Reorganize TEMController

[viljarjf]

Hello,
This reorganizes the TEMController module:

• The TEMController class, which was in the TEMController file, in the TEMController module, is now moved to the controller.py-file in the main folder.
• The TEMController folder is renamed to microscope.
• Specific instrument interfaces are moved to microscope/interface.
• Deflectors, lenses ect. are moved to microscope/components.

Some of the files have been given simpler names, and some functions are renamed as well.
To ensure backwards compatibility, I added a deprecation decorator to warn users that the way things are imported is changing. See e.g. https://github.com/viljarjf/instamatic/blob/efa311ecc536d2724c71207f2fd2cb3c1462ddad/src/instamatic/microscope/microscope.py#L66-L71

Here is a summary:

Opening this as a draft to hear thoughts and suggestions before I go through and update all the documentation, and add more deprecation warnings.
I am unsure about the components-folder, since they are only used by the TEMController-class, which is now placed in a file outside of the microscope-folder. However, placing controller.py inside the microscope-folder seems unfitting, seeing how important the controller class is.
Additionally, should the files not part of the reorganization be left unchanged for now? They will show the deprecation warning, but this reduces the amount of files part of this PR significantly.

[stefsmeets]

Thanks for this. Already looks pretty good to me. I think this is a nice step forward in the organisation of the code, and I'm also happy with the better class / function names.

Opening this as a draft to hear thoughts and suggestions before I go through and update all the documentation, and add more deprecation warnings.

I'm also happy if you want to update the documentation in a follow-up PR.

I am unsure about the components-folder, since they are only used by the TEMController-class, which is now placed in a file outside of the microscope-folder. However, placing controller.py inside the microscope-folder seems unfitting, seeing how important the controller class is.

(TEM)controller.py is meant as a high-level general interface that blends the seperation between the camera and microscope. It makes sense to me to move this to src/instamatic/controller.py. Maybe you could also move ./microscope/components to ./components?

Additionally, should the files not part of the reorganization be left unchanged for now? They will show the deprecation warning, but this reduces the amount of files part of this PR significantly.

As a reviewer, smaller changes are much easier to go through, so feel free to open a new PR with follow-up changes.

Let me know if this PR is finished, I'll be happy to merge it.

[viljarjf]

Should be good to go now! I'll fix the deprecation warnings and update the dcumentation in later PRs, then.

[stefsmeets]

Thanks for this, looks good to me!