_scripts/make_author_graph.py

#!/usr/bin/env python3
"""Generate a self-contained interactive co-authorship graph (D3 force layout).

Nodes are authors (size + color by number of papers in the vault); edges are
co-authorships (width by number of papers shared). Filtered to authors with at
least --min-papers papers, and edges only between kept authors. One HTML file,
D3 from CDN; drag, scroll-zoom, hover a node for the name (the biggest hubs are
labelled always).

    python3 _scripts/make_author_graph.py                       # >=3 papers -> reports/author-graph.html
    python3 _scripts/make_author_graph.py --min-papers 5 --out reports/authors5.html
    python3 _scripts/make_author_graph.py --embed --out graph.html   # header stripped, for <iframe>

Companion to make_graph.py (the idea/paper stance graph); publishing recipe and
the HF-Space upload gotcha are in skills/visualize-graph/SKILL.md.
"""
import argparse
import glob
import json
import os
import re
from collections import Counter
from itertools import combinations

VAULT = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))


def build(min_papers):
    paper_authors = []
    for f in glob.glob(os.path.join(VAULT, "papers", "*.md")):
        m = re.search(r"^authors:\s*\[(.*)\]", open(f, encoding="utf-8").read(), re.M)
        if m:
            paper_authors.append(re.findall(r"\[\[(.+?)\]\]", m.group(1)))
    cnt = Counter(a for auth in paper_authors for a in auth)
    keep = {a for a, c in cnt.items() if c >= min_papers}
    ew = Counter()
    for auth in paper_authors:
        kept = sorted(a for a in auth if a in keep)
        for x, y in combinations(kept, 2):
            ew[(x, y)] += 1
    nodes = [{"id": a, "label": a, "n": cnt[a]} for a in sorted(keep, key=lambda a: -cnt[a])]
    links = [{"source": x, "target": y, "w": w} for (x, y), w in ew.items()]
    return {"nodes": nodes, "links": links, "maxn": max(cnt[a] for a in keep) if keep else 1}


HEADER = '''<div id="hd"><h1>{title}</h1>
<p>Authors with at least {min} papers in the corpus; links are co-authorships (thicker = more papers together). Node size and shade track paper count. Drag, scroll to zoom, hover for a name.</p></div>
'''

TEMPLATE = '''<!doctype html>
<html lang="en"><head>
<meta charset="utf-8"/><meta name="viewport" content="width=device-width,initial-scale=1"/>
<title>{title}</title>
<script src="https://cdn.jsdelivr.net/npm/d3@7/dist/d3.min.js"></script>
<style>
  :root{{--bg:#fbfaf8;--ink:#1a1a1f;--muted:#6b6b78;--line:#e7e4de;}}
  *{{box-sizing:border-box}} html,body{{margin:0;height:100%}}
  body{{background:var(--bg);color:var(--ink);font:15px/1.5 -apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,sans-serif;overflow:hidden}}
  #hd{{position:fixed;top:0;left:0;right:0;padding:14px 20px;z-index:5;pointer-events:none}}
  #hd h1{{font:600 19px/1.2 Georgia,serif;margin:0}}
  #hd p{{margin:3px 0 0;color:var(--muted);font-size:13px;max-width:660px}}
  #legend{{position:fixed;bottom:16px;left:16px;background:#fffdfaee;border:1px solid var(--line);border-radius:10px;padding:11px 13px;font-size:12.5px;z-index:5;box-shadow:0 2px 10px #0000000d}}
  #legend b{{display:block;margin:0 0 6px;font-size:11px;letter-spacing:.05em;text-transform:uppercase;color:var(--muted)}}
  #legend .row{{display:flex;align-items:center;gap:8px;margin:4px 0}}
  #net{{width:100vw;height:100vh;cursor:grab}}
  .link{{stroke:#b9b3a6;stroke-opacity:.5}}
  .node circle{{stroke:#fff;stroke-width:1.2}}
  .lbl{{font-size:11px;fill:var(--ink);pointer-events:none;paint-order:stroke;stroke:#fbfaf8;stroke-width:3px;stroke-linejoin:round}}
</style></head><body>
{header}<div id="legend">
  <b>Node</b>
  <div class="row"><svg width="46" height="16"><circle cx="8" cy="8" r="4" fill="#7fcdbb"/><circle cx="30" cy="8" r="8" fill="#0f5c58"/></svg>papers (size + shade)</div>
  <b style="margin-top:8px">Link</b>
  <div class="row"><svg width="46" height="10"><line x1="2" y1="5" x2="44" y2="5" stroke="#b9b3a6" stroke-width="1"/></svg>1 paper together</div>
  <div class="row"><svg width="46" height="10"><line x1="2" y1="5" x2="44" y2="5" stroke="#b9b3a6" stroke-width="4"/></svg>many together</div>
</div>
<svg id="net"></svg>
<script>
const data={data};
const color=d3.scaleSequential(d3.interpolateYlGnBu).domain([{minp}, data.maxn]);
const R=n=>4+1.15*n, LBL_MIN=5;
const svg=d3.select("#net"),W=innerWidth,H=innerHeight,g=svg.append("g");
const zoom=d3.zoom().scaleExtent([0.15,4]).on("zoom",e=>g.attr("transform",e.transform));svg.call(zoom);
const link=g.append("g").selectAll("line").data(data.links).join("line")
  .attr("class","link").attr("stroke-width",d=>0.6+d.w*0.55);
const node=g.append("g").selectAll("g").data(data.nodes).join("g").attr("class","node");
node.append("circle").attr("r",d=>R(d.n)).attr("fill",d=>color(d.n));
node.append("title").text(d=>d.label+" · "+d.n+" papers");
node.append("text").attr("class","lbl").attr("x",d=>R(d.n)+3).attr("y",4)
  .style("opacity",d=>d.n>=LBL_MIN?1:0).text(d=>d.label);
node.on("mouseover",function(e,d){{d3.select(this).select("text").style("opacity",1)}})
    .on("mouseout",function(e,d){{d3.select(this).select("text").style("opacity",d.n>=LBL_MIN?1:0)}});
node.call(d3.drag()
  .on("start",(e,d)=>{{if(!e.active)sim.alphaTarget(.3).restart();d.fx=d.x;d.fy=d.y}})
  .on("drag",(e,d)=>{{d.fx=e.x;d.fy=e.y}})
  .on("end",(e,d)=>{{if(!e.active)sim.alphaTarget(0);d.fx=null;d.fy=null}}));
function ticked(){{
  link.attr("x1",d=>d.source.x).attr("y1",d=>d.source.y).attr("x2",d=>d.target.x).attr("y2",d=>d.target.y);
  node.attr("transform",d=>`translate(${{d.x}},${{d.y}})`);
}}
const sim=d3.forceSimulation(data.nodes)
  .force("link",d3.forceLink(data.links).id(d=>d.id).distance(d=>82-Math.min(d.w,6)*5).strength(d=>0.14+d.w*0.05))
  .force("charge",d3.forceManyBody().strength(-320).distanceMax(600))
  .force("x",d3.forceX(W/2).strength(.05)).force("y",d3.forceY(H/2).strength(.05))
  .force("collide",d3.forceCollide(d=>R(d.n)+7).strength(.9))
  .stop();
sim.tick(400);          // pre-settle synchronously (no animation race)
ticked();
fit();
sim.on("tick",ticked);  // redraw when drag re-heats the sim
function fit(){{
  const xs=data.nodes.map(d=>d.x),ys=data.nodes.map(d=>d.y);
  const x0=Math.min(...xs),x1=Math.max(...xs),y0=Math.min(...ys),y1=Math.max(...ys);
  const w=(x1-x0)||1,h=(y1-y0)||1,k=Math.min(3,0.9/Math.max(w/W,h/H));
  svg.call(zoom.transform,d3.zoomIdentity.translate(W/2-k*(x0+x1)/2,H/2-k*(y0+y1)/2).scale(k));
}}
</script></body></html>'''


def main():
    ap = argparse.ArgumentParser()
    ap.add_argument("--min-papers", type=int, default=3)
    ap.add_argument("--embed", action="store_true")
    ap.add_argument("--title", default=None)
    ap.add_argument("--out", default="reports/author-graph.html")
    a = ap.parse_args()
    title = a.title or f"Co-authorship — authors with ≥{a.min_papers} papers"

    data = build(a.min_papers)
    header = "" if a.embed else HEADER.format(title=title, min=a.min_papers)
    html = TEMPLATE.format(title=title, header=header, data=json.dumps(data), minp=a.min_papers)
    out = a.out if os.path.isabs(a.out) else os.path.join(VAULT, a.out)
    os.makedirs(os.path.dirname(out), exist_ok=True)
    with open(out, "w", encoding="utf-8") as f:
        f.write(html)
    print(f"wrote {out}: {len(data['nodes'])} authors, {len(data['links'])} co-authorship edges")


if __name__ == "__main__":
    main()