battery: paper_plots.py draws the other figures when no run has REFMAC R-free

The REFMAC check is opt-in, so a battery run without --model-check has no
R-free pairs, and the axis range min()/max() over them crashed the script
before any figure was drawn. The R-free figure is now its own gnuplot block,
left out (with a line in summary.txt saying why) when there is nothing to
draw; d_min and the time figures are drawn as before.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi

tools/battery/paper_plots.py

@@ -21,6 +21,7 @@ Left figure: R-free of the deposited model after the battery's REFMAC check on t
 (x) and on Rugnux's data (y). By default the refined protocol (model_check.py: the same model
 refined against each data set at its own resolution, R-free over the free reflections both data sets
 share); --rfree first-cycle draws the first-cycle rigid-body numbers at the common resolution instead.
+A run without REFMAC values (the check is opt-in, --model-check) gets no R-free figure; the rest are drawn.
 Right figure: the deposited high-resolution limit (x) against Rugnux's own cut
 (y), log axes so the low-resolution entries show. Small molecules (no deposited model) and sets
 whose verdict is `fail` (a wrong lattice: nothing to compare) are left out.
@@ -75,7 +76,10 @@ set style line 2 pt 7 ps 0.35 lc rgb "#0072b2"
 # counts: names left-aligned, numbers right-aligned in a column beside them
 set label 11 "Structures\nFacilities\nBeamlines" at graph 0.05, graph 0.93 left front
 set label 12 "%(n)d\n%(nf)d\n%(nb)d" at graph 0.31, graph 0.93 right front
+"""
 
+# Drawn only where the runs carry REFMAC R-free values; the battery's REFMAC check is opt-in.
+GNUPLOT_RFREE = r"""
 # --- R-free
 set output "%(out)s/rfree.pdf"
 set xlabel "{/:Italic R}_{free}, depositor data"
@@ -86,7 +90,9 @@ set format x "%%.1f"; set format y "%%.1f"
 set label 2 "Within ±%(band).2f: %(within)d/%(n)d" at graph 0.95, graph 0.07 right front
 plot x ls 1, "%(out)s/rfree.dat" using 1:2 ls 2
 unset label 2
+"""
 
+GNUPLOT_REST = r"""
 # --- high-resolution limit
 set output "%(out)s/dmin.pdf"
 set logscale xy
@@ -255,7 +261,8 @@ def main():
             else "set key off")
     params = dict(out=out, tkey=tkey, n=n, nf=nf, nb=nb, dn=dn, dnf=dnf, dnb=dnb, within=within, band=RFREE_BAND,
                   deeper=deeper, shallower=sum(y > x for x, y, _ in dmin),
-                  rlo=0.05 * math.floor((min(values) - 0.01) / 0.05), rhi=0.05 * math.ceil((max(values) + 0.01) / 0.05),
+                  rlo=0.05 * math.floor((min(values, default=0.2) - 0.01) / 0.05),
+                  rhi=0.05 * math.ceil((max(values, default=0.3) + 0.01) / 0.05),
                   dlo=0.5, dhi=8.0,
                   bin=TIME_BIN, thi=TIME_BIN * math.ceil(max(secs) / TIME_BIN), tyhi=10 * math.ceil((tallest + 1) / 10),
                   tmed=tmed, tn=len(times),
@@ -263,9 +270,9 @@ def main():
                   zyhi=5 * math.ceil((max(collections.Counter(math.floor(t / ZOOM_BIN) for t in secs
                                                               if t < ZOOM_MAX).values()) + 1) / 5))
     gp = os.path.join(out, "figures.gp")
-    open(gp, "w").write(GNUPLOT % params)
+    open(gp, "w").write((GNUPLOT + (GNUPLOT_RFREE if rfree else "") + GNUPLOT_REST) % params)
     subprocess.run(["gnuplot", gp], check=True)
-    for fig in ("rfree", "dmin", "time", "time_zoom"):    # the PNG is the PDF rasterised at 600 d.p.i.
+    for fig in (["rfree"] if rfree else []) + ["dmin", "time", "time_zoom"]:    # the PNG is the PDF rasterised at 600 d.p.i.
         subprocess.run(["pdftoppm", "-r", "600", "-png", "-singlefile", os.path.join(out, fig + ".pdf"),
                         os.path.join(out, fig)], check=True)
 
@@ -276,8 +283,10 @@ def main():
             fh.write(f"run {path}\n  label {m.get('label')}  binary git {b.get('source_head')} "
                      f"dirty {b.get('source_dirty')}  sha256 {b.get('sha256')}\n  flags {b.get('flags')}  "
                      f"runner git {m.get('runner_git')} dirty {m.get('runner_dirty')}\n")
-        fh.write(f"R-free: {n} structures, {nf} facilities, {nb} beamlines; within +-{RFREE_BAND}: {within}\n"
-                 f"d_min: {dn} structures, {dnf} facilities, {dnb} beamlines; Rugnux reaches further on "
+        fh.write((f"R-free: {n} structures, {nf} facilities, {nb} beamlines; within +-{RFREE_BAND}: {within}\n"
+                  if rfree else "R-free: no REFMAC values in these runs (run the battery with --model-check); "
+                                "no rfree figure\n")
+                 + f"d_min: {dn} structures, {dnf} facilities, {dnb} beamlines; Rugnux reaches further on "
                  f"{deeper}\n")
         queue_wait = max(time_rows[s]["elapsed_s"] - t for s, _, t, _, _ in times)
         fh.write(f"time: {len(times)} sets of arm(s) {', '.join(a.time_arms)}; field rugnux_wall_s "