Suggestion: Restructure project based on MATLAB Toolbox Best Practices

[ehennestad]

Restructure repository based on the MATLAB Toolbox Best Practices.

Adopting the recommended toolbox structure would make packaging as an .mltbx easier by clearly separating distributable toolbox content from tests, development tools, and repository configuration.
Because this is a MathWorks-maintained repository, it could also serve as a practical example of the toolboxdesign recommendations for a toolbox containing a public MATLAB API, internal implementation code, and a Python dependency.

Preparing the repo for .mltbx based distribution would also provide users with a simpler installation and upgrade path than cloning the repository and manually adding it to the MATLAB path, and it would make it easier for other tools, i.e MatNWB to add the toolbox as a dependency.

What restructuring would mean for this repository:

Step 1: Move all root-level .m files and the PythonModule into a toolbox folder
Step 2: Add buildfile.m, toolbox packaging.prj file (optional/later)

New repository structure after reorganisation:

MATLAB-support-for-Zarr-files/
├── .github/
├── doc/
├── test/
├── toolbox/
│   ├── PythonModule/
│   │   ├── requirements.txt
│   │   └── ZarrPy.py
│   ├── Zarr.m
│   ├── ZarrDatatype.m
│   ├── readZattrs.m
│   ├── zarrcreate.m
│   ├── zarrinfo.m
│   ├── zarrread.m
│   ├── zarrwrite.m
│   └── zarrwriteatt.m
├── .codespellrc
├── .gitignore
├── buildfile.m                 # Proposed
├── codecov.yml
├── license.txt
├── README.md
├── SECURITY.md
└── <project-name>.prj          # Proposed packaging/project file

[ehennestad]

Other changes needed:

1. README installation instructions
   addpath("<repository-root>") -> addpath("<repository-root>/toolbox")
2. PathFixture in tests should target toolbox instead of repository root
3. gitignore
   PythonModule/__pycache__ -> toolbox/PythonModule/__pycache__

[krisfed]

That's a good idea! Maybe something we should have considered from the beginning.

doc can also go under the toolbox, not sure if there is a strict best practice

[ehennestad]

doc can also go under the toolbox, not sure if there is a strict best practice

In the toolbox design guidelines there is a doc folder inside the toolbox folder, but the only example is a GettingStarted.mlx live script. I think it depends on what target audience the documentation is meant for. If it is markdown / rst for online documentation pages, I would keep it out of the toolbox folder, if it is live scripts or documentation to be used within MATLAB it should in the toolbox folder.