build(deps): bump idc-index 0.13.1 -> 0.13.3 (idc-index-data 25.0.4)

[fedorov]

Summary

Bumps the exact idc-index pin to 0.13.3, which pulls idc-index-data 25.0.4. Still IDC v25; collection, series and size totals are unchanged (179 collections, 1,044,191 series, 99.94 TB).

What 25.0.2–25.0.4 change for this server:

• NULL, not '' (idc-index-data#185): index.PatientAge (360 rows), index.SeriesDescription (4), pt_index.SeriesType, collections_index.supporting_data, clinical_index.column_label. SQL testing = '' must test IS NULL. get_clinical_table_schema already maps a NULL column_label to "".
• Descriptions (#146, #183, #186): 19 columns that came through with no description now have one; analysis_result_id and seg_index.segmented_SeriesInstanceUID describe their NULLs. The analysis_result_id fix is the description part of Cohort filters cannot express "original data only" #43.
• volume_geometry_index (#182) adds origin_patient, ImageOrientationPatient, slice_spacing_mm.

Changes

• pyproject.toml — pin idc-index==0.13.3 (+ comment)
• uv.lock — only idc-index / idc-index-data change
• src/idc_api/rest/app.py — /v3/version OpenAPI example → 25.0.4
• dev/deployment.md — example pin
• CHANGELOG.md — Changed and Fixed entries under [Unreleased]

Test plan

• uv sync --locked --extra dev, ruff check, ruff format --check
• uv run pytest tests -q — 112 passed
• Compared the bundled schemas and index stats of 25.0.1 vs 25.0.4 (the figures above)

🤖 Generated with Claude Code

[Copilot]

🟢 Approval recommended

The dependency references are consistent, existing consumers handle the affected NULL values, and no blocking issues remain.

No open issues 🎉

What changed in this PR

Updates the API and MCP server’s bundled index data to 25.0.4 while retaining IDC v25 and unchanged dataset totals.

Changes:

• Pins idc-index to 0.13.3 and updates the lockfile.
• Documents NULL normalization, improved descriptions, and new geometry columns.
• Aligns version examples with the updated dependencies.

File	Description
uv.lock	Locks the updated index and data packages.
src/​idc_api/​rest/​app.py	Updates the OpenAPI version example.
pyproject.toml	Updates the exact dependency pin and explanatory comment.
dev/​deployment.md	Refreshes the example dependency pin.
CHANGELOG.md	Records user-visible data and schema changes.

_{Review effort: Balanced}