Feature/calculate-volumes (#36)

MANIFEST.in

@@ -0,0 +1,2 @@
+include LICENSE
+include requirements.txt

docs/index.md

@@ -1,14 +1,17 @@
 # River-Route
 
-The `river-route` Python package is a tool for routing catchment runoff volumes on vector stream networks using the 
-Matrix Muskingum Cunge Method.
+The `river-route` Python package is a tool for routing catchment runoff volumes on vector stream networks using the
+Matrix Muskingum Cunge Method. It implements a matrix form of the Muskingum Cunge routing method first published by 
+[Cedric David in 2011](https://doi.org/10.1175/2011JHM1345.1) and corrected by Riley Hales in 2024.
 
 ## Installation
 
-It is recommended to install `river-route` in its own environment so you can ensure the latest versions of all the 
-dependencies and to protect the environment that produces your model results from accidents.
+!!! note
+    Refer to the [Basic Tutorial](tutorials/basic-tutorial.md) and [Advanced Tutorial](tutorials/advanced-tutorial.md) 
+    for more complete instructions.
 
-`river-route` is currently only available from source.
+`river-route` is currently only available from source. To get the highest performance, you may want to install in a 
+dedicated conda environment with the latest version of python and the dependencies.
 
 ```commandline
 git clone https://github.com/rileyhales/river-route
@@ -18,16 +21,6 @@ conda activate rr
 python setup.py install
 ```
 
-## Quick Start Guide
-
-In order to use river-route, you will need to
-
-1. Install river-route
-2. Prepare your input data
-3. Create a [Configuration File](configs/config-options.md#example-yaml-file)
-4. Run a simulation
-
-
 ## Computation Process
 
 ```mermaid
@@ -36,7 +29,7 @@ Title: River Route Process Diagram
 ---
 graph LR
     subgraph "Required-Inputs"
-        Inputs["Routing Parameters\nConnectivity File\nRunoff Volumes\nOutflow File"]
+        Inputs["Routing Parameters\nConnectivity File\nCatchment Volumes\nOutflow File"]
     end
 
     subgraph "Compute-Options"
@@ -54,7 +47,7 @@ graph LR
     subgraph "Computations"
         direction TB
         a[Calculate LHS] --> b
-        b[Read Runoff Volumes] --> c
+        b[Read Volumes Array] --> c
         c[Iterate On Routing Intervals] --> d
         d[Solving Matrix\nMuskingum Cunge] --> e
         e[Enforce Positive Flows] --> f & c
@@ -73,6 +66,7 @@ graph LR
     Required-Inputs & Compute-Options & Initialization & Logging-Options ==> Computations
     Computations ==> Main-Output & Cachable-Files
 ```
+
 ## Usage Example
 
 You can pass the configuration options to the `rr.MuskingumCunge` class init by specifying a path to a config file, use
@@ -95,21 +89,21 @@ import river_route as rr
     .MuskingumCunge(**{
         'routing_params_file': '/path/to/routing_params.parquet',
         'connectivity_file': '/path/to/connectivity.parquet',
-        'runoff_volumes_file': '/path/to/runoff.nc',
+        'catchment_volumes_file': '/path/to/volumes.nc',
         'outflow_file': '/path/to/outflow.nc',
     })
     .route()
 )
 
-# Option 3 - Use both a congiuration file and keyword arguments
+# Option 3 - Use both a configuration file and keyword arguments
 (
     rr
     .MuskingumCunge(
         '/path/to/config.yaml',
         **{
             'routing_params_file': '/path/to/routing_params.parquet',
             'connectivity_file': '/path/to/connectivity.parquet',
-            'runoff_volumes_file': '/path/to/runoff.nc',
+            'catchment_volumes_file': '/path/to/volumes.nc',
             'outflow_file': '/path/to/outflow.nc',
         }
     )

docs/references/config-files.md

@@ -0,0 +1,60 @@
+## Configuration File
+
+`river-route` computations are controlled by several variables. You can pass these variables as keyword arguments to the
+corresponding functions or provide a path to a configuration file. Supported file formats for config files are YAML or
+JSON. Config files specify the following parameters:
+
+1. Paths to input and output files
+2. Options to control how the routing is performed
+3. Options to control the numerical solver and tolerances
+4. Information about the structure of the input and output files if non-standard
+5. Logging parameters
+
+## Minimum Required Inputs
+
+Every `river-route` process needs at least the following 4 variables
+
+- `routing_params_file` - path to the [routing parameters file](io-file-schema.md#routing-parameters) (parquet)
+- `connectivity_file` - path to the river network [connectivity file](io-file-schema.md#connectivity-file) (parquet)
+- `catchment_volumes_file` - path to the prepared [catchment volumes file](io-file-schema.md#catchment-volumes-or-runoff-depths) (netCDF)
+- `outflow_file` - path where the [routed flows](io-file-schema.md#routed-discharge) output file will be saved (netCDF)
+
+## Example YAML File
+
+An example yaml file is given below with the default values prepopulated where possible.
+
+```yaml title="Config File Example river-route v0.15.0"
+{% include-markdown "../../examples/config.yaml" %}
+```
+
+## Config Options Table
+
+The following table is a complete list of all configuration options and their purpose.
+
+| Parameter Name         | Required | Type      | Group               | Description                                                            |                                                                                
+|------------------------|----------|-----------|---------------------|------------------------------------------------------------------------|
+| routing_params_file    | True     | File Path | Required Input      | Path to the routing parameters parquet file.                           |                                                
+| connectivity_file      | True     | File Path | Required Input      | Path to the network connectivity parquet file.                         |                                              
+| catchment_volumes_file | True     | File Path | Required Input      | Path to the netCDF with catchment volume values to be routed.          |
+| runoff_depths_files    | True     | File Path | Required Input      | List of paths to netCDF files with runoff depths to be routed.         |
+| weight_table_file      | True     | File Path | Required Input      | Path to the weight table file.                                         |
+| outflow_file           | True     | File Path | Required Input      | Path where the outflows netCDF file should be saved.                   |
+| routing                | False    | String    | Compute Options     | The routing method to use: "linear" or "nonlinear".                    |
+| input_type             | False    | String    | Compute Options     | Specify if runoff files are "sequential" time steps or an "ensemble"   |
+| runoff_type            | False    | String    | Compute Options     | Specify if runoff files are "incremental" or "cumulative"              |
+| dt_routing             | True     | Integer   | Compute Options     | Time interval in seconds between routing computations.                 |                              
+| dt_outflows            | False    | Integer   | Compute Options     | Time interval in seconds between writing flows to disc.                |
+| solver_atol            | False    | Float     | Compute Options     | Absolute tolerance for the solver.                                     |
+| initial_state_file     | False    | File Path | Initialization Data | Path to the initial state file.                                        |                                                     
+| final_state_file       | False    | File Path | Initialization Data | Path where the final state file should be saved.                       |                                    
+| log                    | False    | Boolean   | Logging Options     | Whether to enable logging.                                             |                                       
+| progress_bar           | False    | Boolean   | Logging Options     | Whether to display a progress bar when routing                         |
+| log_level              | False    | String    | Logging Options     | The logging level to print: DEBUG, INFO, CRITICAL, WARNING             |
+| log_stream             | False    | String    | Logging Options     | The destination for log messages: 'stdout', 'stderr', or a file path.  |
+| var_x                  | False    | String    | File Management     | Name of the variable in all files that contains the x coordinates.     |
+| var_y                  | False    | String    | File Management     | Name of the variable in all files that contains the y coordinates.     |
+| var_t                  | False    | String    | File Management     | Name of the variable in all files that contains the time values.       |
+| var_runoff_depths      | False    | String    | File Management     | Name of the variable in files containing runoff depths                 |
+| var_catchment_volumes  | False    | String    | File Management     | Name of the variable in the catchment volumes file containing volumes. |
+| var_river_id           | False    | String    | File Management     | Name of the variable in all files that contains the river IDs.         |
+| var_outflow            | False    | String    | File Management     | Name of the variable in the outflows file that contains the outflows.  |