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Fix for trace of subset of variables #2935

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Merged
fonnesbeck merged 2 commits into from
Apr 20, 2018
Merged

Fix for trace of subset of variables #2935

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7d8aeab
Ensures only variables in trace are summarized in report
fonnesbeck Apr 19, 2018
aa334c9
Added fix to RELEASE-NOTES
fonnesbeck Apr 19, 2018
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10 changes: 9 additions & 1 deletion RELEASE-NOTES.md
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Original file line number Diff line number Diff line change
@@ -1,6 +1,14 @@
# Release Notes

## PyMC 3.4 (unreleased)

## PyMC 3.5 (Unreleaased)


### Fixes

- Fixed `KeyError` raised when only subset of variables are specified to be recorded in the trace.

## PyMC 3.4.1 (April 18 2018)

### New features

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3 changes: 2 additions & 1 deletion pymc3/backends/report.py
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Expand Up @@ -77,7 +77,8 @@ def _run_convergence_checks(self, trace, model):
if is_transformed_name(rv_name):
rv_name2 = get_untransformed_name(rv_name)
rv_name = rv_name2 if rv_name2 in valid_name else rv_name
varnames.append(rv_name)
if rv_name in trace.varnames:
varnames.append(rv_name)

self._effective_n = effective_n = diagnostics.effective_n(trace, varnames)
self._gelman_rubin = gelman_rubin = diagnostics.gelman_rubin(trace, varnames)
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5 changes: 5 additions & 0 deletions pymc3/tests/test_sampling.py
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Expand Up @@ -140,6 +140,11 @@ def test_empty_model():
pm.sample()
error.match('any free variables')

def test_partial_trace_sample():
with pm.Model() as model:
a = pm.Normal('a', mu=0, sd=1)
b = pm.Normal('b', mu=0, sd=1)
trace = pm.sample(trace=[a])

@pytest.mark.xfail(condition=(theano.config.floatX == "float32"), reason="Fails on float32")
class TestNamedSampling(SeededTest):
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