the basin (about 4 minutes)
+
+2. Plot the baseline shortages for specific users or reservoir storage
+
+3. Introduce a statemodify function that samples a specific uncertainty (evaporation, demand, streamflow, water rights, etc.)
+
+4. Create a new set of input files to run through StateMod
+
+5. Run each StateMod simulation (usually about 2 simulations, each at 4 minutes)
+
+6. Plot the new shortages or reservoir levels with respect to the baseline values.
+
+
+The notebooks are hosted in MSD-LIVE containers and can be found at: https:/statemodify.msdlive.org
+
+
+You will be taken to a JupyterLab homepage with "data" and "notebook" buckets on the side.  The "data" directory contains all the StateMod datasets and some other template files. Click on the "notebooks" directory and choose a notebook to start. Press shift + enter to execute the cells in the notebook.
+
+
+.. figure:: ../images/quickstarter_1.png
+  :alt: JupyterLab home screen
+
+  Figure 1: JupyterLab home screen
+
+IMPORTANT: When you finish a notebook and move on to another one, please restart the kernel and clear the outputs as shown below. 
+
+.. figure:: ../images/quickstarter_2.png
+  :alt: Restarting the Kernel 
+
+  Figure 1: Restarting the Kernel 
+
+
+
+.. list-table:: Notebook Topics
+   :widths: 25 50 50 50 50 50
+   :header-rows: 1
+
+   * - Topic
+     - Notebook 1: Getting Started and Using the DDM and DDR modification functions in the San Juan Subbasin
+     - Notebook 2: Using the EVA modification functions in the Gunnison Subbasin
+     - Notebook 3: Using the RES modification function in the Upper Colorado Subbasin
+     - Notebook 4: Using the XBM and IWR modification functions across all basins
+     - Notebook 5: Sampling multiple uncertainties
+
+   * - Description
+     - This notebook has more general intro information on StateModify and shows how changes to demand and water rights can lead to changes to user shortages in the San Juan Subbasin. 
+     - This notebook looks at how changes in evaporation in  reservoirs in the Gunnison subbasin lead to changes to reservoir levels
+     - This notebook looks at how changes in storage in reservoirs in the Upper Colorado subbasin lead to changes to user shortages 
+     - This notebook debuts the stationary Hidden Markov Model to generate alternative streamflow scenarios across the basins. 
+     - This notebook demonstrates how to create a global Latin hypercube sample to consider multiple uncertainties in a basin. Quickstarter
diff --git a/docs/source/getting-started/tutorial.rst b/docs/source/getting-started/tutorial.rst
diff --git a/docs/source/images/figure_1.png b/docs/source/images/figure_1.png
diff --git a/docs/source/images/figure_1_old.png b/docs/source/images/figure_1_old.png
diff --git a/docs/source/images/logo_statemodify.png b/docs/source/images/logo_statemodify.png
diff --git a/docs/source/images/quickstarter_1.png b/docs/source/images/quickstarter_1.png
diff --git a/docs/source/images/quickstarter_2.png b/docs/source/images/quickstarter_2.png
diff --git a/docs/source/index.rst b/docs/source/index.rst
diff --git a/docs/source/reference/api.rst b/docs/source/reference/api.rst
@@ -29,41 +29,60 @@ statemodify.modify_ddm
 
 .. autofunction:: statemodify.modify_ddm
 
+statemodify.modify_single_ddm
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.modify_single_ddm
+
 statemodify.modify_ddr
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. autofunction:: statemodify.modify_ddr
 
+statemodify.modify_single_ddr
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.modify_single_ddr
+
+statemodify.apply_on_off_modification
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.apply_on_off_modification
+
+statemodify.apply_seniority_modification
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.apply_seniority_modification
+
 statemodify.modify_xbm_iwr
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. autofunction:: statemodify.modify_xbm_iwr
 
-Output Modification
----------------------------------
-
-statemodify.convert_xdd
+statemodify.modify_xbm_iwr
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-.. autofunction:: statemodify.convert_xdd
+.. autofunction:: statemodify.modify_single_xbm_iwr
 
-Sampling
----------------------------------
+statemodify.get_reservoir_structure_ids
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-statemodify.build_problem_dict
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. autofunction:: statemodify.get_reservoir_structure_ids
 
-.. autofunction:: statemodify.build_problem_dict
+statemodify.modify_single_res
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-statemodify.generate_samples
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. autofunction:: statemodify.modify_single_res
 
-.. autofunction:: statemodify.generate_samples
+statemodify.modify_res
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-statemodify.validate_modify_dict
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. autofunction:: statemodify.modify_res
 
-.. autofunction:: statemodify.validate_modify_dict
+
+
+HMM Functions
+---------------------------------
 
 statemodify.hmm_multisite_fit
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -75,25 +94,125 @@ statemodify.hmm_multisite_sample
 
 .. autofunction:: statemodify.hmm_multisite_sample
 
+statemodify.get_samples
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.get_samples
+
+statemodify.generate_dry_state_means
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.generate_dry_state_means
+
+statemodify.generate_wet_state_means
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.generate_wet_state_means
+
+statemodify.generate_dry_covariance_matrix
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.generate_dry_covariance_matrix
+
+statemodify.generate_wet_covariance_matrix
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.generate_wet_covariance_matrix
+
+statemodify.generate_transition_matrix
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.generate_transition_matrix 
+
+statemodify.calculate_array_monthly
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.calculate_array_monthly
+
+statemodify.calculate_array_annual
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.calculate_array_annual 
+
+statemodify.calculate_annual_sum
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.calculate_annual_sum 
+
+statemodify.calculate_annual_mean_fractions
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.calculate_annual_mean_fractions
+
+statemodify.fit_iwr_model
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.fit_iwr_model
+
+
+statemodify.generate_hmm_inputs
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.generate_hmm_inputs
+
+statemodify.generate_flows
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.generate_flows 
+
+
+statemodify.generate_modified_file
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.generate_modified_file
+
+
+Output Modification
+---------------------------------
+
+statemodify.convert_xdd
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.convert_xdd
+
 statemodify.read_xre
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. autofunction:: statemodify.read_xre
 
-statemodify.plot_flow_duration_curves
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+statemodify.extract_xre_data
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-.. autofunction:: statemodify.plot_flow_duration_curves
+.. autofunction:: statemodify.extract_xre_data
 
-statemodify.plot_res_quantiles
+
+Sampling
+---------------------------------
+
+statemodify.build_problem_dict
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-.. autofunction:: statemodify.plot_res_quantiles
+.. autofunction:: statemodify.build_problem_dict
 
-statemodify.plot_reservoir_boxes
+statemodify.generate_samples
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-.. autofunction:: statemodify.plot_reservoir_boxes
+.. autofunction:: statemodify.generate_samples
+
+statemodify.validate_modify_dict
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.validate_modify_dict
+
+statemodify.generate_sample_iwr
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.generate_sample_iwr
+
+statemodify.generate_sample_all_params
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.generate_sample_all_params
 
 Modification
 ---------------------------------
@@ -148,6 +267,47 @@ statemodify.Modify
 
 .. autofunction:: statemodify.Modify
 
+Batch Modification
+---------------------------------
+
+statemodify.get_required_arguments
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.get_required_arguments
+
+statemodify.get_arguments_values
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.get_arguments_values 
+
+statemodify.generate_parameters
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.generate_parameters
+
+statemodify.modify_batch
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.modify_batch
+
+Visualization
+---------------------------------
+
+statemodify.plot_flow_duration_curves
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.plot_flow_duration_curves
+
+statemodify.plot_res_quantiles
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.plot_res_quantiles
+
+statemodify.plot_reservoir_boxes
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autofunction:: statemodify.plot_reservoir_boxes
+
 Utilities
 ---------------------------------