UV <---> Pip must stay in sync.

[coreyjadams]

This PR is about dependencies and installation. Goals:

• Ensure uv is first-class
• Ensure pip install works
• Ensure default deps are broadly available and won't hold up other pieces.

To this end, the core deps are listed, and there is linting against them. We can't import non-core deps "bare" any more.

Further, optional deps are almost* entirely protected with check_version_spec, etc., to raise runtime errors at first use only. Meaning, a missing dep will not break the rest of the code, and won't even crash until a user attempts to use it. And I've tried to list out the optional deps per package, too, though some could use versioning.

Everything below is outdated. I left it to show the original design.

Ensure that the pip dependency group exclusively matches the resolution of the dependency-groups from Pep 735 that uv enables.

Requirements are to ensure pip install . still works, with or without uv, even though we want uv to be the sole source of truth. Rather than maintaining two dep lists, especially since one is nested, I made a pre-commit step to ensure that the pip requirements is always exactly what dependency-groups specifies.

Basically, the workflow is this:

• pre-commit will run test/ci_tests/sync_deps.py
• sync_deps.py ingests the pyproject.yaml file.
  • It recurses through the physicsnemo dependency group (no extras) and resolves all the groups and dependencies.
  • It generates a flat list of dependencies.
  • De-duplication is automatic, and if the version strings don't agree it's an error.
• Then:
  • If the list agrees, PASS
  • If the list disagrees, it will overwrite the dependency section of pyproject.toml and fail pre-commit.

This should achieve the following:

• if dependency-group dependencies update, we will be unable to commit that code to the repo unless the pip install . dependencies also update.
• If the pip dependencies update, that update will be destroyed automatically.

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.

Dependencies

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[greptile-apps]

Greptile Overview

Greptile Summary

This PR introduces a pre-commit hook and script to automatically synchronize project.dependencies with the dependency-groups defined in pyproject.toml, ensuring PEP 735 compliance with uv's dependency resolution.

• Added sync_deps.py script that resolves the utils dependency group using DFS traversal, detects cycles, validates version consistency, and auto-generates the dependencies list
• Added pre-commit hook to run this script on every commit, failing if dependencies need updating
• Fixed a bug in the physicsnemo group that referenced domain-parallel (hyphen) instead of the actual group domain_parallel (underscore)
• Restructured dependency hierarchy: models now includes domain_parallel instead of nn directly, and physicsnemo includes models instead of the broken domain-parallel reference

Important Files Changed

File Analysis

Filename	Score	Overview
test/ci_tests/sync_deps.py	4/5	New script that auto-generates project.dependencies from dependency-groups, with DFS resolution and cycle detection. Shebang placement is non-standard but functional.
pyproject.toml	5/5	Fixed broken domain-parallel reference (was missing underscore), added auto-generated dependencies section, and restructured dependency group hierarchy.
.pre-commit-config.yaml	5/5	Added new sync-deps pre-commit hook that runs sync_deps.py on every commit.

[greptile-apps]

_{3 files reviewed, 1 comment}

_{Edit Code Review Agent Settings | Greptile}

[greptile-apps]

style: Shebang line should be at line 1 to work when executing the script directly. Currently it's after the license header, which means ./sync_deps.py won't work, only python sync_deps.py. This is fine since the pre-commit hook calls it via python, but worth noting for consistency.

[pzharrington]

No natten? 😅

[coreyjadams]

We should add it! But unless it's easy to install cross-platform, it needs to go into an optional dep.

[pzharrington]

nn-extras here is optional right? Natten should def be optional regardless, but I think nn-extras is the right place for it

[pzharrington]

It seems the gnns and healpix here are more just general deps groups associated with certain functionality/use-cases but not a part of the base pnm subpackages (nn, models, datapipes ...). Maybe separate them out with a small comment header for clarity? Like

# Use-case Specific Dependency Groups

or something...

[pzharrington]

May want to look at the earth2studio toml to see the various things Nick added to handle earth2grid...I think there is also a need to include --no-build-isolation

[coreyjadams]

Relevant lines appear to be:

no-build-isolation-package = ["earth2grid", "flash-attn", "torch-harmonics"]

[tool.uv.extra-build-dependencies]
earth2grid = ["setuptools", "torch"]

[tool.uv.sources]
...
earth2grid = { git = "https://github.com/NVlabs/earth2grid.git", rev = "661445e2c68edc76f52632aa0528af482357f1b8" }

I can add the missing pieces, though I suspect we don't need to lock to a revision.

[pzharrington]

Yeah I need to double check with Nick when he's back why he pinned version, it may have just been out of "abundance of caution" :)