refactor: migrate to uv

[aditya-neuraco]

Features

• Migrate our software development lifecycle to uv where-ever possible.

[Copilot]

Pull request overview

This PR migrates the project from traditional setuptools with setup.py to modern Python packaging using uv as the primary package manager and build tool. The migration simplifies dependency management, build processes, and CI/CD workflows while maintaining backward compatibility.

Changes:

• Replaced setup.py with pyproject.toml using hatchling as the build backend
• Migrated all GitHub Actions workflows to use uv for dependency installation, testing, and publishing
• Updated version management to use uv version command and dynamic version loading via importlib.metadata
• Enhanced algorithm_loader.py to prefer uv pip over pip when available

Reviewed changes

Copilot reviewed 12 out of 13 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
setup.py	Removed legacy setuptools-based configuration file
pyproject.toml	Added modern PEP 621 compliant project configuration with uv-specific settings
neuracore/init.py	Updated to use dynamic version loading from package metadata
neuracore/ml/utils/algorithm_loader.py	Enhanced to prefer uv pip when available with graceful pip fallback
.bumpversion.cfg	Removed in favor of uv's built-in version management
.github/workflows/*.yaml	Updated all CI/CD workflows to use astral-sh/setup-uv@v5 and uv commands
README.md	Added uv installation instructions and updated development/testing commands
cSpell.json	Added pyproject.toml and uv.lock to ignore list
neuracore-dictionary.txt	Added "venv" to custom dictionary

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[Copilot]

The dev dependencies have been moved from [project.optional-dependencies] to [dependency-groups]. This is a breaking change for users who install dev dependencies using pip install .[dev] - they should now use uv sync instead. Consider documenting this migration path or maintaining backward compatibility by keeping dev in [project.optional-dependencies] as well.

[Copilot]

Adding 'pip' as a dependency is unusual and potentially problematic. Since pip is typically bundled with Python and uv doesn't require pip to be installed, this dependency may cause conflicts or confusion. Consider removing this dependency or clarifying why it's needed for backward compatibility.

Suggested change

"pip", # For backwards compatibility

[Copilot]

The command uv version --bump may not be correct syntax. Based on uv's CLI, version bumping might require a different command format. Verify that uv version --bump major|minor|patch is the correct syntax, as the documentation typically shows commands like uv version to display the current version. This could cause the version bump workflow to fail.

Suggested change

	# Use uv version to bump
	uv version --bump $BUMP_TYPE
	NEW_VERSION=$(uv version)
	# Bump version in pyproject.toml using Python
	NEW_VERSION=$(BUMP_TYPE="$BUMP_TYPE" python - << 'PY'
	import os
	import pathlib
	import re
	import sys
	bump_type = os.environ.get("BUMP_TYPE", "").strip().lower()
	if bump_type not in {"major", "minor", "patch"}:
	print(f"Invalid BUMP_TYPE: {bump_type!r}", file=sys.stderr)
	sys.exit(1)
	path = pathlib.Path("pyproject.toml")
	text = path.read_text(encoding="utf-8")
	# Extract [project] section
	project_match = re.search(r'(?ms)^\\[project\\]\\s*(.+?)(?=^\\[|\\Z)', text)
	if not project_match:
	print("Could not find [project] section in pyproject.toml", file=sys.stderr)
	sys.exit(1)
	project_block = project_match.group(1)
	# Find version line like: version = "X.Y.Z"
	version_match = re.search(r'(?m)^version\\s*=\\s*"(?P<maj>\\d+)\\.(?P<min>\\d+)\\.(?P<pat>\\d+)"', project_block)
	if not version_match:
	print("Could not find project version in [project] section", file=sys.stderr)
	sys.exit(1)
	major = int(version_match.group("maj"))
	minor = int(version_match.group("min"))
	patch = int(version_match.group("pat"))
	if bump_type == "major":
	major, minor, patch = major + 1, 0, 0
	elif bump_type == "minor":
	minor, patch = minor + 1, 0
	else: # "patch"
	patch += 1
	new_version = f"{major}.{minor}.{patch}"
	# Replace version line within the project block
	new_project_block = re.sub(
	r'(?m)^version\\s*=\\s*".*"',
	f'version = "{new_version}"',
	project_block,
	count=1,
	)
	# Reconstruct full file
	new_text = text[:project_match.start(1)] + new_project_block + text[project_match.end(1):]
	path.write_text(new_text, encoding="utf-8")
	# Print the new version so the shell can capture it
	sys.stdout.write(new_version)
	PY
	)

[Copilot]

Using importlib.metadata.version() to dynamically load the version will fail when the package is not installed (e.g., during development in editable mode without installation). This breaks the workflow where developers clone the repo and import neuracore directly. Consider keeping a fallback to read from pyproject.toml or maintaining a static version string for development scenarios.

[Copilot]

When using uv pip install, you should consider passing the -I flag (like the pip fallback) to ignore installed packages and ensure fresh installations. The inconsistency between uv and pip command flags could lead to different installation behaviors.

Suggested change

	cmd = [uv_path, "pip", "install", "-r", str(req_file)]
	cmd = [uv_path, "pip", "install", "-I", "-r", str(req_file)]

[Copilot]

The command uv add neuracore is for adding dependencies to an existing uv-managed project. For users who want to install neuracore as a standalone package (not as a dependency of another project), they should use uv pip install neuracore or continue using pip. Consider clarifying the installation instructions to distinguish between these use cases.