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use chain serial rather than logical index with _DefaultTrace.insert #1590

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Merged
OriolAbril merged 2 commits into from
Mar 3, 2021
Merged

use chain serial rather than logical index with _DefaultTrace.insert #1590

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9762c3a
use chain serial rather than logical index with _DefaultTrace.insert
Spaak Mar 1, 2021
5b68722
add PR #1590 to changelog
Spaak Mar 3, 2021
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -13,6 +13,7 @@
* Integrate `index_origin` with all the library ([1201](https://github.com/arviz-devs/arviz/pull/1201))
* Fix pareto k threshold typo in reloo function ([1580](https://github.com/arviz-devs/arviz/pull/1580))
* Preserve shape from Stan code in `from_cmdstanpy` ([1579](https://github.com/arviz-devs/arviz/pull/1579))
* Correctly use chain index when constructing PyMC3 `DefaultTrace` in `from_pymc3` ([1590](https://github.com/arviz-devs/arviz/pull/1590))

### Deprecation
* Deprecated `index_origin` and `order` arguments in `az.summary` ([1201](https://github.com/arviz-devs/arviz/pull/1201))
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4 changes: 2 additions & 2 deletions arviz/data/io_pymc3.py
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Expand Up @@ -243,12 +243,12 @@ def _extract_log_likelihood(self, trace):
"`pip install pymc3>=3.8` or `conda install -c conda-forge pymc3>=3.8`."
) from err
for var, log_like_fun in cached:
for chain in trace.chains:
for k, chain in enumerate(trace.chains):
log_like_chain = [
self.log_likelihood_vals_point(point, var, log_like_fun)
for point in trace.points([chain])
]
log_likelihood_dict.insert(var.name, np.stack(log_like_chain), chain)
log_likelihood_dict.insert(var.name, np.stack(log_like_chain), k)
return log_likelihood_dict.trace_dict

@requires("trace")
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