markdownlint fix

91361307 · Clayton, Brandon Scott · 3377ba10 · 91361307 · 91361307 · 91361307
Commit 91361307 authored 2 years ago by Clayton, Brandon Scott
--- a/README.md
+++ b/README.md
 # GeoPhys ![Shear-wave velocity model in the LA area, looking north. Color scale is 100 to 1000 m/s Vs30 on the top and 100 to 5000 m/s shear-wave velocity on the sides. Vertical exageration is a factor of 10.](images/LACrossSectionVelocitySmall.png)
-This set of utilities is used to extract geophysical information from the NCM (Boyd, 2020) 
-including, for example, S-wave, P-wave, and density profiles, as well as attributes for ground 
-motions models including *V*S30,  *Z*1.0, and *Z*2.5. Running the code in either MATLAB or 
+
+This set of utilities is used to extract geophysical information from the NCM (Boyd, 2020)
+including, for example, S-wave, P-wave, and density profiles, as well as attributes for ground
+motions models including *V*S30,  *Z*1.0, and *Z*2.5. Running the code in either MATLAB or
 Python requires all of the NCM databases:

 [GeoPhys](https://code.usgs.gov/ghsc/nshmp/ncm/GeoPhys)
-* NCM_AuxData.nc (https://doi.org/10.5066/P9GO3CP8)
+
+* NCM_AuxData.nc (<https://doi.org/10.5066/P9GO3CP8>)

 [GeoFram](https://code.usgs.gov/ghsc/nshmp/ncm/GeoFram)

@@ -21,19 +23,23 @@ Python requires all of the NCM databases:

 * MineralPhysicsDatabase.nc

-These codes are part of an effort to produce a three dimensional national crustal model for use with seismic hazard studies. (https://doi.org/10.5066/P9T96Q67)
+These codes are part of an effort to produce a three dimensional national crustal model for use with seismic hazard studies. (<https://doi.org/10.5066/P9T96Q67>)

 ## Python
+
 See the [README](geophys/README.md) file in the [geophys](geophys) directory for instructions
 on installing the database and running in Python.

 ## Matlab
+
 See the [README](matlab/README.md) file in the [matlab](matlab) directory for running in MATLAB.

 ## Help
+
 Any questions regarding the code can be directed to olboyd@usgs.gov.

 ## References
+
 *Boyd, O.S., 2020, Calibration of the U.S. Geological Survey
 National Crustal Model: U.S. Geological Survey Open-File
-Report 2020–1052, 23 p., https://doi.org/10.3133/ofr20201052*
+Report 2020–1052, 23 p., <https://doi.org/10.3133/ofr20201052>*
--- a/geophys/README.md
+++ b/geophys/README.md
 # GeoPhys Python routines ![Shear-wave velocity model in the LA area, looking north. Color scale is 100 to 1000 m/s Vs30 on the top and 100 to 5000 m/s shear-wave velocity on the sides. Vertical exageration is a factor of 10.](../images/LACrossSectionVelocitySmall.png)
-This set of utilities is used to extract geophysical profiles from the NCM (Boyd, 2020). Running the code requires the NCM Calibration dataset (https://doi.org/10.5066/P9GO3CP8), NCM Geologic Framework databases (https://doi.org/10.5066/P9SBQENM), NCM thermal model, NCM_TemperatureGrids.nc (https://doi.org/10.5066/P935DT1G), and the NCM Petrologic and Mineral Physics database (https://doi.org/10.5066/P9HN170G). These codes and datasets are part of an effort to produce a three dimensional national crustal model for use with seismic hazard studies. (https://doi.org/10.5066/P9T96Q67)
+
+This set of utilities is used to extract geophysical profiles from the NCM (Boyd, 2020). Running the code requires the NCM Calibration dataset (<https://doi.org/10.5066/P9GO3CP8>), NCM Geologic Framework databases (<https://doi.org/10.5066/P9SBQENM>), NCM thermal model, NCM_TemperatureGrids.nc (<https://doi.org/10.5066/P935DT1G>), and the NCM Petrologic and Mineral Physics database (<https://doi.org/10.5066/P9HN170G>). These codes and datasets are part of an effort to produce a three dimensional national crustal model for use with seismic hazard studies. (<https://doi.org/10.5066/P9T96Q67>)

 Profiles can be returned from roughly -126 degrees to -100 degrees longitude and 22 to 53 degrees latitude. If the requested location is outside of the bounds of the NCM, a message to that effect will be returned.

@@ -9,19 +10,23 @@ Profiles can be returned from roughly -126 degrees to -100 degrees longitude and
 * [Poetry](https://python-poetry.org/) Python dependency manager

 ### Poetry Install
+
 See [Poetry installation](https://python-poetry.org/docs/) instructions for more.

 #### osx / linux / bashonwindows install instructions
+
 ```bash
 curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python
 ```

 #### windows powershell install instructions
+
 ```bash
 (Invoke-WebRequest -Uri https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py -UseBasicParsing).Content | python
 ```

 #### pip
+
 ```bash
 pip install --user poetry
 ```
@@ -29,22 +34,27 @@ pip install --user poetry
 ## Usage

 ### Install Dependenices
+
 ```bash
 poetry install
 ```

 ### Install GeoPhys Database
+
 The following will install the GeoPhys database only:
+
 ```bash
 poetry run database --GeoPhys
 ```

 To download all databases:
+
 ```bash
 poetry run database
 ```

 The output directory for the database can be specified using the `--output` argument:
+
 ```bash
 poetry run database --output="/path/to/database"

@@ -52,8 +62,9 @@ poetry run database --output="/path/to/database"
 poetry run database --output="~/NCM_DATA"
 ```

-The output directory can additionally be specified using the environmental variable 
+The output directory can additionally be specified using the environmental variable
 `NCM_DATABASE_PATH`:
+
 ```bash
 export NCM_DATABASE_PATH="/path/to/database"

@@ -62,13 +73,16 @@ export NCM_DATABASE_PATH="~/NCM_DATA"
 ```

 ### Remove Database
+
 To remove database directory:
+
 ```bash
 poetry run database --clean
 ```

 ### Examples
-Geophysical profile at a latitude and longitude of 36, -118 from the 
+
+Geophysical profile at a latitude and longitude of 36, -118 from the
 surface to 30 m depth in increments of 1 m.

 ```bash
@@ -82,6 +96,7 @@ poetry run geophys -f geophys/resources/example.Input
 ```

 ### Help
+
 Please see or query the code for help.

 ```bash
@@ -90,32 +105,39 @@ poetry run help

 Any questions regarding the code and data can be directed to olboyd@usgs.gov.

-# Development
+## Development

 ### Git Hooks
+
 The GeoPhys project contains githooks on pre-commit and pre-push that
 will check the Python code format using [Black](https://github.com/psf/black),
-check the import sorting using [isort](https://github.com/timothycrosley/isort), and 
+check the import sorting using [isort](https://github.com/timothycrosley/isort), and
 lints the code using [Flake8](https://gitlab.com/pycqa/flake8).

 The GitHooks are configured with:
-```
+
+```bash
 poetry run setup
 ```

 ### Checking the Format
+
 To check the format of the code against Black and isort run:
-```
+
+```bash
 poetry run format_check
 ```

 ### Formatting the Code
+
 To automatically format the code using Black and isort run:
+
 ```bash
 poetry run format
 ```

 ## References
+
 *Boyd, O.S., 2020, Calibration of the U.S. Geological Survey
 National Crustal Model: U.S. Geological Survey Open-File
-Report 2020–1052, 23 p., https://doi.org/10.3133/ofr20201052*
+Report 2020–1052, 23 p., <https://doi.org/10.3133/ofr20201052>*
--- a/matlab/README.md
+++ b/matlab/README.md
 # GeoPhys MATLAB routines ![Shear-wave velocity model in the LA area, looking north. Color scale is 100 to 1000 m/s Vs30 on the top and 100 to 5000 m/s shear-wave velocity on the sides. Vertical exageration is a factor of 10.](images/LACrossSectionVelocitySmall.png)
-This program is used to extract geophysical profiles from the NCM (Boyd, 2020). Running the code requires the NCM Calibration dataset (https://doi.org/10.5066/P9GO3CP8), NCM Geologic Framework databases (https://doi.org/10.5066/P9SBQENM), NCM thermal model, NCM_TemperatureGrids.nc (https://doi.org/10.5066/P935DT1G), and the NCM Petrologic and Mineral Physics database (https://doi.org/10.5066/P9HN170G). These codes and datasets are part of an effort to produce a three dimensional national crustal model for use with seismic hazard studies. (https://doi.org/10.5066/P9T96Q67)
+
+This program is used to extract geophysical profiles from the NCM (Boyd, 2020). Running the code requires the NCM Calibration dataset (<https://doi.org/10.5066/P9GO3CP8>), NCM Geologic Framework databases (<https://doi.org/10.5066/P9SBQENM>), NCM thermal model, NCM_TemperatureGrids.nc (<https://doi.org/10.5066/P935DT1G>), and the NCM Petrologic and Mineral Physics database (<https://doi.org/10.5066/P9HN170G>). These codes and datasets are part of an effort to produce a three dimensional national crustal model for use with seismic hazard studies. (<https://doi.org/10.5066/P9T96Q67>)

 Profiles can be returned from roughly -126 degrees to -100 degrees longitude and 22 to 53 degrees latitude. If the requested location is outside of the bounds of the NCM, a message to that effect will be returned.

 ## Installation
+
 Within matlab, add to your path the location of the GeoPhys matlab scripts. The LoadNCMData.m script assumes that the databases (mentioned above) are installed in NCMBase/database where NCMBase is ../../(Location of LoadNCMData.m). For example, GeoPhys.m might be located in Path/NCM/GeoPhys/matlab. The database directory would then be in Path/NCM/database. LoadNCMData.m can be edited to allow for a different location of the database.

 ## Example
+
 See example.m for an example.

 ## Help
+
 Please see or query the code for help.

 **matlab>> help GeoPhys**
@@ -17,6 +21,7 @@ Please see or query the code for help.
 Any questions regarding the code and data can be directed to olboyd@usgs.gov.

 ## References
+
 *Boyd, O.S., 2020, Calibration of the U.S. Geological Survey
 National Crustal Model: U.S. Geological Survey Open-File
-Report 2020–1052, 23 p., https://doi.org/10.3133/ofr20201052*
+Report 2020–1052, 23 p., <https://doi.org/10.3133/ofr20201052>*