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name: publication-chart-skill
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description: This skill should be used when the user asks for a publication-quality scientific figure or table, wants help choosing the right chart for results, needs a paper-ready pubfig or pubtab workflow, wants a figure + companion table for a results section, wants an Excel sheet turned into publication-ready LaTeX, or wants an existing scientific figure/table reviewed and upgraded.
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version: 0.2.0
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---
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# Publication Chart Skill
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## Goal
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Use this skill to turn research results into **publication-grade figures and tables** with an end-to-end workflow.
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Primary production stack:
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- **`pubfig`** for figures
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- **`pubtab`** for publication tables
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This skill covers the full delivery chain:
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1. understand the scientific communication goal,
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2. choose the right artifact type,
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3. map the task to `pubfig`, `pubtab`, or both,
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4. generate concrete runnable instructions,
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5. export paper-ready assets,
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6. run publication QA,
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7. propose targeted revisions.
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## Use this skill when
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Trigger this skill for requests like:
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- “make a publication-quality figure”
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- “choose the right chart for these results”
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- “turn these results into a paper-ready figure”
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- “make a benchmark / ablation / calibration / forest / heatmap / scatter / line / bar figure”
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- “make a benchmark / appendix / ablation table from Excel”
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- “convert this Excel table into publication-ready LaTeX”
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- “prepare one summary figure plus one companion table for the results section”
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- “review and improve this scientific figure/table”
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- “I already have a weak chart / screenshot / draft plot — make it publication-ready”
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- “export panels for a paper figure”
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## Do not use this skill for
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Do **not** use this skill when the task is mainly:
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- manuscript prose writing,
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- statistical testing without artifact design,
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- raw exploratory analysis with no publication deliverable,
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- Figma-first layout work before the figure/table content is solid.
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For simple composite assembly after the figure content is already strong, use the optional secondary workflow in `references/composite-assembly.md`.
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## Primary contract
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### Inputs
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Expect some combination of:
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- the scientific communication goal,
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- available data shape,
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- venue or style constraints,
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- whether the artifact is a figure, table, or mixed deliverable,
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- optional existing assets such as code, spreadsheets, `.tex`, screenshots, or draft plots,
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- whether the user needs a first draft, a publication-ready artifact, or a review/revision pass.
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### Outputs
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The minimum useful output is:
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- the recommended figure/table form,
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- the recommended `pubfig` / `pubtab` route,
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- a minimal runnable code snippet or CLI command,
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- explicit export filenames and formats,
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- a publication QA summary,
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- and, when needed, a revision plan.
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## Default workflow
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### 0. Probe the environment and artifact state
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Before generating anything, identify:
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- whether `pubfig` or `pubtab` is actually available,
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- whether the user already has code / spreadsheets / `.tex` / screenshots,
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- whether the deliverable is a fresh build or a revision,
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- whether the result needs exact values, fast visual perception, or both.
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Prefer the smallest environment check that helps execution. When the bundled helper script is available, use it first:
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- `python3 scripts/ensure_publication_tooling.py --require pubfig --json`
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- `python3 scripts/ensure_publication_tooling.py --require pubtab --json`
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Equivalent manual checks are still acceptable when needed:
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- `python -c "import pubfig; print(pubfig.__version__)"`
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- `python -c "import pubtab; print(pubtab.__version__)"`
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- `pubtab --help`
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Report the result clearly as **available** or **missing**.
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If a dependency is missing and the task requires runnable execution:
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- **auto-install it by default**,
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- prefer the user’s active environment instead of guessing a random global interpreter,
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- use `python3 scripts/ensure_publication_tooling.py --require ...` as the default bundled route when the script is present,
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- let that helper choose `uv` vs `python -m pip` against the active interpreter,
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- re-run the availability probe after installation,
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- and only then continue with the artifact workflow.
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Equivalent concrete commands include:
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- `python3 scripts/ensure_publication_tooling.py --require pubfig`
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- `python3 scripts/ensure_publication_tooling.py --require pubtab`
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- `uv pip install pubfig`
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- `uv pip install pubtab`
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- `python -m pip install pubfig`
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- `python -m pip install pubtab`
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If auto-install fails, report the exact failure and then degrade gracefully.
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Do not block on a full environment audit.
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### 1. Classify the task
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Classify the request along these axes:
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- **artifact type**: figure / table / mixed deliverable
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- **maturity**: exploratory draft / publication-ready generation / revision of an existing artifact
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- **structure**: single panel / multi-panel / figure-plus-table package
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- **evidence mode**: pattern perception / exact value lookup / both
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Do not jump into plotting code before the communication target is clear.
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Before plotting research results, lock the evidence contract:
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- primary scientific claim,
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- unit of analysis,
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- primary metric and metric direction,
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- whether repeated rows are independent,
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- missing cells or incomplete comparison blocks,
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- error-bar basis: subject, subject-task, fold, seed, run, or bootstrap sample,
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- whether exact values need a companion table,
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- whether the current evidence allows a winner/significance claim.
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If these are unclear, ask or produce an audit recommendation instead of a polished figure. Do not create a paper-ready plot while the unit of analysis, missing-cell handling, or error-bar basis is unresolved.
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### 2. Choose the representation
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Choose the representation based on the scientific claim, not novelty or visual flair.
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Common families:
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- **comparison** — grouped scatter, bar, line comparison, benchmark summary, companion table
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- **ablation** — grouped comparison, dumbbell, paired comparison, compact table
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- **distribution** — box, violin, raincloud, histogram, density, ECDF, QQ
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- **relationship** — scatter, bubble, contour2d, hexbin
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- **trend** — line, area
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- **evaluation / diagnostic** — calibration, ROC, PR, Bland–Altman, forest plot, volcano
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- **composition / hierarchy** — UpSet, stacked ratio, donut, radial hierarchy, circular grouped or stacked bars
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- **table** — benchmark table, ablation table, dataset summary, appendix table, error breakdown
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Avoid weak defaults:
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- avoid pie/donut when exact comparison matters and a bar/table is clearer,
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- avoid radar unless the comparison is genuinely profile-like and low-cardinality,
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- avoid 3D, decorative gradients, and dense legends used only for style,
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- avoid forcing every result into a figure when a publication table communicates the evidence better.
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If the request is ambiguous, explicitly state what scientific claim the artifact is supposed to support.
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### 3. Map to the toolchain
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Default mapping:
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- **Figures** → `pubfig`
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- **Tables** → `pubtab`
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- **Mixed deliverables** → use both, with each artifact carrying a distinct role
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Tool roles:
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- `pubfig` is the default figure engine for scientific plots and paper-ready export.
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- `pubtab` is the default table engine for Excel ↔ LaTeX workflows, preview, and publication-ready table export.
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- Figma/composite assembly is an **optional secondary branch** for multi-panel finishing.
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Route selection rules:
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- prefer **Python** for `pubfig` figure generation,
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- prefer **CLI** for `pubtab` when the task is file-driven,
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- prefer **Python** for `pubtab` when the task is already inside a notebook or scripted pipeline,
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- keep the figure and table responsibilities separate in mixed requests.
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### 4. Generate concrete artifact instructions
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Prefer the smallest production-ready artifact first:
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- minimal runnable Python for `pubfig`, or
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- minimal CLI/Python for `pubtab`
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Then add publication parameters only when justified:
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- labels, caption, width, export format, backend, preview, panel packaging, or composite layout.
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Keep filenames and suffixes explicit.
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Good defaults:
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- figures: one `pubfig` call + one `save_figure(...)`
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- multiple figure outputs: `batch_export(...)`
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- tables: one `pubtab xlsx2tex ...` or `pubtab.preview ...`
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- mixed requests: one figure route + one table route, clearly separated
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### 5. Define the delivery contract
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For every response, make these explicit when possible:
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- the claim the artifact supports,
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- which part is handled by `pubfig` and which by `pubtab`,
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- the output filenames,
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- the output formats,
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- whether the artifact is draft / final / revision,
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- what still needs user-provided data or manuscript context.
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### 6. Run publication QA
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After generation, check:
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- title and legend density,
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- axis labels and units,
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- category ordering and baseline clarity,
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- color accessibility and grayscale robustness,
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- font / line-weight consistency,
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- caption readiness,
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- figure/table readability after downscaling,
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- panel consistency for multi-panel figures,
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- venue-fit issues such as width, crowding, or over-annotation.
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The QA output must be concrete. Do not say “looks better” without naming why.
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### 7. Revise
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If the result is weak, revise with specific changes such as:
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- switch chart family,
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- remove chartjunk,
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- reorder categories,
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- move exact values into a table,
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- split a crowded panel,
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- add or simplify the caption,
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- change export width,
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- or convert the deliverable from figure-first to table-first.
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## Missing dependency behavior
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If `pubfig` or `pubtab` is not available:
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- do **not** fail immediately,
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- first attempt automatic installation into the active environment,
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- prefer `python3 scripts/ensure_publication_tooling.py --require ...` when the bundled script exists,
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- explicitly state which dependency is missing,
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- state which install command or helper route is being used,
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- re-check availability after installation,
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- if installation succeeds, continue with the runnable workflow,
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- if installation fails, degrade to a design/specification workflow,
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- provide pseudocode or draft commands,
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- preserve the recommended figure/table structure,
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- still provide QA and revision guidance.
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## Composite assembly rule
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Treat composite or Figma assembly as **secondary**:
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- use it when the user explicitly wants a multi-panel paper figure,
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- or when panel-level export and layout polishing are genuinely needed.
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Do not escalate simple figure tasks into composite/Figma workflows by default.
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## Output style rules
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- Prefer direct, implementation-usable outputs.
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- Explain the **why** of chart/table choice briefly, then give the runnable route.
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- When execution matters, include a short environment status block such as `pubfig: available/missing`, `pubtab: available/missing`.
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- If a dependency is missing, state the exact helper command or install command, perform the installation, and report the post-install status.
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- When a table is stronger than a figure, say so explicitly.
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- When a figure is stronger than a table, say so explicitly.
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- When both are needed, assign them different communication roles.
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- Keep revision guidance actionable and falsifiable.
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## Recommended response shape
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A strong response using this skill usually has 6 parts:
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1. **Artifact decision** — figure / table / paired deliverable, and why
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2. **Tool route** — `pubfig`, `pubtab`, or both
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3. **Minimal implementation** — runnable code or CLI
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4. **Export plan** — filenames, formats, width/backend/preview choices
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5. **Publication QA** — what to verify before paper submission
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6. **Revision plan** — what to change if the current artifact is weak
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## Resources
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Load these as needed:
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- `references/workflow.md` — full end-to-end decision order and delivery contract
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- `references/chart-selection.md` — task-to-chart mapping and anti-patterns
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- `references/execution-and-verification.md` — environment probing, forced install behavior, and runnable verification
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- `scripts/ensure_publication_tooling.py` — bundled probe + auto-install helper for `pubfig` / `pubtab`
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- `references/pubfig-recipes.md` — shortest useful figure patterns and export routes
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- `references/pubtab-recipes.md` — shortest useful table routes and backend guidance
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- `references/source-guides/pubfig-architecture.md` — package layout and figure-generation boundaries from source
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- `references/source-guides/pubfig-api-map.md` — stable public pubfig surface and chart-family map from `__init__.py`
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- `references/source-guides/pubfig-export-flow.md` — figure export, publication sizing, and panel-export flow from source
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- `references/source-guides/pubtab-architecture.md` — package layout and forward/reverse conversion architecture from source
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- `references/source-guides/pubtab-cli-api-flow.md` — CLI-to-API control flow and batch/sheet behavior from source
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- `references/source-guides/pubtab-backend-and-preview.md` — backend/theme split and real preview compile pipeline from source
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- `references/publication-qa-checklist.md` — figure/table QA checklist
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- `references/composite-assembly.md` — optional multi-panel and Figma branch
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For prompt-shaped examples, see `examples/`.
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