Migrate to uv as primary package manager for Python

[JohT]

🚀 Feature

• ⚠️ Breaking: Use uv as primary package manager for Python: Switch default Python package manager to uv; update scripts, workflows, and add uv.lock.

⚙️ Optimization

• Add instructions for renovate.json: Add usage instructions for renovate.json and update related docs.

🛠 Fix

• Reintroduce package to run Jupyter notebooks: Restore required notebook package in environment/requirements so Jupyter notebooks run.

• Fix plotly kaleido orjson type issues: Resolve typing issues for plotly/kaleido and orjson in visualization scripts.

[Copilot]

Pull request overview

This PR migrates the pipeline’s Python environment management from requirements.txt/venv-first workflows to uv using pyproject.toml + uv.lock, while keeping Conda as an optional supported path. It updates activation scripts, CI workflows, Renovate config, and documentation to align with the new dependency source of truth.

Changes:

• Introduces pyproject.toml + uv.lock and removes requirements.txt, making uv the default Python environment path.
• Adds activateUvEnvironment.sh and updates report compilation + compatibility checks to use uv (with Conda still supported via PYTHON_PACKAGE_MANAGER=conda).
• Updates GitHub workflows (new uv/conda checks; public reusable workflow gets a new python-package-manager input) plus docs and Renovate rules.

Reviewed changes

Copilot reviewed 19 out of 21 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
scripts/reports/compilations/PythonReports.sh	Switch Python report environment activation from venv script to uv activation script.
scripts/checkCompatibility.sh	Update compatibility checks to reflect uv/conda environment options and remove standalone python/pip requirements.
scripts/activateUvEnvironment.sh	Add uv-based environment sync + .venv activation (cross-platform).
scripts/activatePythonEnvironment.sh	Remove venv-based activation script.
scripts/activateCondaEnvironment.sh	Gate Conda activation behind PYTHON_PACKAGE_MANAGER=conda and document deprecation of old var.
requirements.txt	Delete legacy pip requirements file.
renovate.json	Switch Renovate’s “stable Python versions” rule to use the uv manager; enable conda env regex updates.
README.md	Document uv as primary Python manager; Conda as optional path with PYTHON_PACKAGE_MANAGER=conda.
pyproject.toml	Add canonical Python dependency list and uv tool section.
conda-environment.yml	Sync versions/packages with pyproject.toml (e.g., pandas, neo4j) and update header note.
COMMANDS.md	Add uv setup instructions and keep Conda setup path.
AGENTS.md	Update instruction applicability table to reference pyproject.toml instead of requirements.txt.
.github/workflows/public-analyze-code-graph.yml	Add python-package-manager input and uv setup step; pass PYTHON_PACKAGE_MANAGER into analysis.
.github/workflows/internal-typescript-code-analysis.yml	Remove requirements.txt path override from workflow triggers.
.github/workflows/internal-java-code-analysis.yml	Remove requirements.txt path override from workflow triggers.
.github/workflows/internal-check-python-venv-support.yml	Remove obsolete venv environment check workflow.
.github/workflows/internal-check-python-uv-support.yml	Add CI check that uv sync --frozen works and key imports succeed.
.github/workflows/internal-check-conda-support.yml	Add CI check for Conda environment activation + key imports.
.github/prompts/plan-uvAsPrimaryPackageManager.prompt.md	Add implementation plan for the migration (prompt/documentation artifact).
.github/instructions/python-dependencies.instructions.md	Update dependency conventions: pyproject.toml canonical; uv/conda verification steps.

[Copilot]

Pull request overview

Copilot reviewed 23 out of 25 changed files in this pull request and generated 9 comments.