Code clean-up

[NikoOinonen]

There seems to be a lot of unused code and old/alternative versions of functions and modules that could probably be deleted. Additionally, some things could be renamed and reorganized to be cleaner. I'm afraid to just go and delete things, so I'll list here the things that I would change, and we can discuss it.

• Organize OCL-related code into submodules #19
• Single function for reading xyz and writing xyz files #24
• Delete all functions related to old procedural version of the OCL code. #25
• Rename GeneratorOCL_Simple2 -> Generator and delete other versions. #23
• Delete old_gui. #18
• Delete all commented-out lines of code. #20
• Rename GUILJ to something simpler like 'ppm' or 'ppm-gui'. #21
• Clean-up repository root #22
• Pass flake8 test #26

[NikoOinonen]

I also tried running flake8 to detect problems in the code. The report is in the attachment. There seems to be many cases (113) of undefined variables and a couple of syntax errors. These lines of code will never run, so I guess they have never been tested or are remainders from earlier versions. Maybe @ProkopHapala could look through these to see if they should be fixed or just deleted.

flake8_test.txt

[ProkopHapala]

flake8_test.txt
Thank you Niko, I did not know about such tool

[NikoOinonen]

All of the listed issues have been resolved, so closing this issue.