Update README.md

Readme updates

Author: RyanJField

README.md

@@ -17,7 +17,6 @@ The two external dependancies not included are:
 [gnuplot](http://www.gnuplot.info/download.html), gnuplot is required to run the executable and should be installed and the gnuplot executable available in the system path.
 
 And [HDF5](https://support.hdfgroup.org/ftp/HDF5/current/src/), this should be installed and the HDF5_ROOT environment variable defined.
-
 ### HDF5
 #### Windows
 HDF5 can be installed for windows 10 64bit windows using a precompiled installer available [here](https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.1/bin/windows/hdf5-1.12.1-Std-win10_64-vs14.zip)
@@ -27,19 +26,16 @@ Or by compiling it using the [source code](https://www.hdfgroup.org/downloads/hd
 The HDF5_ROOT should then be set to the installation directory eg.:`C:\Program Files (x86)\HDF_Group\HDF5\1.12.1`
 
 ** Note: The architecture of your compiler should match the installation of HDF5.
-
 #### Linux
 HDF5 can be install on linux through APT:
 ```
-sudo apt=get install libhdf5-dev
+sudo apt-get install libhdf5-dev
 ```
-
 #### Mac OS
 HDF5 can be installed on mac using homebrew:
 ```
 brew install hdf5
 ```
-
 ### gnuplot
 gnuplot can be installed using the following commands:
 
@@ -48,27 +44,22 @@ gnuplot can be installed on windows using chocolatey:
 ```
 choco install gnuplot
 ```
-
 #### Linux
 gnuplot can be installed on linux using apt:
 ```
 sudo apt-get install gnuplot
 ```
-
 #### Mac OS
 gnuplot can be installed on mac using homebrew:
 ```
 brew install gnuplot
 ```
-
 ## Compiling
 Compile the executable by running:
-
 ```
 $ cmake -Bbuild
 $ cmake --build build
 ```
-
 **Important** For multi-config compilers such as Visual Studio xcode or ninja the config type needs to be set to `Release` otherwise the API will not build for example:
 ```
 $ cmake -Bbuild
@@ -77,35 +68,35 @@ $ cmake --build build --config=Release
 
 ## Usage
 The executable is located in the `build/bin[/release]` directory
-
 The executable is designed to be run independently using the `--local` flag and taking one parameter:
-
-## on Unix
+### on Unix
 ```
 build/bin/cppSimpleModel --local data/static_params_SEIRS.csv
 ```
-## or on windows:
+### or on windows:
 ```
 build/bin/release/cppSimpleModel.exe --local data\static_params_SEIRS.csv"
 ```
 
-Or conjuction with the [fair cli](#Fair CLI) like so:
-(From a fair cli poetry shell within the repo)
-## Unix
+### or conjuction with the [fair cli](#Fair-CLI):
+
+(From a virtual environment within the repo directory)
+
+#### Fair CLI
+The [FAIR commandline interface]("https://github.com/FAIRDataPipeline/FAIR-CLI") is available to install using pip:
+```
+pip install fair-cli
+```
+Once installed the model can be run using the following:
+### Unix
 ```
 fair init --ci
 fair pull data/seirs_config.yaml
 fair run data/seirs_config.yaml
 ```
-## Windows
+### Windows
 ```
 fair init --ci
 fair pull data/seirs_config_windows.yaml
 fair run data/seirs_config_windows.yaml
 ```
-
-## Fair CLI
-The [FAIR commandline interface]("https://github.com/FAIRDataPipeline/FAIR-CLI") is available to install using pip:
-```
-pip install fair-cli
-```