Added pre-commit and CI

[jjomier]

Added pre-commit script and fixing linting errors

[greptile-apps]

Greptile Summary

Adds pre-commit hooks and CI workflow to enforce code quality standards, along with automated linting fixes across 46 files. The changes introduce ruff for Python linting/formatting and markdownlint for documentation, then apply those tools to fix existing style issues including import ordering, modern type hints, trailing whitespace, and markdown formatting.

Confidence Score: 5/5

• This PR is safe to merge with minimal risk
• All changes are automated linting/formatting fixes that don't alter logic. The new CI infrastructure follows best practices and will prevent future style inconsistencies
• No files require special attention

Important Files Changed

Filename	Overview
.pre-commit-config.yaml	New pre-commit configuration with standard hooks for trailing whitespace, file formatting, YAML/JSON validation, ruff for Python linting/formatting, and markdownlint
.github/workflows/ci.yml	New CI workflow that runs pre-commit checks on pushes and PRs to main branch
pyproject.toml	New ruff configuration targeting Python 3.11, 150 char line length, standard linting rules with E501 ignored
.markdownlint.yaml	New markdownlint configuration with relaxed line length (700 chars) to accommodate existing docs
README.md	Formatting fixes: trailing whitespace removed, image syntax converted from HTML to markdown, blank lines normalized
NV-Segment-CT/scripts/trainer.py	Import reordering per ruff standards (collections.abc imports separated from typing), minor line reformatting
NV-Segment-CTMR/brain_t1_preprocess/intensity_normalization/normalize/base.py	Import reordering, modern type hints (typing.Optional →
NV-Segment-CT/docs/README.md	Markdown formatting improvements: added blank lines between sections, improved link syntax, better heading hierarchy, code block language tags

_{Last reviewed commit: 5938a58}

[greptile-apps]

_{46 files reviewed, 4 comments}

_{Edit Code Review Agent Settings | Greptile}

[greptile-apps]

Comment references NV-Generate-CTMR but the repository is nv-segment-ctmr

Suggested change

	# Pre-commit hooks for NV-Generate-CTMR
	# Pre-commit hooks for NV-Segment-CTMR

[greptile-apps]

Comment references NV-Generate-CTMR but the repository is nv-segment-ctmr

Suggested change

	# CI for NV-Generate-CTMR: lint and format checks via pre-commit
	# CI for NV-Segment-CTMR: lint and format checks via pre-commit

[greptile-apps]

Comment references NV-Generate-CTMR but the repository is nv-segment-ctmr

Suggested change

	# Minimal config for tooling (pre-commit, ruff). NV-Generate-CTMR has no installable package.
	# Minimal config for tooling (pre-commit, ruff). NV-Segment-CTMR has no installable package.

[greptile-apps]

Comment references NV-Generate-CTMR but the repository is nv-segment-ctmr

Suggested change

	# Markdownlint config for NV-Generate-CTMR
	# Markdownlint config for NV-Segment-CTMR

[greptile-apps]

_{46 files reviewed, no comments}

_{Edit Code Review Agent Settings | Greptile}