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add distribution details to GraphViz output #4159

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merged 8 commits into from
Oct 8, 2020
Merged

add distribution details to GraphViz output #4159

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44d600a
use new str() representations in GraphViz output
Spaak Oct 7, 2020
006e930
typo
Spaak Oct 7, 2020
c52547f
updating tests
Spaak Oct 7, 2020
401686e
add debug print info for Travis-CI
Spaak Oct 8, 2020
7b60ab0
fix failing test due to floating point numerical accuracy
Spaak Oct 8, 2020
44b6b14
another attempt at fixing float accuracy test fail
Spaak Oct 8, 2020
cccedbe
ensure string format as proper floatX
Spaak Oct 8, 2020
e2bcefd
Merge branch 'master' into improved-graph-labels
ColCarroll Oct 8, 2020
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22 changes: 12 additions & 10 deletions pymc3/model_graph.py
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Original file line number Diff line number Diff line change
Expand Up @@ -134,20 +134,22 @@ def _make_node(self, var_name, graph):
if isinstance(v, SharedVariable):
attrs["style"] = "rounded, filled"

# Get name for node
# determine the shape for this node (default (Distribution) is ellipse)
if v in self.model.potentials:
distribution = "Potential"
attrs["shape"] = "octagon"
elif hasattr(v, "distribution"):
distribution = v.distribution.__class__.__name__
attrs['shape'] = 'octagon'
elif isinstance(v, SharedVariable) or not hasattr(v, 'distribution'):
# shared variables and Deterministic represented by a box
attrs['shape'] = 'box'

if v in self.model.potentials:
label = f'{var_name}\n~\nPotential'
elif isinstance(v, SharedVariable):
distribution = "Data"
attrs["shape"] = "box"
label = f'{var_name}\n~\nData'
else:
distribution = "Deterministic"
attrs["shape"] = "box"
label = str(v).replace(' ~ ', '\n~\n')

graph.node(var_name.replace(':', '&'), label, **attrs)

graph.node(var_name.replace(":", "&"), f"{var_name}\n~\n{distribution}", **attrs)

def get_plates(self):
"""Rough but surprisingly accurate plate detection.
Expand Down
8 changes: 5 additions & 3 deletions pymc3/tests/test_data_container.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
# limitations under the License.

import pymc3 as pm
from ..theanof import floatX
from .helpers import SeededTest
import numpy as np
import pandas as pd
Expand Down Expand Up @@ -174,7 +175,8 @@ def test_model_to_graphviz_for_model_with_data_container(self):
x = pm.Data("x", [1.0, 2.0, 3.0])
y = pm.Data("y", [1.0, 2.0, 3.0])
beta = pm.Normal("beta", 0, 10.0)
pm.Normal("obs", beta * x, np.sqrt(1e-2), observed=y)
obs_sigma = floatX(np.sqrt(1e-2))
pm.Normal("obs", beta * x, obs_sigma, observed=y)
pm.sample(1000, init=None, tune=1000, chains=1)

g = pm.model_to_graphviz(model)
Expand All @@ -183,9 +185,9 @@ def test_model_to_graphviz_for_model_with_data_container(self):
text = 'x [label="x\n~\nData" shape=box style="rounded, filled"]'
assert text in g.source
# Didn't break ordinary variables?
text = 'beta [label="beta\n~\nNormal"]'
text = 'beta [label="beta\n~\nNormal(mu=0.0, sigma=10.0)"]'
assert text in g.source
text = 'obs [label="obs\n~\nNormal" style=filled]'
text = f'obs [label="obs\n~\nNormal(mu=f(f(beta), x), sigma={obs_sigma})" style=filled]'
assert text in g.source

def test_explicit_coords(self):
Expand Down