Remove Tau from Pixelator

[johandahlberg]

Description

Remove the retired Tau aggregate-calling implementation from Pixelator and stop writing tau, tau_type, and tau_thresholds to newly generated AnnData objects. Prevent legacy Tau observation fields from being restored when denoise or sample calling rebuilds AnnData. Remove the associated CLI option, plotting API, report metrics, and tests/snapshots.

Linear: PNA-1953

Type of change

• Breaking change (fix or feature that would cause existing functionality to not work as expected)

How Has This Been Tested?

• uv run ruff format --check src tests
• uv run ruff check src tests
• 92 focused tests across AnnData generation, MPX annotation/plotting, PNA denoising, graph recovery/reporting, legacy graph generation, and sample calling: 90 passed, 2 skipped
• 31 follow-up tests for legacy Tau cleanup, sample calling, and denoising: all passed

PR checklist:

• This comment contains a description of changes (with reason).
• I have performed a self-review of my own code
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• If a new tool or package is included, I have updated dependencies in pyproject.toml and cited it properly (not applicable)
• I have checked my code and documentation and corrected any misspellings