General long-term notes

[pcolaianni]

I will collect info from multiple PRs into this issue:

• we are using #pragma once instead of define guards
• we keep using OpenMS:: namespace explicitly, avoiding using namespace OpenMS;
• using namespace std; is fine where it actually increases readability
• convert python to c++ first, and then take care of improving code
• rename "Targeted" to "TargetedExperiment" for identifiers and methods in code
• .cpp/.h C++ files should indented using two spaces
• .cmake (or other cmake related files), build scripts, and docker files should be indented using tab/4 spaces
• will need to correct EOF consistency

[pcolaianni]

About getters/setters:

Non constant versions should only be implemented if there is a desire to modify the underlying value. If not, a copy should be returned.

If performance becomes an issue, then we can start thinking about breaking the above rule. However, I suspect that this will not be the case.