medsci-skills 4.1.0

package/skills/render-pdf-doc/scripts/infer_colwidths.py

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+#!/usr/bin/env python3
+"""
+infer_colwidths.py — Replace pandoc pipe-table separator rows with dash-ratios
+proportional to per-column content width.
+
+Pandoc pipe tables interpret the dash count in the separator row as relative
+column widths (when the total exceeds the line width). This script replaces:
+
+    | Label | Long data column            | Other |
+    |-------|-----------------------------|-------|
+
+with widths derived from the maximum display-width of header + cells per column.
+CJK glyphs count as 2 cells (East-Asian wide), ASCII as 1.
+
+Usage:
+    python infer_colwidths.py input.md [--out output.md] [--min 5] [--total 80]
+
+If --out is omitted, writes to stdout.
+"""
+from __future__ import annotations
+
+import argparse
+import re
+import sys
+import unicodedata
+from pathlib import Path
+
+
+def display_width(s: str) -> int:
+    """East-Asian-aware char width. Wide/Fullwidth = 2, else = 1."""
+    w = 0
+    for ch in s:
+        if unicodedata.east_asian_width(ch) in ("W", "F"):
+            w += 2
+        else:
+            w += 1
+    return w
+
+
+SEPARATOR_RE = re.compile(r"^\s*\|?[\s:\-|]+\|[\s:\-|]+\s*$")
+PIPE_ROW_RE = re.compile(r"^\s*\|.*\|\s*$")
+
+
+def split_row(line: str) -> list[str]:
+    s = line.strip()
+    if s.startswith("|"):
+        s = s[1:]
+    if s.endswith("|"):
+        s = s[:-1]
+    return [c.strip() for c in s.split("|")]
+
+
+def is_separator(line: str) -> bool:
+    if not SEPARATOR_RE.match(line):
+        return False
+    cells = split_row(line)
+    if len(cells) < 2:
+        return False
+    for c in cells:
+        if not re.match(r"^:?-{3,}:?$", c.strip()):
+            return False
+    return True
+
+
+def parse_alignment(sep_cell: str) -> str:
+    s = sep_cell.strip()
+    left = s.startswith(":")
+    right = s.endswith(":")
+    if left and right:
+        return "center"
+    if right:
+        return "right"
+    if left:
+        return "left"
+    return "default"
+
+
+def make_separator(widths: list[int], aligns: list[str]) -> str:
+    parts = []
+    for w, a in zip(widths, aligns):
+        body = "-" * max(3, w)
+        if a == "center":
+            cell = ":" + body[1:-1] + ":" if len(body) >= 3 else ":-:"
+        elif a == "left":
+            cell = ":" + body[1:] if len(body) >= 2 else ":--"
+        elif a == "right":
+            cell = body[:-1] + ":" if len(body) >= 2 else "--:"
+        else:
+            cell = body
+        parts.append(cell)
+    return "| " + " | ".join(parts) + " |"
+
+
+def find_table_blocks(lines: list[str]) -> list[tuple[int, int, int]]:
+    """Return list of (header_idx, sep_idx, end_idx_exclusive) for pipe tables."""
+    blocks = []
+    i = 0
+    while i < len(lines) - 1:
+        if PIPE_ROW_RE.match(lines[i]) and is_separator(lines[i + 1]):
+            header = i
+            sep = i + 1
+            j = sep + 1
+            while j < len(lines) and PIPE_ROW_RE.match(lines[j]):
+                j += 1
+            blocks.append((header, sep, j))
+            i = j
+        else:
+            i += 1
+    return blocks
+
+
+def infer_widths_for_block(
+    lines: list[str], header: int, sep: int, end: int, min_dashes: int
+) -> tuple[list[int], list[str]]:
+    header_cells = split_row(lines[header])
+    sep_cells = split_row(lines[sep])
+    n = len(header_cells)
+
+    aligns = [parse_alignment(c) for c in sep_cells]
+    if len(aligns) < n:
+        aligns += ["default"] * (n - len(aligns))
+    aligns = aligns[:n]
+
+    widths = [display_width(h) for h in header_cells]
+    for r in range(sep + 1, end):
+        cells = split_row(lines[r])
+        for k in range(min(n, len(cells))):
+            widths[k] = max(widths[k], display_width(cells[k]))
+
+    widths = [max(min_dashes, w) for w in widths]
+    return widths, aligns
+
+
+def process(text: str, min_dashes: int, scale: float) -> str:
+    lines = text.splitlines()
+    blocks = find_table_blocks(lines)
+    for header, sep, end in blocks:
+        widths, aligns = infer_widths_for_block(lines, header, sep, end, min_dashes)
+        if scale != 1.0:
+            widths = [max(min_dashes, int(round(w * scale))) for w in widths]
+        lines[sep] = make_separator(widths, aligns)
+    return "\n".join(lines) + ("\n" if text.endswith("\n") else "")
+
+
+def main() -> int:
+    ap = argparse.ArgumentParser(description=__doc__)
+    ap.add_argument("input", type=Path, help="Input markdown file")
+    ap.add_argument("--out", type=Path, default=None, help="Output path (default: stdout)")
+    ap.add_argument("--min", type=int, default=5, help="Minimum dashes per column (default: 5)")
+    ap.add_argument("--scale", type=float, default=1.0, help="Multiply all widths (default: 1.0)")
+    args = ap.parse_args()
+
+    text = args.input.read_text(encoding="utf-8")
+    out = process(text, min_dashes=args.min, scale=args.scale)
+    if args.out:
+        args.out.write_text(out, encoding="utf-8")
+        print(f"[infer_colwidths] {args.input} → {args.out}", file=sys.stderr)
+    else:
+        sys.stdout.write(out)
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())

package/skills/render-pdf-doc/scripts/render_pdf.sh

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+#!/usr/bin/env bash
+# render_pdf.sh — pandoc + xelatex wrapper for Korean academic markdown.
+#
+# Usage:
+#   render_pdf.sh -i input.md [-o output.pdf] [--infer-colwidths]
+#                 [--font "Apple SD Gothic Neo"] [--cjk-font "Apple SD Gothic Neo"]
+#                 [-- <extra pandoc args>]
+#
+# Defaults:
+#   - macOS: mainfont/CJKmainfont = "Apple SD Gothic Neo"
+#   - Linux: mainfont = "Noto Serif CJK KR", CJKmainfont = "Noto Sans CJK KR"
+#   - Output path = <input>.pdf
+#   - geometry = margin=0.85in, fontsize = 11pt (override via frontmatter)
+#
+# The frontmatter in input.md takes precedence over CLI/auto-detected defaults.
+
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+
+INPUT=""
+OUTPUT=""
+INFER_COLWIDTHS=0
+MAINFONT=""
+CJKFONT=""
+EXTRA=()
+
+usage() {
+  cat >&2 <<EOF
+Usage: $(basename "$0") -i <input.md> [-o <output.pdf>] [options] [-- <pandoc args>]
+
+Options:
+  -i  Input markdown
+  -o  Output PDF (default: <input>.pdf)
+  --infer-colwidths     Run scripts/infer_colwidths.py on a temp copy first
+  --font NAME           mainfont (default: OS-detected)
+  --cjk-font NAME       CJKmainfont (default: OS-detected)
+  -h | --help           Help
+
+Pass-through: any args after '--' go directly to pandoc.
+EOF
+  exit 1
+}
+
+while [[ $# -gt 0 ]]; do
+  case "$1" in
+    -i) INPUT="$2"; shift 2 ;;
+    -o) OUTPUT="$2"; shift 2 ;;
+    --infer-colwidths) INFER_COLWIDTHS=1; shift ;;
+    --font) MAINFONT="$2"; shift 2 ;;
+    --cjk-font) CJKFONT="$2"; shift 2 ;;
+    -h|--help) usage ;;
+    --) shift; EXTRA=("$@"); break ;;
+    *) EXTRA+=("$1"); shift ;;
+  esac
+done
+
+[[ -z "$INPUT" ]] && usage
+[[ -f "$INPUT" ]] || { echo "ERROR: input not found: $INPUT" >&2; exit 2; }
+[[ -z "$OUTPUT" ]] && OUTPUT="${INPUT%.md}.pdf"
+
+# OS-based font defaults
+if [[ -z "$MAINFONT" || -z "$CJKFONT" ]]; then
+  if [[ "$(uname)" == "Darwin" ]]; then
+    : "${MAINFONT:=Apple SD Gothic Neo}"
+    : "${CJKFONT:=Apple SD Gothic Neo}"
+  else
+    : "${MAINFONT:=Noto Serif CJK KR}"
+    : "${CJKFONT:=Noto Sans CJK KR}"
+  fi
+fi
+
+command -v pandoc >/dev/null || { echo "ERROR: pandoc not installed" >&2; exit 3; }
+command -v xelatex >/dev/null || { echo "ERROR: xelatex not installed (install mactex / texlive-xetex)" >&2; exit 3; }
+
+WORK="$INPUT"
+TMPDIR=""
+if [[ "$INFER_COLWIDTHS" == "1" ]]; then
+  TMPDIR="$(mktemp -d)"
+  trap 'rm -rf "$TMPDIR"' EXIT
+  WORK="$TMPDIR/$(basename "$INPUT")"
+  python3 "$SCRIPT_DIR/infer_colwidths.py" "$INPUT" --out "$WORK"
+fi
+
+ARGS=(
+  --pdf-engine=xelatex
+  -V "mainfont=${MAINFONT}"
+  -V "CJKmainfont=${CJKFONT}"
+  -V "geometry:margin=0.85in"
+  -V "fontsize=11pt"
+  -V "linestretch=1.25"
+  -V "colorlinks=true"
+  -o "$OUTPUT"
+)
+
+echo "[render_pdf] in=$INPUT out=$OUTPUT mainfont='$MAINFONT' CJK='$CJKFONT' infer=$INFER_COLWIDTHS" >&2
+pandoc "${ARGS[@]}" ${EXTRA[@]+"${EXTRA[@]}"} "$WORK"
+echo "[render_pdf] ok → $OUTPUT" >&2

package/skills/render-pdf-doc/skill.yml

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+schema_version: 2
+name: render-pdf-doc
+layer: A
+owner_domain: document_layout
+when_to_use:
+  - Render a non-bibliography Korean/English academic markdown to publication-quality PDF
+  - Research proposals, IRB cover letters, briefing handouts, anchor docs, reference tables
+  - Auto-infer pipe-table column widths for content-proportional layout
+  - CJK-font-aware PDF on macOS (Apple SD Gothic Neo) or Linux (Noto Sans CJK KR)
+when_NOT_to_use:
+  - Manuscripts with bibliography (use /manage-refs scripts/render_pandoc.sh — owns CSL pipeline)
+  - Filling institutional Word form templates (use /fill-protocol)
+  - Figures, plots, or PPTX (use /make-figures or /present-paper)
+  - Hand-typing CSV data into tables (forbidden — see numerical-safety rule)
+inputs:
+  - markdown_file (non-bibliography academic doc — proposal, briefing, anchor doc, IRB cover, reference table)
+  - frontmatter (optional; mainfont, CJKmainfont, geometry, fontsize, linestretch)
+outputs:
+  - pdf_file (default: same dir, same stem, .pdf)
+  - intermediate.colwidths.md (optional, when --infer-colwidths is run as separate step)
+deterministic_scripts:
+  - scripts/render_pdf.sh
+  - scripts/infer_colwidths.py
+  - scripts/check_deps.sh
+side_effects:
+  - writes_pdf_artifacts
+  - reads_os_font_table  # for CJK font detection (Apple SD Gothic Neo / Noto Sans CJK KR)
+downstream_consumers:
+  - intake-project
+  - manage-project
+  - write-protocol  # when no institutional .docx form exists; see fill-protocol for the form-fill alternative
+forbidden_actions:
+  - bibliography_rendering  # delegate /manage-refs scripts/render_pandoc.sh
+  - citation_key_modification
+  - institutional_word_form_filling  # delegate /fill-protocol
+  - figure_or_pptx_generation  # delegate /make-figures or /present-paper
+  - hand_typing_csv_data_into_tables  # ~/.claude/rules/numerical-safety.md
+provenance:
+  origin: "P3 spinoff from /write-paper Phase 7.6 split (2026-05-01)"
+  precedent: "an education-research calibration anchor PDF — manual fix x2 → skill"
+quality_gates:
+  - check_deps.sh: hard exit if pandoc + xelatex + CJK-font dependencies are not installed
+  - infer_colwidths.py: enforce content-proportional dashes unless the equal-split (--equal) option is specified
+  - circulation_redaction: for circulation PDFs, enforce frontmatter `redact_internal: true` or keep change history / version numbers / PI attribution out of the body
+
+# v2.1 quality card
+purpose: "Render a Markdown manuscript to a styled DOCX/PDF (tables, column widths, dependencies checked)."
+safety_boundaries:
+  - "Delegates bibliography rendering to manage-refs and figures/PPTX to make-figures/present-paper; does not modify citation keys."
+  - "Does not hand-type CSV data into tables (numerical-safety)."
+known_limitations:
+  - "Output fidelity depends on installed render dependencies (checked by check_deps.sh)."
+  - "Institutional Word forms are out of scope (use fill-protocol)."
+validation_commands:
+  - "bash scripts/check_deps.sh"
+  - "bash scripts/render_pdf.sh <manuscript.md>"
+evidence_surface: bundled_script

package/skills/render-pdf-doc/templates/anchor-doc.md

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+---
+title: "<!-- TODO: Document title -->"
+author: "<!-- TODO: Author / Working Group -->"
+date: "<!-- TODO: YYYY-MM-DD -->"
+mainfont: "Apple SD Gothic Neo"
+CJKmainfont: "Apple SD Gothic Neo"
+geometry: "margin=0.85in"
+fontsize: 11pt
+linestretch: 1.25
+colorlinks: true
+---
+
+<!-- English-default template. For a Korean starter, see anchor-doc_ko.md. -->
+
+# <!-- TODO: Section 1 -->
+
+<!-- TODO: one-paragraph summary (background / purpose). In a circulation PDF, do not expose change history or internal versions. -->
+
+## Q&A alignment grid
+
+| Axis | Question | Agreed answer |
+|------|----------|---------------|
+| Definition | <!-- TODO: question text --> | <!-- TODO: answer --> |
+| Scope | <!-- TODO --> | <!-- TODO --> |
+| Measurement | <!-- TODO --> | <!-- TODO --> |
+
+> `scripts/infer_colwidths.py` auto-replaces the pipe-table separator row with content-proportional dash ratios.

package/skills/render-pdf-doc/templates/anchor-doc_ko.md

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+---
+title: "<!-- TODO: Document title -->"
+author: "<!-- TODO: Author / Working Group -->"
+date: "<!-- TODO: YYYY-MM-DD -->"
+mainfont: "Apple SD Gothic Neo"
+CJKmainfont: "Apple SD Gothic Neo"
+geometry: "margin=0.85in"
+fontsize: 11pt
+linestretch: 1.25
+colorlinks: true
+---
+
+# <!-- TODO: Section 1 -->
+
+<!-- TODO: 한 단락 요약 (배경·목적). 회람 PDF에서는 변경이력·내부 버전 노출 금지. -->
+
+## Q&A 정렬표
+
+| Axis | 질문 | 합의 답변 |
+|------|------|-----------|
+| 정의 | <!-- TODO: 질문 텍스트 --> | <!-- TODO: 답변 --> |
+| 범위 | <!-- TODO --> | <!-- TODO --> |
+| 측정 | <!-- TODO --> | <!-- TODO --> |
+
+> Pipe table 분리 행은 `scripts/infer_colwidths.py`가 content-proportional 대시 비율로 자동 교체.

package/skills/render-pdf-doc/templates/briefing-handout.md

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+---
+title: "<!-- TODO: meeting / briefing title -->"
+author: "<!-- TODO: author -->"
+date: "<!-- TODO: YYYY-MM-DD -->"
+mainfont: "Apple SD Gothic Neo"
+CJKmainfont: "Apple SD Gothic Neo"
+geometry: "margin=0.75in"
+fontsize: 10pt
+linestretch: 1.2
+---
+
+<!-- English-default template. For a Korean starter, see briefing-handout_ko.md. -->
+
+# <!-- TODO: meeting topic -->
+
+**Date/time**: <!-- TODO --> · **Location**: <!-- TODO --> · **Attendees**: <!-- TODO -->
+
+## Key decisions (1 line each)
+
+1. <!-- TODO -->
+2. <!-- TODO -->
+3. <!-- TODO -->
+
+## Discussion / action items
+
+| # | Item | Owner | Due |
+|---|------|-------|-----|
+| 1 | <!-- TODO --> | <!-- TODO --> | <!-- TODO --> |
+| 2 | <!-- TODO --> | <!-- TODO --> | <!-- TODO --> |
+
+## Next meeting
+
+<!-- TODO: date/time + one-line agenda -->

package/skills/render-pdf-doc/templates/briefing-handout_ko.md

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+---
+title: "<!-- TODO: Meeting / Briefing 제목 -->"
+author: "<!-- TODO: 작성자 -->"
+date: "<!-- TODO: YYYY-MM-DD -->"
+mainfont: "Apple SD Gothic Neo"
+CJKmainfont: "Apple SD Gothic Neo"
+geometry: "margin=0.75in"
+fontsize: 10pt
+linestretch: 1.2
+---
+
+# <!-- TODO: 미팅 주제 -->
+
+**일시**: <!-- TODO --> · **장소**: <!-- TODO --> · **참석**: <!-- TODO -->
+
+## 핵심 결정 (1-line each)
+
+1. <!-- TODO -->
+2. <!-- TODO -->
+3. <!-- TODO -->
+
+## 논의 / 액션 아이템
+
+| # | 항목 | 담당 | 기한 |
+|---|------|------|------|
+| 1 | <!-- TODO --> | <!-- TODO --> | <!-- TODO --> |
+| 2 | <!-- TODO --> | <!-- TODO --> | <!-- TODO --> |
+
+## 다음 미팅
+
+<!-- TODO: 일시 + 어젠다 1줄 -->

package/skills/render-pdf-doc/templates/proposal-cover.md

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+---
+title: "<!-- TODO: research title -->"
+subtitle: "<!-- TODO: subtitle (optional) -->"
+author: "<!-- TODO: principal investigator / affiliation -->"
+date: "<!-- TODO: YYYY-MM-DD -->"
+mainfont: "Apple SD Gothic Neo"
+CJKmainfont: "Apple SD Gothic Neo"
+geometry: "margin=1in"
+fontsize: 11pt
+linestretch: 1.5
+---
+
+<!-- English-default template. For a Korean starter, see proposal-cover_ko.md. -->
+
+# Research Proposal Cover
+
+| Item | Content |
+|------|---------|
+| Research title | <!-- TODO --> |
+| Principal investigator | <!-- TODO --> |
+| Co-investigators | <!-- TODO --> |
+| Institution | <!-- TODO --> |
+| Study period | <!-- TODO: YYYY-MM-DD ~ YYYY-MM-DD --> |
+| IRB approval no. | <!-- TODO --> |
+| Funding source | <!-- TODO --> |
+
+## Summary
+
+<!-- TODO: one paragraph (200-300 words) — background / purpose / methods / expected impact -->
+
+## Keywords
+
+<!-- TODO: keyword 1, keyword 2, keyword 3 -->

package/skills/render-pdf-doc/templates/proposal-cover_ko.md

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+---
+title: "<!-- TODO: 연구 제목 -->"
+subtitle: "<!-- TODO: 부제 (생략 가능) -->"
+author: "<!-- TODO: 책임연구자 / 소속 -->"
+date: "<!-- TODO: YYYY-MM-DD -->"
+mainfont: "Apple SD Gothic Neo"
+CJKmainfont: "Apple SD Gothic Neo"
+geometry: "margin=1in"
+fontsize: 11pt
+linestretch: 1.5
+---
+
+# 연구계획서 표지
+
+| 항목 | 내용 |
+|------|------|
+| 연구 제목 | <!-- TODO --> |
+| 책임연구자 | <!-- TODO --> |
+| 공동연구자 | <!-- TODO --> |
+| 소속기관 | <!-- TODO --> |
+| 연구 기간 | <!-- TODO: YYYY-MM-DD ~ YYYY-MM-DD --> |
+| IRB 승인번호 | <!-- TODO --> |
+| 연구비 출처 | <!-- TODO --> |
+
+## 연구 요약
+
+<!-- TODO: 한 단락 (200-300 자) — 배경·목적·방법·기대효과 -->
+
+## 핵심 키워드
+
+<!-- TODO: 키워드 1, 키워드 2, 키워드 3 -->

package/skills/render-pdf-doc/templates/reference-table.md

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+---
+title: "<!-- TODO: comparison-table title -->"
+author: "<!-- TODO -->"
+date: "<!-- TODO: YYYY-MM-DD -->"
+mainfont: "Apple SD Gothic Neo"
+CJKmainfont: "Apple SD Gothic Neo"
+geometry: "margin=0.75in"
+fontsize: 10pt
+linestretch: 1.15
+---
+
+<!-- English-default template. For a Korean starter, see reference-table_ko.md. -->
+
+# <!-- TODO: table title -->
+
+| Dimension | Option A | Option B | Option C |
+|-----------|----------|----------|----------|
+| <!-- TODO --> | <!-- TODO --> | <!-- TODO --> | <!-- TODO --> |
+| <!-- TODO --> | <!-- TODO --> | <!-- TODO --> | <!-- TODO --> |
+| <!-- TODO --> | <!-- TODO --> | <!-- TODO --> | <!-- TODO --> |
+
+> Pipe-table widths are distributed content-proportionally via `--infer-colwidths`.

package/skills/render-pdf-doc/templates/reference-table_ko.md

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+---
+title: "<!-- TODO: 비교표 제목 -->"
+author: "<!-- TODO -->"
+date: "<!-- TODO: YYYY-MM-DD -->"
+mainfont: "Apple SD Gothic Neo"
+CJKmainfont: "Apple SD Gothic Neo"
+geometry: "margin=0.75in"
+fontsize: 10pt
+linestretch: 1.15
+---
+
+# <!-- TODO: 표 제목 -->
+
+| 차원 | 옵션 A | 옵션 B | 옵션 C |
+|------|--------|--------|--------|
+| <!-- TODO --> | <!-- TODO --> | <!-- TODO --> | <!-- TODO --> |
+| <!-- TODO --> | <!-- TODO --> | <!-- TODO --> | <!-- TODO --> |
+| <!-- TODO --> | <!-- TODO --> | <!-- TODO --> | <!-- TODO --> |
+
+> Pipe table 폭은 `--infer-colwidths`로 content-proportional 자동 분배.