Bug fix in pyromixin for posterior sampling #1158
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Codecov Report
@@ Coverage Diff @@
## master #1158 +/- ##
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+ Coverage 90.27% 90.74% +0.46%
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Files 93 95 +2
Lines 7341 7668 +327
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+ Hits 6627 6958 +331
+ Misses 714 710 -4
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@adamgayoso please have a look at this |
adamgayoso
requested changes
Sep 14, 2021
scvi/model/base/_pyromixin.py
Outdated
| @@ -262,7 +262,7 @@ def _get_obs_plate_return_sites(self, return_sites, obs_plate_sites): | |||
| else: | |||
| return obs_plate_sites | |||
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| def _get_obs_plate_sites(self, args, kwargs): | |||
| def _get_obs_plate_sites(self, args, kwargs, sample_observed): | |||
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can you document this function and add relevant typing?
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I think this is done now. |
adamgayoso
requested changes
Sep 22, 2021
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Yes, you are right actually - these arguments are not optional and don't
have default values. I will change this.
…On Wed, 22 Sep 2021, 05:56 Adam Gayoso, ***@***.***> wrote:
***@***.**** requested changes on this pull request.
------------------------------
In scvi/model/base/_pyromixin.py
<#1158 (comment)>:
> + args: Optional[list],
+ kwargs: Optional[dict],
usually optional has a None default. Don't believe this is the case here?
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adamgayoso
approved these changes
Oct 1, 2021
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The method
._get_obs_plate_sites()should discard observed variables (unless requested otherwise) and plates. Current code always performs posterior sampling even if unobserved local variables do not exist in the model, e.i. code never enters this statement:This PR addresses the issue by adding a check for observed and plates.