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.

• Delete pixelator.common.annotate.aggregates (specificity_tau, call_aggregates) and the TAU_* constants.
• Drop the call_aggregates calls in the PNA graph, denoise, and sample calling paths, so new AnnData no longer carries Tau fields.
• Remove the Tau-derived aggregate metrics from GraphStatistics / GraphSampleReport and the graph report snapshot, since they were computed solely from tau_type.
• Exclude legacy tau / tau_type columns in add_missing_adata_info, which otherwise copies them from an old AnnData back into a rebuilt one during denoise and sample calling. _add_missing_adata_info in sample calling was a duplicate of that helper and now delegates to it.

Replaces #444, which was based on dev before the MPX removal in #439. The MPX portions of that branch (annotate step, --aggregate-calling CLI flag, scatter_umi_per_upia_vs_tau plot, annotate report fields) are obsolete now that the MPX tree is gone.

This branch has since been merged up to current dev. The only conflict was src/pixelator/pna/graph_legacy/connected_components.py, which #443 deleted while this branch had edited it to remove its Tau usage; resolved by accepting the deletion.

Linear: PNA-1953

Type of change

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

Existing PXL files remain readable; their stored Tau columns are simply no longer produced or propagated on rewrite.

How Has This Been Tested?

• uv run ruff format --check src tests and uv run ruff check src tests — all pass
• uv run pytest tests — 644 passed, 3 skipped, 1 failed
• The single failure is tests/cli/test_integration.py::test_command_line_interface, which is pre-existing on dev and unrelated to this PR: #443 removed the graph_legacy CLI command but left it listed in that test's expected commands. It reproduces identically (AssertionError: graph_legacy) on an unmodified dev checkout, so it is not fixed here.
• Assertions were added that newly written AnnData omits tau, tau_type, and tau_thresholds in tests/common/data_generator/test_pixelfile.py and tests/pna/denoise/test_denoise.py, plus a regression test that add_missing_adata_info does not restore legacy Tau columns.

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
• I have checked my code and documentation and corrected any misspellings

  

[cursor]

Cursor Bugbot has reviewed your changes using high effort and found 1 potential issue.

^{❌ Bugbot Autofix is OFF. To automatically fix reported issues with cloud agents, enable autofix in the Cursor dashboard.}

^{Reviewed by Cursor Bugbot for commit 19ee885. Configure here.}