Temp train cleaning

[laserkelvin]

ALCHEMI Toolkit Pull Request

Description

Removes residuals

Type of Change

• Bug fix (non-breaking change that fixes an issue)
• New feature (non-breaking change that adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Performance improvement
• Documentation update
• Refactoring (no functional changes)
• CI/CD or infrastructure change

Related Issues

Changes Made

• Removes dependency from pyproject.toml
• Removes documentation mentions of feature

Testing

• Unit tests pass locally (make pytest)
• Linting passes (make lint)
• New tests added for new functionality meets coverage expectations?

Checklist

• I have read and understand the Contributing Guidelines
• I have updated the CHANGELOG.md
• I have performed a self-review of my code
• I have added docstrings to new functions/classes
• I have updated the documentation (if applicable)

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[greptile-apps]

Greptile Summary

This PR removes the training optional dependency (which pulled in nvidia-physicsnemo[datapipes-extras]>=2.0.0) from pyproject.toml and scrubs associated documentation references across README.md, docs/index.md, docs/userguide/dynamics_sinks.md, and docs/userguide/zarr_compression.md. The uv.lock is regenerated accordingly.

• The dependency removal and all documentation text changes are correct and coherent.
• A minor indentation regression was introduced in the quick-start code block of docs/userguide/zarr_compression.md (lines 24–27): core= gained an extra leading space, and both the closing ) and writer = statement ended up with a spurious single-space prefix, making the example visually misleading. A fix is suggested inline.
• CHANGELOG.md was not updated; the PR checklist item for it was left unchecked — consider adding an entry for the removal of the training extra.

Important Files Changed

Filename	Overview
pyproject.toml	Removes the training optional dependency group (which pulled in nvidia-physicsnemo[datapipes-extras]>=2.0.0); change is clean and self-contained.
README.md	Removes the pip install nvalchemi-toolkit[training] line from the optional-extras section, consistent with the dependency removal.
docs/index.md	Replaces "training data" with "simulation data" in the ML Researchers card; clean wording update.
docs/userguide/dynamics_sinks.md	Replaces three "training" references with "dynamics" / "analysis"; straightforward text cleanup with no issues.
docs/userguide/zarr_compression.md	Removes training-specific language across several sections; however the first quick-start code block has incorrect indentation introduced by this PR (5-space indent on core=, 1-space prefix on ) and writer =).
uv.lock	Lock file regenerated to reflect removal of nvidia-physicsnemo and its transitive dependencies; no issues.

_{Reviews (1): Last reviewed commit: "docs: descriptions" | Re-trigger Greptile}

[greptile-apps]

Inconsistent indentation introduced in code block

This PR changed the example path from /data/training.zarr to /data/example.zarr, but also accidentally shifted the indentation: core= now has 5 leading spaces (instead of 4) and the closing ) and writer = assignment each have a spurious leading space. The writer = line in particular visually appears to sit inside the ZarrWriteConfig(...) call. Compare with the correctly-indented Recipe 1 block at line 312.

Suggested change

	config = ZarrWriteConfig(
	core=ZarrArrayConfig(compressors=(ZstdCodec(level=3),)),
	)
	writer = AtomicDataZarrWriter("/data/training.zarr", config=config)
	core=ZarrArrayConfig(compressors=(ZstdCodec(level=3),)),
	)
	writer = AtomicDataZarrWriter("/data/example.zarr", config=config)
	config = ZarrWriteConfig(
	core=ZarrArrayConfig(compressors=(ZstdCodec(level=3),)),
	)
	writer = AtomicDataZarrWriter("/data/example.zarr", config=config)