Update API docs and structure.

[coreyjadams]

PhysicsNeMo Pull Request

This PR brings the API section of the docs in line with the refactor work. To-dos remain:

• mesh @peterdsharpe
• diffusion @CharlelieLrt
• datapipes @coreyjadams
• nn @loliverhennigh

We also need to check models are all listed in the API section, I think we are missing some.

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

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[greptile-apps]

Greptile Summary

This PR restructures the API documentation to align with a broader codebase refactor: removing old physicsnemo.launch.*, physicsnemo.deploy, and physicsnemo.distributed.shardtensor docs in favor of new pages for physicsnemo.core, physicsnemo.diffusion, physicsnemo.domain_parallel, physicsnemo.nn, and physicsnemo.mesh. However, several of the newly added automodule directives reference modules that do not exist, causing Sphinx build warnings and empty documentation sections.

Key issues found:

• docs/api/models/weather.rst: GraphCast utils directives reference physicsnemo.graphcast.utils.*, but this package doesn't exist; the correct prefix is physicsnemo.models.graphcast.utils.*. Additionally, data_utils and loss modules don't exist in the repository.

• docs/api/physicsnemo.diffusion.rst: References non-existent modules physicsnemo.diffusion.samplers.deterministic_sampler and stochastic_sampler (actual files are samplers.py, solvers.py, and legacy variants).

• docs/api/models/operators.rst: References physicsnemo.utils.domino.utils which doesn't exist; correct path is physicsnemo.models.domino.utils.

• docs/api/physicsnemo.nn.rst: All four referenced modules don't exist under physicsnemo.nn, and the file lacks a required top-level RST document title.

• docs/api/physicsnemo.mesh.rst: Completely empty file included in toctree will cause Sphinx build error; needs at minimum a placeholder title.

• docs/api/physicsnemo.core.rst: Ends with a dangling cross-reference label and missing trailing newline.

_{Last reviewed commit: 3405928}

[greptile-apps]

Additional Comments (1)

docs/api/physicsnemo.mesh.rst
The file is completely empty but is included in api_index.rst's toctree. Sphinx requires every file in a toctree to have at least a document title, otherwise it will produce a build error.

Add a minimal placeholder since mesh documentation is a pending TODO:

PhysicsNeMo Mesh
================

.. note::

   Documentation for ``physicsnemo.mesh`` is coming soon.

[peterdsharpe]

Reviewing only the changes to the Mesh API docs - this migration looks good to me! Thanks!

[loliverhennigh]

Checked the image moves and it looks good to me. I read through the other doc changes. They make sense to me and happy to approve although I know others might know a bit better about the distributed stuff and diffusion.