generate_plate_overview() core function (PR2 of #7)

[ferrinm]

Closes #9. Part of #7.

Summary

• New module src/pyphenix/_overview.py exposing generate_plate_overview(). No napari/Qt imports.
• Produces 2**N − 1 PNGs (one per channel combo) plus a JSON provenance sidecar.
• Plate-wide per-channel contrast: 99.5th percentile of nonzero, downsampled, max-projected pixels — single pass through the wells (per ADR-0001).
• Singletons rendered in viridis; merges use each channel's colormap from _colormaps.channel_color with additive RGB blending.
• Layout: title (plate ID + combo) and objective subtitle on top, plate grid with row-letter and column-number labels, per-channel colorbars stacked on the right, scale bar in µm at the bottom.
• matplotlib and tqdm added to base dependencies; generate_plate_overview exported from the package.
• README usage example added under the headless install section.

Test plan

• tests/test_overview.py — 9 new tests covering:
  • combo count (2^N − 1) and JSON sidecar presence
  • filename conventions (ch{X}.png, ch{X}+ch{Y}.png, merge_all.png)
  • JSON sidecar contents (plate ID, layout, computed contrast limits, channel colormaps, channel names, objective, pyphenix version, pixel size)
  • channels= filter constrains the combo set
  • contrast_limits= override is applied and recorded in the sidecar
  • PNGs are non-empty
  • _overview.py source contains no import napari / from napari
  • module imports correctly in a subprocess with napari blocked at sys.meta_path
  • empty wells still produce all PNGs (blank cell + labels render)
• Full suite passes: 51 passed (9 new + 42 existing)
• Manual visual check of generated PNGs on a real Phenix experiment before merge

🤖 Generated with Claude Code