Organize Helpers and Project Structure

[philipc2]

Closes #291, #247, #101, #86

Overview

• Project structure has been refactored, splitting the Grid into a separate directory with specific modules that contain Grid-Only functionality.
• Helper functions have been organized out of utils.helpers into specific modules
• General refactoring (cleaning up imports, organizing functions in terms of Pubic vs Private in each file, etc)

Original Project Structure

.
├── ...
├── core                    
│   ├── api.py               # API
│   └── dataarray.py         # Dataarray Object
│   └── dataset.py           # Dataset Object
│   └── grid.py              # Grid Object
├── io                       
│   ├── _ugrid.py            # UGRID I/O
│   └── _exodus.py           # Exodus I/O
│   └── _mpas.py             # MPAS I/O
│   └── _scrip.py            # Scrip I/O
│   └── _shapefile.py        # Shapefile I/O
├── utils                     
│   ├── constants.py             # Top-Level constants 
│   └── get_quadratureDG.py      # Functions working with connectivity variables
│   └── helpers.py               # Assorted helper functions from all modules

New Project Structure

.
├── ...
├── core                     
│   ├── api.py               # API
│   └── dataarray.py         # Dataarray Object
│   └── dataset.py           # Dataset Object
├── grid                     
│   ├── grid.py              # Grid Object
│   └── connectivity.py      # Functions working with connectivity variables
│   └── coordinates.py       # Functions working with coordinates
│   └── area.py              # Functions working with face area
├── io                       
│   ├── _ugrid.py            # UGRID I/O
│   └── _exodus.py           # Exodus I/O
│   └── _mpas.py             # MPAS I/O
│   └── _scrip.py            # Scrip I/O
│   └── _shapefile.py        # Shapefile I/O
│   └── utils.py             # General I/O helpers
└── constants.py             # Top-Level constants 
├── utils   # General Helper Functions

PR Checklist

General

• An issue is linked created and linked
• Add appropriate labels
• Filled out Overview and Expected Usage (if applicable) sections

Documentation

• Docstrings have been added to all new functions
• Docstrings have updated with any function changes
• Internal functions have a preceding underscore (_) and have been added to docs/internal_api/index.rst
• User functions have been added to docs/user_api/index.rst

[ifranda]

This looks good as far as I can tell!

[rajeeja]

API docs seem to be broken: https://uxarray--370.org.readthedocs.build/en/370/user_api/index.html

[philipc2]

API docs seem to be broken: https://uxarray--370.org.readthedocs.build/en/370/user_api/index.html

Will fix this.

[philipc2]

@anissa111

Would you have an idea to why the API isn't rendering?

[philipc2]

@rajeeja

Documentation is fixed now.

[rajeeja]

where do you think the Analysis Operators would go?
in core - based on if they operate on dataset or dataarray etc?

integrate currently resides in dataset.py..

[rajeeja]

good work overall, helpers.py was getting cumbersome and this organization is better than the previous one.

[philipc2]

where do you think the Analysis Operators would go? in core - based on if they operate on dataset or dataarray etc?

integrate currently resides in dataset.py..

Correct, I envision that operators that interface with both the data and grid will be housed under the core directory, with grid being used for functions that only operate on the grid and it's geometry/topology.