Adds PhysicsNeMo-Mesh API Docs

[peterdsharpe]

PhysicsNeMo Pull Request

Description

Checklist

• I am familiar with the Contributing Guidelines.
• New or existing tests cover these changes.
• The documentation is up to date with these changes.
• The CHANGELOG.md is up to date with these changes.
• An issue is linked to this pull request.
• If I am implementing a new model or modifying any existing model, I have followed the Models Implementation Coding Standards.

Dependencies

Review Process

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[peterdsharpe]

/blossom-ci

[greptile-apps]

Greptile Summary

This PR adds a comprehensive Sphinx API documentation section for the PhysicsNeMo-Mesh library (docs/mesh/), covering 16 submodules (core mesh class, I/O, discrete calculus, curvature, geometry, boundaries, neighbors, spatial queries, sampling, transformations, subdivision, smoothing, remeshing, repair, validation, and visualization) plus a top-level index page wired into docs/api_index.rst.

The documentation is well-structured, accurate against the source code, and provides useful conceptual overviews and runnable code examples for each module. One issue was found:

• Missing mesh initialization in calculus.rst example — the code block uses a mesh variable immediately after imports without ever constructing one, which would produce a NameError if a user tried to run the snippet verbatim. All other pages in this PR correctly instantiate a mesh (typically via sphere_icosahedral.load(...)) before using it.

Important Files Changed

Filename	Overview
docs/mesh/index.rst	Main landing page for the Mesh API docs; overview, data model, quick-start, key features, and toctree all look accurate and well-structured.
docs/mesh/calculus.rst	Code example uses mesh before it is instantiated, causing a NameError if run verbatim; the Mesh import is present but never used to create an object.
docs/mesh/core.rst	Correctly documents the Mesh tensorclass with a working example; autoclass:: Mesh under the right currentmodule.
docs/mesh/boundaries.rst	Accurate description of boundary detection, facet extraction, and topology checking; methods and module path match the implementation.
docs/mesh/repair.rst	Documents the repair pipeline accurately; all functions listed (merge_duplicate_points, remove_degenerate_cells, fix_orientation, fill_holes) are exported from physicsnemo.mesh.repair.
docs/mesh/transformations.rst	Covers geometric transformations and projections in a single file with two currentmodule resets; both submodules exist and export the documented symbols.
docs/mesh/visualization.rst	Correctly documents draw_mesh under physicsnemo.mesh.visualization.draw_mesh; backends (matplotlib / PyVista) and usage examples match the implementation.

_{Last reviewed commit: d2ec699}

[greptile-apps]

_{18 files reviewed, 1 comment}

_{Edit Code Review Agent Settings | Greptile}

[greptile-apps]

Additional Comments (1)

docs/mesh/calculus.rst
mesh used before it is defined in code example

The code block imports Mesh and the calculus functions, but then immediately uses mesh (e.g. mesh.point_data["T"] = ...) without ever constructing a Mesh instance. Running this snippet verbatim produces a NameError: name 'mesh' is not defined.

A mesh creation step is needed before the first use of mesh. For example, inserting the following after the imports would fix it:

from physicsnemo.mesh.primitives.surfaces import sphere_icosahedral
mesh = sphere_icosahedral.load(subdivisions=2)

The same pattern (importing Mesh but creating the instance via sphere_icosahedral.load) is already used consistently in boundaries.rst, curvature.rst, geometry.rst, and other pages in this PR.

[peterdsharpe]

/blossom-ci

[megnvidia]

Well done. I just have what probably feels like a lot of very minor requested changes.

[megnvidia]

Well done. I just have what probably feels like a lot of very minor requested changes.

[peterdsharpe]

/blossom-ci