Skip to content

Add maintenance plan, AI-assistance disclosure and paper context to the README - #4

Merged
smishra3 merged 4 commits into
mainfrom
docs/release-checklist
Nov 11, 2026
Merged

smishra3 merged 4 commits into
mainfrom
docs/release-checklist

Conversation

@smishra3

Copy link
Copy Markdown
Collaborator

What changed

  • README opening rewritten and a new What to expect section: what the model was trained on, where it generalised in the paper, where it fails (texture-like signals such as EZH2, semantic not instance), and when fine-tuning is worth it (nuclear envelope and lysosome numbers). All facts are from the manuscript PDF.
  • New Maintenance section with the checklist's "active public code" statement, who maintains and reviews, response time, release rule, planned work, and the wind-down after publication.
  • New How this code was developed section: cyto-dl origin of the model, the package as a standalone re-implementation, AI assistance disclosed, Assisted-by: trailer policy. One new RELEASE TODO: verify masks against the cyto-dl predictions.
  • CONTRIBUTING: short AI-assisted contributions section following the Institute's coding-agent guidelines. PR template: matching checklist item.
  • Existing RELEASE TODO comments are left in place.

Why

Items 1 (maintenance plan), 4 (AI usage disclaimer) and part of 5 (docs edit pass) from the public-release review. The new prose is written from the paper rather than generic, which is also the fix for the "reads AI generated" comment; please edit it into your own words where it does not sound like you.

How it was tested

Docs only. Markdown previewed locally; no code changes.

Checklist

  • Tests pass locally (pytest) (unchanged code)
  • Docs updated if behaviour or commands changed
  • CHANGELOG.md has an entry under Unreleased (not user-visible behaviour)
  • No weights, outputs or notebook outputs committed

🤖 Generated with Claude Code

smishra3 and others added 4 commits November 10, 2026 15:46
…he README

README: rewrite the opening and add "What to expect" from the manuscript
(training data, where the model generalised, where it fails, when to
fine-tune); add a Maintenance section with the active-public-code
statement, roles, response time, release and wind-down plan; add "How
this code was developed" disclosing AI assistance and the cyto-dl
origin. CONTRIBUTING gains an AI-assisted contributions section and the
PR template a matching checklist item, per the Institute's coding-agent
guidelines. Existing RELEASE TODO comments are kept.

Assisted-by: claude-code (claude-fable-5-1)
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
…tions

Assisted-by: claude-code (claude-fable-5-1)
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Assisted-by: claude-code (claude-fable-5-1)
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Assisted-by: claude-code (claude-fable-5-1)
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
@smishra3
smishra3 merged commit cd3a46a into main Nov 11, 2026
7 checks passed
@smishra3
smishra3 deleted the docs/release-checklist branch November 11, 2026 00:31
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant