[WIP] Fix quick setup issues in code

[Copilot]

Summary

Fixed the setup_dev.sh script to properly handle pre-commit installation from requirements-dev.txt.

Changes Made:

• Updated grep pattern in setup_dev.sh to include both 'sphinx' and 'pre-commit' packages (line 64)
• Added error handling if pre-commit command is not available after installation attempt (lines 76-85)
• Improved error and info messages to accurately reference requirements-dev.txt
• Investigated CI failures - found pre-existing mypy type annotation errors (214 errors unrelated to setup script changes)
• Replied to user explaining the fix and CI failure root cause
• Completed code review with no outstanding issues
• Verified no security vulnerabilities introduced

CI Failures Note:

The pre-commit CI workflow is failing due to 214 pre-existing mypy type annotation errors in test files, examples, and benchmarks. These errors existed before this PR and are caused by disallow_untyped_defs = true in pyproject.toml. The setup script changes are correct and address the issues identified in code review comments.

Security Summary:

No security vulnerabilities were introduced or discovered during this change.

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[Copilot]

Pull request overview

This PR fixes the setup_dev.sh script to properly handle pre-commit installation and improves error handling when pre-commit is unavailable after installation attempts.

Key Changes:

• Updated the grep pattern to extract both sphinx and pre-commit dependencies from requirements-dev.txt
• Added conditional check with error handling when pre-commit command is not available
• Cleaned up trailing whitespace in CONTRIBUTING.md and setup_dev.bat

Reviewed changes

Copilot reviewed 2 out of 3 changed files in this pull request and generated 2 comments.

File	Description
setup_dev.sh	Updated dependency extraction logic to include pre-commit, renamed variables for clarity, and added error handling for missing pre-commit command
setup_dev.bat	Removed trailing newline
CONTRIBUTING.md	Removed trailing whitespace on line 193

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[Copilot]

The error handling assumes that pre-commit should have been installed from requirements-dev.txt, but the script only attempts to install it if requirements-dev.txt exists AND contains a line matching the grep pattern. If requirements-dev.txt doesn't exist or doesn't contain pre-commit, the error message will be misleading. Consider checking if requirements-dev.txt exists and contains pre-commit before assuming it should have been installed from there.

Suggested change

	echo "This should have been installed from requirements-dev.txt."
	echo "Please ensure pre-commit is listed in requirements-dev.txt or install it manually:"
	echo " pip install pre-commit"
	if [ -f "requirements-dev.txt" ] && grep -q -E '^[[:space:]]*pre-commit' requirements-dev.txt; then
	echo "pre-commit appears to be listed in requirements-dev.txt but was not installed."
	echo "You may need to rerun this script or install it manually:"
	echo " pip install pre-commit"
	else
	echo "pre-commit is not installed and does not appear to be listed in requirements-dev.txt."
	echo "Please add pre-commit to your development dependencies (e.g., requirements-dev.txt) or install it manually:"
	echo " pip install pre-commit"
	fi

[Copilot]

The exit 1 here will terminate the script if pre-commit is not available, which may be too strict. If pre-commit is truly optional or can be installed later, consider making this a warning instead of a fatal error. Alternatively, the script could attempt to install pre-commit directly if it's missing.

Suggested change

	echo "❌ Error: pre-commit is not installed in this environment."
	echo "This should have been installed from requirements-dev.txt."
	echo "Please ensure pre-commit is listed in requirements-dev.txt or install it manually:"
	echo " pip install pre-commit"
	exit 1
	echo "⚠️ Warning: pre-commit is not installed in this environment."
	echo " Pre-commit hooks will not be installed automatically."
	echo " To enable pre-commit hooks, ensure 'pre-commit' is listed in requirements-dev.txt"
	echo " or install it manually in this environment with:"
	echo " pip install pre-commit"