Instructions to get python notebooks working on a Mac

Author: scottprahl

README.md

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-Jupyter notebooks to call the VTS using Python
+# Jupyter notebooks to call the VTS using Python
+
+This is likely to change once `python` scripting is formally supported by `VTS`.  
+
+## Getting things working on a Mac
+
+I did not have a .NET installation and do most things from the command line.  This is a record of how I got `vts` working in `JupyterLab`.
+
+### Step 1: Install .NET 6
+
+You will need version 6 of .NET which is available from Microsoft below
+
+https://dotnet.microsoft.com/en-us/download/dotnet/6.0
+
+I saved everything to `$HOME/Documents/Code/dotnet6`
+
+Do not forget to update your `.bash_profile` or whatever you use so that this directory is in your path.  Also define `DOTNET_ROOT` 
+
+    PATH=$PATH:$HOME/Documents/Code/dotnet6
+  
+    export DOTNET_ROOT=$HOME/Documents/Code/dotnet6
+
+### Step 2: Install VTS
+
+Follow the guidelines at https://github.com/VirtualPhotonics/VTS/wiki/Getting-Started-on-Mac  Briefly, clone the `.git` repo 
+
+    git clone https://github.com/VirtualPhotonics/vts.git
+
+This will create the director `vts` that we will use in the next step
+
+When you are using `brew` you might as well install `nuget` at the same time
+
+    brew install powershell
+    brew install nuget
+
+Now build VTS.  If you don't have `matlab` don't worry, it seemed to work fine without completing the `matlab` tests
+
+    pwsh
+    cd vts
+    ./BuildTestRelease.ps1 
+    exit
+    
+### Step 3: Install .NET dlls
+
+Navigate to the release version of vts.dll
+
+    cd vts/src/Vts/bin/Release/net6.0
+
+Now use `nuget` to install the extra required libraries
+
+    nuget install MathNet.Numerics.dll
+    nuget install Newtonsoft.Json.dll
+    nuget install Nlog.dll
+    nuget install System.Reactive.dll
+
+rummage through all the folders and move the net6.0 `*.dll` to  `vts/src/Vts/bin/Release/net6.0` .  Doing `ls` in this directory should show
+
+    MathNet.Numerics.dll
+    Newtonsoft.Json.dll
+    Nlog.dll
+    System.Reactive.dll
+    Vts.dll
+
+### Step 4: Install pythonnet
+
+    pip install pythonnet
+
+Now because `pythonnet` assumes that you're using `mono` and not `.NET`, we need to update a few more things in .bash_profile
+
+    export PYTHONNET_RUNTIME=coreclr
+    export PYTHONNET_PYDLL=/usr/local/bin/python3   
+    
+Change the path for python to that for your system  (try `which python3` if you don't know)
+
+Start a `JupyterLab` notebook and verify that things are installed correctly
+
+    import clr
+    
+    clr.AddReference("System")
+    from System import Console
+    Console.WriteLine("Hello from .NET 6!")
+
+Once this works the next step will be to add the `Vts.dll`
+
+    import sys
+    
+    dll_directory = "/path/to/vts/src/Vts/bin/Release/net6.0"
+    sys.path.append(dll_directory)
+    clr.AddReference("Vts")
+
+Once this is working, verify that the other dlls you downloaded load properly
+
+    clr.AddReference("Newtonsoft.Json")
+    clr.AddReference("Mathnet.Numerics")
+    clr.AddReference("NLog")
+    clr.AddReference("System.Reactive");
+
+And now you should be able to run `VTS` programs in `python` with the header
+
+    import sys
+    dll_directory = "/path/to/vts/src/Vts/bin/Release/net6.0"
+    sys.path.append(dll_directory)
+    
+    import clr
+    clr.AddReference("Vts")
+    clr.AddReference("Newtonsoft.Json")
+    clr.AddReference("Mathnet.Numerics")
+    clr.AddReference("NLog")
+    clr.AddReference("System.Reactive")
+    
+    from Vts import *
+    from Vts.Common import *
+    from Vts.Extensions import *
+    from Vts.Modeling.Optimizers import *
+    from Vts.Modeling.ForwardSolvers import *
+    from Vts.Factories import *
+    from Vts.MonteCarlo import *
+    from Vts.MonteCarlo.Sources import *
+    from Vts.MonteCarlo.Tissues import *
+    from Vts.MonteCarlo.Detectors import *
+    from Vts.MonteCarlo.Factories import *
+    from Vts.MonteCarlo.PhotonData import *
+    from Vts.MonteCarlo.PostProcessing import *
+    from System import Array, Double
+
+