83 clear up classes in sample

[andped10]

This PR only consists only code refactoring and typing.

Entry to all sample classes should be fetched directly from sample

This is obtained by the __init__.py file in the sample folder. By doing so we will be free to make changes to the internal structure of the module in the future.

The internal structure of the sample folder is now:

sample

• elementals
  • layers (layer consists of a material)
    • layer
    • layer_apm
  • materials (most fundamental element)
    • material
    • material_density
    • material_mixture
• assemblies (these are constructs of layers)
  • gradient_layer
  • multilayer
  • repeating_multilayer
  • surfactant_layer

However from a user perspective you would get the Multilayer class implemented in sample.assemblies.multilayer by executing:
from sample import Multiplayer

or for Layer implemented in sample.elementals.layers.layer:
from sample import Layer

Other Changes

The modules for material and layer been split into several files only containing a single class per file.

Class renaming:

• Structure has been renamed to Sample
• Layers has been renamed to LayerCollection
• Materials has been renamed to MaterialCollection

Base classes introduced in elementals:

• BaseElement
• BaseElementCollection

ADR is created in #89

[rozyczko]

Small comment on naming consistency.

module surfactant_layer contains class SurfactantLayer.
module gradient_layer contains class GradientLayer

so it is sensible to assume that PascalCase for classes converts into snake_case for modules.

This doesn't seem to hold for MultiLayer class which module you named multilayer.
Is there any reason or should the class name be just Multilayer (lower case l)?

[rozyczko]

A couple of base.py modules should also be renamed according to the class name inside.
I.e.
sample/assemblies/base.py -> base_assembly.py
sample/elementals/base.py -> base_element.py

[rozyczko]

The base class names in sample/elementals/base.py are BaseElement and BaseElementCollection.
Should the folder name be elements then?

[andped10]

The base class names in sample/elementals/base.py are BaseElement and BaseElementCollection. Should the folder name be elements then?

Changed folder name to elements

[andped10]

Small comment on naming consistency.

module surfactant_layer contains class SurfactantLayer. module gradient_layer contains class GradientLayer

so it is sensible to assume that PascalCase for classes converts into snake_case for modules.

This doesn't seem to hold for MultiLayer class which module you named multilayer. Is there any reason or should the class name be just Multilayer (lower case l)?

Changed class names containing MultiLayer to Multilayer

[andped10]

A couple of base.py modules should also be renamed according to the class name inside. I.e. sample/assemblies/base.py -> base_assembly.py sample/elementals/base.py -> base_element.py

Renamed files and extracted base for base_element_collection.py

[rozyczko]

I think this is now ready for mergig.