Update README.md

README.md

@@ -54,26 +54,47 @@ The following input data sources should be downloaded and preprocessed prior to
 
 ## Usage
 
-1. Run Docker Container : `docker run --rm -it -v <path/to/data>:/data -v <path/to/repository>:/foss_fim <image_name>:<tag>`
-2. Acquire and Prepare Data : `/foss_fim/lib/acquire_and_preprocess_inputs.py -u <huc4s_to_process>`
-    - `-u` can be a single HUC4, series of HUC4s (e.g. 1209 1210), path to line-delimited file with HUC4s.
-    - Please run `/foss_fim/lib/acquire_and_preprocess_inputs.py --help` for more information.
-    - See United States Geological Survey (USGS) National Hydrography Dataset Plus High Resolution (NHDPlusHR) [site](https://www.usgs.gov/core-science-systems/ngp/national-hydrography/nhdplus-high-resolution) for more information
-3. Aggregate NHD HR streams and create NWM headwater points : /foss_fim/lib/aggregate_vector_inputs.py
-4. Produce Hydrofabric : `fim_run.sh -u <huc4,6,or8s> -c /foss_fim/config/<your_params_file.env> -n <name_your_run>`
-    - `-u` can be a single huc, a series passed in quotes, or a line-delimited file
-        i. To run entire domain of available data use one of the `/data/inputs/included_huc[4,6,8].lst` files
-    - Outputs can be found under `/data/outputs/<name_your_run>`
+### Run Docker Container
+```
+docker run --rm -it -v <path/to/data>:/data -v <path/to/repository>:/foss_fim <image_name>:<tag>
+```
+
+### Acquire and Prepare Data
+```
+/foss_fim/lib/acquire_and_preprocess_inputs.py -u <huc4s_to_process>
+```
+- `-u` can be a single HUC4, series of HUC4s (e.g. 1209 1210), path to line-delimited file with HUC4s.
+- Please run `/foss_fim/lib/acquire_and_preprocess_inputs.py --help` for more information.
+- See United States Geological Survey (USGS) National Hydrography Dataset Plus High Resolution (NHDPlusHR) [site](https://www.usgs.gov/core-science-systems/ngp/national-hydrography/nhdplus-high-resolution) for more information
+
+### Aggregate NHD HR streams and create NWM headwater points 
+```
+/foss_fim/lib/aggregate_vector_inputs.py
+```
+### Produce Hydrofabric 
+```
+fim_run.sh -u <huc4,6,or8s> -c /foss_fim/config/<your_params_file.env> -n <name_your_run>
+```
+- `-u` can be a single huc, a series passed in quotes, or a line-delimited file
+    i. To run entire domain of available data use one of the ```/data/inputs/included_huc[4,6,8].lst``` files
+- Outputs can be found under ```/data/outputs/<name_your_run>```
+
+----
 
 ## Evaluating Inundation Map Performance
 After `fim_run.sh` completes, you are ready to evaluate the model's skill.
 
-**Please note:** You will need access to the test_cases benchmark data. Similar to the other non-publicly available datasets, you can acquire the benchmark data from Brad Bates (bradford.bates@noaa.gov). (A longer term data sharing solution is in the works).
+**Please note:** You will need access to the test_cases benchmark data. You can acquire the benchmark data from Brad Bates (bradford.bates@noaa.gov). As mentioned before, a long term data sharing solution is still in the works.
 
 To evaluate model skill, run the following:
-`python /foss_fim/tests/synthesize_test_cases.py -c DEV -v <fim_run_name> -m <path/to/output/metrics.csv> -j [num_of_jobs]`
+```
+python /foss_fim/tests/synthesize_test_cases.py -c DEV -v <fim_run_name> -m <path/to/output/metrics.csv> -j [num_of_jobs]
+```
 
-More information can be found by running `python /foss_fim/tests/synthesize_test_cases.py --help`
+More information can be found by running:
+```
+python /foss_fim/tests/synthesize_test_cases.py --help
+```
 
 ## Dependencies