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Draft JOSS paper for ZnDraw#910

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PythonFZ wants to merge 5 commits intomainfrom
feature/joss-paper-design
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Draft JOSS paper for ZnDraw#910
PythonFZ wants to merge 5 commits intomainfrom
feature/joss-paper-design

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@PythonFZ PythonFZ commented Apr 2, 2026

Summary

  • Adds paper/paper.md and paper/bibliography.bib following JOSS format
  • Covers: Summary, Statement of Need, State of the Field, Software Design, Features & Implementation, Related Software
  • ~1100 words, within JOSS 750–1750 limit
  • Design spec at docs/superpowers/specs/2026-04-02-joss-paper-design.md

TODOs

  • Rokas ORCID and affiliation
  • molify DOI (pending JOSS publication)
  • MolecularWebXR DOI (verify)
  • Figure (paper/zndraw_ui.png) — composite screenshot of browser UI
  • AI usage disclosure sentence
  • Rokas funding acknowledgement
  • Verify code snippets run against current API
  • CONTRIBUTING.md and CODE_OF_CONDUCT.md (JOSS review requirement)

🤖 Generated with Claude Code

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coderabbitai bot commented Apr 2, 2026

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PythonFZ and others added 5 commits April 2, 2026 13:49
Replace the shared-password model for the internal worker user with
per-task JWT tokens minted at dispatch time, eliminating the well-known
default credential that grants superuser access on unpatched deployments.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Rely on fastapi-users' built-in "user already exists" rejection for
registration — a custom guard is YAGNI.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Section-by-section design for a ZnDraw JOSS submission covering
summary, statement of need, state of the field, software design,
features/implementation, and related software.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Initial paper.md and bibliography.bib following JOSS format.
Covers summary, statement of need, state of the field, software
design, features/implementation, and related software sections.

TODOs remaining:
- Rokas ORCID and affiliation
- molify DOI (pending publication)
- MolecularWebXR DOI
- Figure (zndraw_ui.png)
- AI usage disclosure

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@PythonFZ PythonFZ force-pushed the feature/joss-paper-design branch from 03c8fe2 to 4355ece Compare April 2, 2026 11:50
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.68%. Comparing base (06cab0d) to head (4355ece).
✅ All tests successful. No failed tests found.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #910      +/-   ##
==========================================
- Coverage   91.78%   91.68%   -0.11%     
==========================================
  Files         246      246              
  Lines       22881    22881              
==========================================
- Hits        21001    20978      -23     
- Misses       1880     1903      +23     

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2 participants