Refactoring

Objectives

Per issue #8 (closed) - cleaner code organization, with io module for loading/saving annotations, volumes and projects, model module for managing the dataclasses, and less stuff in utils.

Major changes

• Add model module with AnnotationModel, ProjectModel, VolumeModel dataclasses
• Remove utils.project, put Project I/O in io.project
• Remove volumeio module, put Volume I/O in io.volume
• Remove utils.annotations, put Annotations I/O in io.annotations
• Put skimage and sitk filters in utils
• Split Volume/Annotation load Windows.

Minor changes

• Add filename to bruker and dicom volumes
• Remove hardcoded paths from test

Checklist

Make sure that all items in the checklist are checked before submitting.

• New code is accompanied by relevant unit tests.
• make clean, then make test leads to all tests passing.
• make run correctly starts the GUI.
• make docs has been run to update API documentation (and all documentation files have been committed)
• New or modified user functionalities are documented in the User manual