V2.0 refactor #1235

coreyjadams · 2025-11-19T21:46:12Z

PhysicsNeMo Pull Request

Rearchitecture of core physicsnemo components. Highlights:

Break circular deps in internal imports, and ensure they can't come back via a linting step.
Organize external dependencies via dependency groups. Note that models and metrics have a few "-extra" dependencies that are unprotected still, to be fixed before merge.
Add linting to ensure we can not add external dependencies unless they are accounted for in pyproject.toml
Update tests to handle new structure.
- Tests organization mirrors physicsnemo.
Update examples with changed imports. Biggest breaking change is the deprecation of launch. Logging utilities moved into physicsnemo.utils.logging.
Main build and install method is now uv.

Overall, this should lower the installation challenges and lay the groundwork for the rest of v2.0.

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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.

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No tests fixed yet.

phsyicsnemo.utils, launch.config is just gone. It was empty.

coreyjadams · 2025-12-03T20:14:41Z

/blossom-ci

CharlelieLrt

It seems some imports haven't been fixed. For instance I still see in the examples some imports like:

from physicsnemo.models import Module

Those are not expected to work anymore I think.

* Ensure that the pip dependency group exclusively matches the resolution of the dependency-groups from Pep 735 that uv enables. * Revert some dependency tracking. Now, we allow unbare external imports anywhere. But the import list is smaller, and more easily managed with uv / pip equally. extras are now chained and built in the optional deps. * Add dev deps. Add docstring for ci script. * Update pyproject with small changes from review.

coreyjadams · 2025-12-08T19:41:13Z

/blossom-ci

- Update links to physicsnemo-curator examples in DoMINO and Transolver READMEs. - Update link to CachedDoMINODataset and path reference for cache_data.py script.

coreyjadams · 2025-12-08T19:58:03Z

/blossom-ci

Alexey-Kamenev

Checked some of the models, LGTM.

Alexey-Kamenev · 2025-12-08T23:40:29Z

pyproject.toml

-include = ["physicsnemo", "physicsnemo.*"]
+#####################################################################
+# Linting configuration
+#####################################################################

 [tool.ruff]
 # Enable flake8/pycodestyle (`E`), Pyflakes (`F`), flake8-bandit (`S`),


Below on the line 173 it says "Never enforce E402," but E402 is not in the ignore list.

Alexey-Kamenev · 2025-12-08T23:45:49Z

physicsnemo/models/fno/fno.py

@@ -901,6 +899,9 @@ def __init__(
        )

    def getFNOEncoder(self):


Such non-standard naming will be addressed later I guess?

@Alexey-Kamenev can you elaborate on what you mean by "non-standard" naming? I can see two things wrong there:

This method should be private

This method name should be using snake case

So, essentially _get_fno_encoder instead of getFNOEncoder.
Were you thinking of anything else?

@ktangsali for viz, since he is assigned to this task

@CharlelieLrt - that's right, _get_fno_encoder is exactly what I meant!

Alexey-Kamenev · 2025-12-08T23:51:37Z

physicsnemo/models/meshgraphnet/meshgraphkan.py

@@ -221,7 +200,7 @@ def forward(
        self,
        node_features: Tensor,
        edge_features: Tensor,
-        graph: Union[DGLGraph, List[DGLGraph], CuGraphCSC],
+        graph: Union[GraphType, List[GraphType]],


Thank you, I forgot to change it to a more appropriate type.

coreyjadams · 2025-12-10T18:09:40Z

/blossom-ci

coreyjadams · 2025-12-10T19:45:29Z

/blossom-ci

CharlelieLrt · 2025-12-11T00:27:49Z

pyproject.toml

-[tool.uv]
-no-build-isolation-package = ["torch_scatter"]
-managed = false
+

 [project.entry-points."physicsnemo.models"]
 AFNO = "physicsnemo.models.afno:AFNO"


@coreyjadams I realized something wrong with the automatic registration of Modules. Now the registration happens at (sub)class definition. This might lead to unexpected behaviors.

For instance:

from physicsnemo.core import ModelRegistry model_registry = ModelRegistry() model_registry.list_models() # ['AFNO', 'DLWP', 'EDMPrecondSR', 'FNO', 'Fengwu', 'FullyConnected', 'GraphCastNet', 'MeshGraphNet', 'One2ManyRNN', 'Pangu', 'Pix2Pix', 'SRResNet', 'SwinRNN', 'UNet']

If after that I do:

from physicsnemo.models.diffusion import SongUNet # Defines multiple Module subclasses: SongUNet, SongUNetPosEmdb, etc... model_registry.list_models() # ['AFNO', 'DLWP', 'EDMPrecondSR', 'FNO', 'Fengwu', 'FullyConnected', 'GraphCastNet', 'MeshGraphNet', 'One2ManyRNN', 'Pangu', 'Pix2Pix', 'SRResNet', 'SwinRNN', 'UNet', 'SongUNet', 'SongUNetPosEmbd', 'SongUNetPosLtEmbd', 'DhariwalUNet', 'StormCastUNet', 'VPPrecond', 'VEPrecond', 'iDDPMPrecond', 'EDMPrecond', 'EDMPrecondSuperResolution']

This type of implicit stateful is very counter-intuitive. This could be changed by having all the models from the zoom put here in the entry points. Not sure it's the best option though.

peterdsharpe

Discussed most of our open questions in the refactor meetings + over Slack, this looks good to me! I've been building on top of this for a few weeks now and haven't experienced any issues. The addition of uv-compatibility for pyproject.toml is particularly nice!

CharlelieLrt · 2025-12-12T01:06:11Z

physicsnemo/models/dlwp_healpix_layers/healpix_layers.py

@coreyjadams those are layers, shouldn't they go into physicsnemo.nn instead?

Or maybe they are not general purpose enough to put them in physicsnemo.nn? In that case maybe a better place is in physicsnemo/models/dlwp_healpix instead of the upper level physicsnemo.models (since these layers are really not models that are part of the zoo)

@pzharrington maybe you know?

Eventually yes, but I'm gonna request we postpone that migration until the follow-up work of addressing models which do not conform to standards.

CharlelieLrt

Bumped into a wrong import: from physicsnemo.models.meta import ModelMetaData

* Adding cpu ci * Make sure to get dev deps * target tests properly, maybe fix uv build * make sure radius search passes on CPU * maybe fix uv sync. Hopefully fix ubuntu testing. * Fix a test typo * Matrix to more python versions * drop support for python < 3.11 * fix link, enable nightly, target only selected branches * Only run python 3.12 on PRs, ubuntu and mac os, uv and pip * Add coverage to devs * Limit to one test path for PRs. nightly CI is consistent to all tests. uv install gets a retry.

…amples (#1276) * Remove TensorFlow dependency in Vortex Shedding and Lagrangian MGN examples * Update READMEs

coreyjadams added 30 commits November 3, 2025 08:02

Move filesystems and version_check to core

46d2880

Fix version check tests

c6d04ad

Reorganize distributed, domain_parallel, and begin nn / utils cleanup.

6f36f03

Move modules and meta to core. Move registry to core.

7824091

No tests fixed yet.

Add missing init files

f753573

Update build system and specify some deps.

2ef835e

Merge branch 'main' into refactor

1603067

Reorganize tests.

1e8df52

Update init files

2e1195c

Clean up neighbor tools.

a698685

Update testing

258d988

Fix compat tests

0638b97

Move core model tests to tests/core/

b6327cb

Add import lint config

3ce049a

Relocate layers

95fa450

Move graphcast utils into model directory

ba6813d

Relocating util functionalities.

3f10463

Further clean up and organize tests.

339b484

Merge branch 'NVIDIA:main' into refactor

18df402

utils tests are passing now

d6946d9

Cleaning up distributed tests

66f8d15

Patching tests working again in nn

2ee76db

Fix sdf test

33d525d

Fix zenith angle tests

a06ad0a

Some organization of tests. Checkpoints is moved into utils.

4c845cc

Remove launch.utils and launch.config. Checkpointing is moved to

3bb64f4

phsyicsnemo.utils, launch.config is just gone. It was empty.

Most nn tests are passing

4aa332e

Further cleanup. Getting there!

45686cc

Remove constants file

bbc54f6

Add import linting to pre-commit.

8453fea

Merge branch 'refactor' into v2.0-refactor

6c9cebd

coreyjadams added 2 commits December 3, 2025 15:15

fix import error from wandb

7422e4c

remove instance check

75490ea

CharlelieLrt requested changes Dec 5, 2025

View reviewed changes

coreyjadams and others added 3 commits December 8, 2025 13:49

Fix broken imports

ab46322

Fix README links in transolver and domino examples (#1259)

c8c4da6

- Update links to physicsnemo-curator examples in DoMINO and Transolver READMEs. - Update link to CachedDoMINODataset and path reference for cache_data.py script.

Merge branch 'main' into v2.0-refactor

9132858

CharlelieLrt self-requested a review December 8, 2025 21:40

Add xarray, timm to core deps

770589b

Alexey-Kamenev reviewed Dec 8, 2025

View reviewed changes

coreyjadams removed the request for review from CharlelieLrt December 9, 2025 17:53

coreyjadams added 5 commits December 9, 2025 12:59

update import

e07fbd2

Somehow, a number of import protections got broken

6f92470

Automatically select CPU or CPU+CUDA instead of decorating every test.

de56395

ensure te installed for serialization test

281e90c

All CPU tests are passing

289c11d

Remove DGL/PyG equivalency tests (#1273)

d07eab2

CharlelieLrt reviewed Dec 11, 2025

View reviewed changes

peterdsharpe approved these changes Dec 11, 2025

View reviewed changes

CharlelieLrt reviewed Dec 12, 2025

View reviewed changes

CharlelieLrt self-requested a review December 12, 2025 02:08

CharlelieLrt reviewed Dec 12, 2025

View reviewed changes

coreyjadams and others added 2 commits December 12, 2025 09:37

Remove TensorFlow dependency in Vortex Shedding and Lagrangian MGN ex…

ea5ab3a

…amples (#1276) * Remove TensorFlow dependency in Vortex Shedding and Lagrangian MGN examples * Update READMEs

V2.0 refactor #1235

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V2.0 refactor #1235

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PhysicsNeMo Pull Request

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coreyjadams commented Nov 19, 2025 •

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