Update readme

README.md

@@ -1,55 +1,56 @@
 [![DOI](https://zenodo.org/badge/487911703.svg)](https://zenodo.org/badge/latestdoi/487911703)
+[![codecov](https://codecov.io/gh/IMMM-SFA/naturf/graph/badge.svg?token=SoIfjdS6BL)](https://codecov.io/gh/IMMM-SFA/naturf)
+[![build](https://github.com/IMMM-SFA/naturf/actions/workflows/build.yml/badge.svg)](https://github.com/IMMM-SFA/naturf/actions/workflows/build.yml)
 
+# naturf
 
-## naturf
+#### `naturf` (Neighborhood Adaptive Tissues for Urban Resilience Futures) is an open-source geospatial Python package for calculating urban building parameters to be compiled and input to the Weather Research and Forecasting model (WRF).
 
-NATURF: Neighborhood Adaptive Tissues for Urban Resilience Futures
+### Purpose
+`naturf` was created to:
 
-## Description
+  - Calculate 132 urban parameters based on building footprints and height,
+  - Compile the parameters at sub-kilometer resolutions into binary files,
+  - Prepare binary files to be fed into WRF to understand the effect of building morphology on the urban microclimate.
 
-The Neighborhood Adaptive Tissues for Urban Resilience Futures tool (NATURF) is
-a Python workflow that generates data readable by the Weather Research and
-Forecasting (WRF) model. The NATURF Python modules use shapefiles containing
-building footprint and height data as input to calculate 132 building parameters
-at any resolution and converts the parameters into a binary file format.
+### Install `naturf`
 
-NATURF was created to:
+```bash
+pip install naturf
+```
+### Check out a quickstart tutorial to run `naturf`
 
-  - addresses the knowledge gap of the effect of the geometry of a neighborhood on the local meteorology and
-  -  translate neighborhood morphology (building footprints, heights, spacing, etc.) representations to the WRF-readable urban parameters so that meteorological processes at urban scale can interact with the built environment.
+Run `naturf` using the quickstart tutorial: [`naturf` Quickstarter](https://immm-sfa.github.io/naturf/quickstarter.html)
 
-## Example Data
+### Getting started
 
-The example data provided with this package includes a shapefile containing building footprints and heights for one 3.2km by 3.2km tile of
-Washington, D.C. (C-5.shp) and a CSV file that lists the index name for each tile in Washington, D.C. (DC_Indices.csv).
+New to `naturf`? Get familiar with what `naturf` is all about in our [Getting Started](https://immm-sfa.github.io/naturf/getting_started.html)
 
-NATURF requires the center latitude and longitude of the study area in order to correctly project the output data,
-but these values are already included in `scripts/workflow.py` for the example data.
+### User guide
 
-Outputs from the example data should include a binary file named `00065-00096.00065-00096`, an `index` file,
-a CSV file with urban parameter values for each building, two NumPy files, several pickle files that are
-used in the compilation of the binary file, and a directory of TIF rasters that represent each of the
-132 calculated urban parameters.
+Our user guide provides in-depth information on the key concepts of `naturf` with useful background information and explanation. See our [User Guide](https://immm-sfa.github.io/naturf/user_guide.html)
 
-## Workflow
+### Contributing to `naturf`
 
-1. Example data is provided in this repository in the `example` directory
-2. Setup paths and settings in `scripts/workflow.py`
-3. Run `scripts/workflow.py` in a Python 3.8 or greater environment
+Whether you find a typo in the documentation, find a bug, or want to develop functionality that you think will make `naturf` more robust, you are welcome to contribute! See our [Contribution Guidelines](https://immm-sfa.github.io/naturf/contributing.html)
 
-## Citation
+### API reference
 
-> Allen-Dumas, Melissa Ree, Sweet-Breu, Levi, Seals, Matthew, Berres, Andy, Vernon, Chris R., Rexer, Emily, and USDOE Office of Science. NATURF. Computer software. https://www.osti.gov//servlets/purl/1879628. Vers. 0. USDOE Office of Science (SC), Biological and Environmental Research (BER). Earth and Environmental Systems Science Division. 31 Aug. 2022. Web. doi:10.11578/dc.20220803.4.
+The reference guide contains a detailed description of the `naturf` API. The reference describes how the methods work and which parameters can be used. It assumes that you have an understanding of the key concepts. See [API Reference](https://immm-sfa.github.io/naturf/modules.html)
 
+### Developer Setup
 
-# Developer Setup
-To get started on development, install the pre-commit hooks to format code.
+To get started on development, install the pre-commit hooks to format code. Instructions for installation can be found [here](https://pre-commit.com/). Then install the hooks within the repo:
 
-```bash
-$ brew install pre-commit
-```
-Then install the hooks within the repo:
 ```bash
 $ cd /PATH/TO/NATURF
 $ pre-commit install
 ```
+
+### Code citation
+
+> Allen-Dumas, Melissa Ree, Sweet-Breu, Levi, Seals, Matthew, Berres, Andy, Vernon, Chris R., Rexer, Emily, and USDOE Office of Science. NATURF. Computer software. https://www.osti.gov//servlets/purl/1879628. Vers. 0. USDOE Office of Science (SC), Biological and Environmental Research (BER). Earth and Environmental Systems Science Division. 31 Aug. 2022. Web. doi:10.11578/dc.20220803.4.
+
+### Sample data citation
+
+> OpenDataDC (2021) Open Data DC. URL https://opendata.dc.gov/datasets