Mesh improvements

[jojoelfe]

This improves the reading/writing of meshes. One issue that I stumbled upon is that in the mod format the vertices actually contain vertices+normals (most of the time anyway). I modified the vertices and indices properties to remove the normals, which are now available through the normal property.

I also added support for writing of meshes. It's still a bit clunky, but functional

I also started to create some example notebooks under docs/examples

Read meshes
Write meshes

Minor refactors

Dependency Updates:

• Added numpydantic to the dependencies in pyproject.toml to support new data structures.

Model Enhancements:

• Updated the MeshHeader class to use the new MeshFlags class and added a field_validator for the flags attribute.
• Modified the Mesh class to initialize with default values, added a model_validator to update sizes, and added new properties and setters for vertices, normals, and indices. [1] [2]

Code Refactoring:

• Replaced the flag attribute with flags in the ModFileSpecification class.
• Updated the Contour class to use NDArray from numpydantic for the points attribute.

Testing Enhancements:

• Added new test test_read_write_read_roundtrip_mesh to verify the roundtrip read and write of mesh data.
• Added new test test_mesh_flags to check the mesh flags property.

[Copilot]

Pull Request Overview

This PR improves mesh reading and writing by updating the mesh model, header, and flag handling while adding new tests and example notebooks. Key changes include:

• New tests in tests/test_model_api.py for mesh roundtrip and flag behavior.
• Updates in src/imodmodel/models.py to introduce MeshFlags, interleave vertices and normals, and adjust indices handling.
• Refactors in writers, binary specification, and pyproject.toml along with an added example notebook.

Reviewed Changes

Copilot reviewed 8 out of 9 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tests/test_model_api.py	Added new tests to verify mesh read/write roundtrips and flag property functionality.
src/imodmodel/writers.py	Changed mesh header serialization from .dict() to dict(header) in header writing logic.
src/imodmodel/models.py	Introduced MeshFlags, updated MeshHeader defaults and validators, and refined vertices/indices properties.
src/imodmodel/binary_specification.py	Updated field name from 'flag' to 'flags' to support the new MeshFlags implementation.
pyproject.toml	Added "numpydantic" to support new data structures.
docs/examples/smiley.ipynb	Added an example notebook demonstrating mesh export functionality.

Files not reviewed (1)

• docs/examples/export_mesh.ipynb: File too large

Comments suppressed due to low confidence (1)

src/imodmodel/writers.py:64

• Using dict(header) instead of header.dict() may bypass pydantic's custom processing; please confirm that the intended fields are correctly serialized.

_write_to_specification(file, ModFileSpecification.MESH_HEADER, dict(header))

[jojoelfe]

• Using dict(header) instead of header.dict() may bypass pydantic's custom processing; please confirm that the intended fields are correctly serialized.

Yes, Mr. AI, this is intentional to avoid converting the Flags submodel into a dictionary

[alisterburt]

looks fantastic! Minor suggestion would be to move the obj into examples/data

Thanks for adding the notebooks too - is it easy to render notebooks in mkdocs do you know?

[alisterburt]

what made you remove numpydantic? I assume it avoids having to set up the custom model config when fields are numpy arrays? neat!

[jojoelfe]

is it easy to render notebooks in mkdocs do you know?

I think so, let me try.

what made you remove numpydantic? I assume it avoids having to set up the custom model config when fields are numpy arrays? neat!

Yeah, I thought it would be neat to specify array shapes that way instead of using validators. There seem to be two packages numpydantic and pydantic-numpy. numpydantic seemed to have the cleaner API, but I haven't really looked into advantages/diadvantages. Removed it for now because it is incompatible with python 3.8 and broke the tests.

[jojoelfe]

is it easy to render notebooks in mkdocs do you know?

I think so, let me try.

Yes, super simple, just added a plugin. Looks great, too, the trimesh web-thing renders properly.

[alisterburt]

Removed it for now because it is incompatible with python 3.8 and broke the tests.

if you want to add it back in and deprecate 3.8 that's fine by me! I follow NEP29 for python versions

amazing re: docs, look forward to seeing these online