displaCy saving to SVG produces un-renderable output

[serenalotreck]

Redirect from #11875.

I'm looking to save an svg of a displaCy doc for a paper figure. I can render it correctly within Jupyter, but when I disable Jupyter mode to save it, I get a weird output that doesn't create an image. Here's a minimal reproducible example:

# Imports
import spacy
from spacy import displacy

# Data
text = """
INTERSPECIFIC VARIATION IN DESICCATION SURVIVAL-TIME OF AEDES (STEGOMYIA) MOSQUITO EGGS IS CORRELATED WITH HABITAT AND EGG SIZE | Survival times of eggs under three humidity conditions (42%, 68%, 88% RH) were investigated among Aedes (Stegomyia) mosquitoes from temperate and tropical zones (5 species and 20 geographical strains). This subgenus tends to occupy small aquatic sites as larvae, where desiccation resistance of eggs is necessary during habitat drought. Interspecific comparison showed that the egg survival time was correlated with egg volume and dryness of source locality, and probably with habitat. Aedes aegypti is associated most with arid climate and human-disturbed habitats - its large eggs survived the longest periods at all humidities. Aedes albopictus ranges from tropics to temperate zones and inhabits both disturbed and forest habitats - its eggs were less desiccation-resistant than A. aegypti eggs. The survival times for forest species eggs (A. riversi, A. galloisi, A.flavopictus) were variable at high humidities but at the lowest humidity were consistently shorter than for eggs of A. aegypti and A. albopictus."""

dygiepp_entities = [[[6, 11, 'Plant_region', 5.0459, 0.9856],
  [42, 46, 'Multicellular_organism', 10.709, 1.0]],
 [],
 [],
 [[107, 108, 'Multicellular_organism', 13.4504, 1.0]],
 [[130, 131, 'Multicellular_organism', 10.2215, 1.0],
  [152, 154, 'Plant_region', 3.2924, 0.8773]],
 [[160, 162, 'Multicellular_organism', 4.018, 0.9615],
  [164, 165, 'Multicellular_organism', 7.943, 0.9996],
  [167, 168, 'Multicellular_organism', 10.6862, 1.0],
  [189, 190, 'Multicellular_organism', 9.6409, 0.9999],
  [192, 193, 'Multicellular_organism', 11.921, 1.0]]]

# Process text data and entities
nlp = spacy.load("en_core_sci_sm", disable=['ner'])
doc = nlp(text)
doc_ents = []
for sent in dygiepp_entities:
    prev_idxs = (0, 0)
    for ent in sent:
        span = spacy.tokens.Span(doc, ent[0], ent[1]+1, ent[2])
        ent_types.append(ent[2])
        if not (prev_idxs[0] <= ent[0] < prev_idxs[1]):
            doc_ents.append(span)
            prev_idxs = (ent[0], ent[1]+1)
doc.set_ents(entities=doc_ents)

# Use displacy in Jupyter
cmap = matplotlib.cm.get_cmap('Set3')
ent_colors = {ent_type: rgb2hex(cmap(i)) for i, ent_type in enumerate(sorted(set(ent_types), reverse=True))}
svg = displacy.render(doc, style='ent', options={'colors': ent_colors}, jupyter=True)

# Use displacy to save image
svg = displacy.render(doc, style='ent', options={'colors': ent_colors}, jupyter=False)
with open('test_displacy.svg', 'w') as f:
    f.write(svg)

I've attached the weird output here as well. Any thoughts appreciated!

EDIT: here's the file