The three variants

All variants share AGENTS.md, TASK.md, CHANGELOG.md, context/, standards/, diagrams/, figures/, and scripts/. They differ in the deliverable folder and in the variant-specific section of AGENTS.md.

investigation: notebook with a handful of plots

notebooks/01_analysis.ipynb
requirements.txt

  • The notebook starts with a setup cell that moves to the workspace root and imports teamplot, plus a figure-pattern cell and a “Findings” cell.

  • Each plot is followed by a markdown cell: the takeaway, then the settings line from teamplot.settings_text(settings).

  • The agent must leave the notebook runnable top to bottom (Restart & Run All).

  • Display saved figures with teamplot.figure_path(name) so human annotations win.

docs: Markdown grounded in Confluence

docs/writeup.md      Summary / Background / Details / Open questions
context/confluence-<id>-<title>.md

  • Sources are snapshotted into context/ at creation. The agent cites page titles, summarizes rather than copies, and lists gaps under “Open questions” instead of guessing.

  • Figures: ![caption](../figures/name.png) followed by an italic caption line with the settings. Run python scripts/check_figures.py before finishing.

  • The Markdown converts cleanly to Confluence, Word, or PDF with pandoc if needed.

paper: Tufte-style LaTeX

paper/main.tex           tufte-handout (article) or tufte-book (report)
paper/sections/*.tex     abstract, introduction, methods, results, conclusion
paper/references.bib
paper/.latexmkrc         finds standards/latex/, tolerates "no citations yet"

  • Typography and layout come from standards/latex/teamtufte.sty; see LaTeX papers.

  • report style adds front matter, table of contents, and chapters.

  • Build with cd paper && latexmk main.tex; the agent must leave it compiling cleanly.

../_images/handout-page2.png

A full-width figure (figure* + teamplot.figure("full")) spanning text and margin, with x/y/z colored by axis, and the bibliography appearing once something is cited.