Allow array to be input, update documentation, minor fixes

[genisplaja]

• In this PR, I first updated most of the tools so that an input array can input (now you could only input a filepath). The extract function automatically adapts to the input type now (path or data array).
• Then, we have a more complete contribution guidelines page
• Minor fixes (variable names, improve dataset list in readme which is badly formatted now)

[genisplaja]

Thanks @thomasgnuttall! Minor comments fixed. Maybe we can merge this one, which is quite dense already, and we can then create a separate PR for the print/logger comments you left while fixing this issue through the package. I will copy past the comments you left here, in the logger issue #82, so that we can have them listed for fixing them.