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v0.1.5 — Quickstart rewrite, paper plan untracked

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@emcramer emcramer released this 15 May 00:08
· 36 commits to main since this release
v0.1.5
cfc563a

Highlights

This release fixes minor v0.1.4 fallout and refreshes the user-facing onboarding doc.

docs/quickstart.md

Full rewrite for the v0.1.x feature surface. Adds:

  • A runnable five-minute tour that walks through tissue generation, slicing, spatial-network construction, and CSV export. Verified end-to-end on the real package: 495 cells, 2424 edges, ~5 s.
  • A Headline workflows section pointing at replicate generation, graph coloring, the PhysiCell bridge, convergence and power analysis, MCP, and the GUI.
  • A Reproducibility note covering the v0.1.2 seed plumbing and the nan divergence semantics.

The previous quickstart was pre-v0.1.1 and only documented TissueSection.

Reference fixes from v0.1.4

docs/api/{mcp,replicate-generation,slicing,spatial-analysis}.md and docs/guides/{mcp,complete-workflow}.md had stale links to GUIDE.md / SLICING.md / SPATIAL_ANALYSIS.md / MCP_GUIDE.md / GRAPH_COLORING_GUIDE.md from before the v0.1.4 docs reorganization. All updated to point at the new docs/api/ and docs/guides/ paths.

Example config

mcp_config_claude_desktop.example.json now uses /ABSOLUTE/PATH/TO/... as a placeholder instead of a hard-coded developer path, matching the intent of the .example.json rename.

Internal-only docs

PAPER_PLAN_REPORT.md is no longer tracked. It remains on disk as a local-only paper-planning artifact and is now listed in .gitignore alongside TODO.md and REPO_SUMMARY.md.

Validation

  • 120 / 120 tests pass.
  • Result-1 demo produces identical divergence numbers as v0.1.3 / v0.1.4 (mean 0.0843, std 0.0243).
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