pre publish code tidy

[alexallmont]

Ticket to capture easy wins in code before publication. This change will not have any functional changes, just additionaly safety guards before we move onto imputation. Work includes:

• Run tests directly via python rather than run.subprocess for proper error reporting
• Rename L to neighborhood_size
• Remove commented-out code
• Fix FutureWarning: The 'delim_whitespace' when running tests
• Ensure all member variables initialised. Non initialised values can lead to non-deterministic behaviour
• Warnings as errors. A dry run on these indicates that most are size_t to int warnings, should be very fast fix.
• License (GPL)
• Copyright headers in python, cpp, hpp and cmake files
• Formatting
• Class order
• const-correctness
• change heavy operator& to named method
• Replace -7 and -9 references