Joss 2025 revisions

[subravvr]

Software update for JOSS.

Dependency update

• Included pandas, pyvista for handling morphology data and visualization respectively

API update

• cleaned up morphology data computation and writing functions
• added a visualization function

Examples update

• added morphology and visualization to the api example
• changed parameters slightly

Tests update

• added integration test to ensure all parts of the API work together (from grid creation to .vti writing)
• added integration test to ensure morphology output was correct
• removed redundant integration test

README update

• Some capitalization changed to match JOSS manuscript
• Reworded CLI/API example description
• Added an image highlighting defect formation due to local under melting between paths/layers

CONTRIBUTING update

• Added file

[subravvr]

Failed PR due to missing a filename in input.yaml. closed this one. will reopen a different one.