Merge pull request #5 from scottprahl/main

alternate notebook implementation

Author: Lisa Malenfant

README.md

@@ -1,10 +1,10 @@
-# Jupyter notebooks to call the VTS using Python
+# Using VTS in a Jupyter notebook
 
 This is likely to change once `python` scripting is formally supported by `VTS`.  
 
-## Getting things working on a Mac
+## macOS installation details
 
-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`.
+This is a record of how I got `vts` working in `JupyterLab`.
 
 ### Step 1: Install .NET 6
 
@@ -14,7 +14,7 @@ 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` 
+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
 
@@ -26,9 +26,9 @@ Follow the guidelines at https://github.com/VirtualPhotonics/VTS/wiki/Getting-St
 
     git clone https://github.com/VirtualPhotonics/vts.git
 
-This will create the director `vts` that we will use in the next step
+This will create the directory `vts` that is needed for the next step
 
-When you are using `brew` you might as well install `nuget` at the same time
+Install both `powershell` and `nuget` using [Homebrew](https://brew.sh)
 
     brew install powershell
     brew install nuget
@@ -39,74 +39,40 @@ Now build VTS.  If you don't have `matlab` don't worry, it seemed to work fine w
     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
+### Step 3: 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
+Because `pythonnet` under macOS (or linux) defaults to `mono`, two more things need to added to `~/.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)
+Obviously use the path for python on your system  (`which python3` will tell you)
 
-Start a `JupyterLab` notebook and verify that things are installed correctly
+Next start a `JupyterLab` notebook to 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`
+The final test is importing from `Vts.dll`
 
-    import sys
-    
-    dll_directory = "/path/to/vts/src/Vts/bin/Release/net6.0"
-    sys.path.append(dll_directory)
-    clr.AddReference("Vts")
+    import clr
+    clr.AddReference("/path/to/vts/src/Vts/publish/local/Vts.dll")    
+    from Vts import *
 
-Once this is working, verify that the other dlls you downloaded load properly
+where, of course, "/path/to" above has been adapted to your system
 
-    clr.AddReference("Newtonsoft.Json")
-    clr.AddReference("Mathnet.Numerics")
-    clr.AddReference("NLog")
-    clr.AddReference("System.Reactive");
+### Step 4: Run programs
 
-And now you should be able to run `VTS` programs in `python` with the header
+To run `VTS` programs in `python` include the following 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")
+    clr.AddReference("/path/to/vts/src/Vts/publish/local/Vts.dll")    
 
     from Vts import *
     from Vts.Common import *
@@ -121,6 +87,4 @@ And now you should be able to run `VTS` programs in `python` with the header
     from Vts.MonteCarlo.Factories import *
     from Vts.MonteCarlo.PhotonData import *
     from Vts.MonteCarlo.PostProcessing import *
-    from System import Array, Double
-
-
+    from System import Array, Double