Thorough use of distributions to clean module-level code #1356

PierreBoyeau · 2022-02-15T22:10:41Z

…distribution_outs

codecov · 2022-02-15T23:17:56Z

Codecov Report

Merging #1356 (c581d14) into master (0ced5d1) will decrease coverage by 0.01%.
The diff coverage is 93.29%.

@@            Coverage Diff             @@
##           master    #1356      +/-   ##
==========================================
- Coverage   91.03%   91.01%   -0.02%     
==========================================
  Files         113      113              
  Lines        9023     8996      -27     
==========================================
- Hits         8214     8188      -26     
+ Misses        809      808       -1

Impacted Files	Coverage Δ
scvi/distributions/__init__.py	`100.00% <ø> (ø)`
scvi/model/base/_vaemixin.py	`92.30% <66.66%> (-0.29%)`	⬇️
scvi/module/_multivae.py	`91.32% <75.00%> (+2.31%)`	⬆️
scvi/distributions/_negative_binomial.py	`87.11% <80.00%> (-0.59%)`	⬇️
scvi/module/_peakvae.py	`93.93% <80.00%> (+1.78%)`	⬆️
scvi/module/_vae.py	`94.76% <89.65%> (+0.34%)`	⬆️
scvi/module/_vaec.py	`85.71% <90.90%> (+1.80%)`	⬆️
scvi/model/base/_rnamixin.py	`91.57% <91.66%> (-0.53%)`	⬇️
scvi/external/gimvi/_module.py	`80.00% <100.00%> (-0.27%)`	⬇️
scvi/model/_autozi.py	`98.79% <100.00%> (-0.05%)`	⬇️
... and 9 more

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scvi/model/_autozi.py

scvi/module/_vae.py

scvi/module/_totalvae.py

scvi/module/_amortizedlda.py

justjhong · 2022-02-16T00:58:53Z

nit: please make the title of the PR more meaningful (since it's the commit message for squash merge)

for more information, see https://pre-commit.ci

scvi/nn/_base_components.py

scvi/module/_vae.py

…distributions_outb

…istributions_outb

justjhong

looks good to me, needs to be added to release note

justjhong · 2022-04-27T02:00:50Z

scvi/distributions/_negative_binomial.py

+    Parameters
+    ----------
+    rate
+        rate of the Poisson distribution.


improve docs on optional args

sorry wasnt clear, just meant to expand on the definitions which looks good now. You can remove ": optional" because sphinx takes care of that for us

scvi/distributions/_negative_binomial.py

scvi/module/_totalvae.py

scvi/distributions/_negative_binomial.py

scvi/model/base/_rnamixin.py

scvi/module/_autozivae.py

scvi/model/_autozi.py

adamgayoso · 2022-05-04T00:46:01Z

@PierreBoyeau can you also add a new v0.17.0 release note and get it started in this PR?

PierreBoyeau · 2022-05-04T02:30:42Z

Sure!

…istributions_outb

PierreBoyeau · 2022-05-13T01:34:14Z

i addressed the points you raised @jjhong922 @adamgayoso

justjhong

final minor comments, but i think its good to go

justjhong · 2022-05-19T21:48:39Z

docs/release_notes/v0.17.0.md

@@ -3,6 +3,7 @@
 ## Changes

 - Experimental MuData support for {class}`~scvi.model.TOTALVI` via the method {meth}`~scvi.model.TOTALVI.setup_mudata`. For several of the existing `AnnDataField` classes, there is now a MuData counterpart with an additional `mod_key` argument used to indicate the modality where the data lives (e.g. {class}`~scvi.data.fields.LayerField` to {class}`~scvi.data.fields.MuDataLayerField`). These modified classes are simply wrapped versions of the original `AnnDataField` code via  the new {method}`scvi.data.fields.MuDataWrapper` method [#1474].
+- Modification of the `generative` method's outputs to return prior and likelihood properties as `torch.Distribution` objects. Concerned modules are `_amortizedlda.py`, `_autozivae.py`, `multivae.py`, `_peakvae.py`, `_scanvae.py`, `_vae.py`, and `_vaec.py`. This allows facilitating the manipulation of these distributions for model training and inference [#1356].


Use the api doc notation e.g. {class}~scvi.module.VAE instead of _vae.py

justjhong · 2022-05-19T21:50:09Z

scvi/distributions/_negative_binomial.py

+    Parameters
+    ----------
+    rate
+        rate of the Poisson distribution.


sorry wasnt clear, just meant to expand on the definitions which looks good now. You can remove ": optional" because sphinx takes care of that for us

* replace normal parameters in inference by distribution * totalVI changes * merge fixes * fix totalvi * fixes * fix gimvi * pyro * clean * clean * dummy * log prob sum * fix conversion * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * simplication log_prob_sum * rename px * px * Optional return_dist * feat generative refactor * updates * precommit * docstring * docstring * docstring * release note Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

adamgayoso · 2022-07-01T08:02:06Z

scvi/distributions/_negative_binomial.py

+    validate_args : optional
+        whether to validate input.
+    scale : optional
+        Normalized mean expression of the distribution.
+        This optional parameter is not used in any computations, but allows to store
+        normalization expression levels.


@PierreBoyeau @jjhong922 can we fix this?

are you talking about the docs or the optional parameter here? I can remove the :optional in the docs now

PierreBoyeau added 7 commits August 30, 2021 11:45

replace normal parameters in inference by distribution

9884cda

totalVI changes

998c345

Merge branch 'master' of https://github.com/YosefLab/scvi-tools into …

2a0c1d1

…distribution_outs

merge fixes

c9bf152

fix totalvi

c1ebcd4

fixes

493ff5d

fix gimvi

0e1d07f

PierreBoyeau closed this Feb 15, 2022

merge from main

3761bb6

PierreBoyeau reopened this Feb 15, 2022

PierreBoyeau changed the title ~~Distributions outb~~ [WIP]: Distributions outb Feb 15, 2022

adamgayoso requested a review from justjhong February 15, 2022 22:29

pyro

abffd8f

PierreBoyeau changed the title ~~[WIP]: Distributions outb~~ Distributions outb Feb 15, 2022

PierreBoyeau added 3 commits February 15, 2022 15:36

clean

ce1b4b4

clean

1227323

dummy

7d9be42

justjhong reviewed Feb 16, 2022

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adamgayoso changed the title ~~Distributions outb~~ Thorough use of distributions to clean module-level code Feb 16, 2022

PierreBoyeau and others added 3 commits February 17, 2022 11:10

log prob sum

41d9b0f

fix conversion

4868898

[pre-commit.ci] auto fixes from pre-commit.com hooks

6566c0e

for more information, see https://pre-commit.ci

justjhong mentioned this pull request Feb 17, 2022

[AmortizedLDA] Unintentionally lower bounded cell_topic_posterior_sigma #1359

Closed

simplication log_prob_sum

65df0aa

adamgayoso requested changes Feb 17, 2022

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adamgayoso added this to the 0.16.0 milestone Feb 18, 2022

PierreBoyeau added 2 commits February 18, 2022 11:49

rename px

de172e7

px

ea225a5

PierreBoyeau added 5 commits February 18, 2022 15:53

Optional return_dist

fbae55f

Merge branch 'master' of https://github.com/YosefLab/scvi-tools into …

04c4138

…distributions_outb

feat generative refactor

fedf805

updates

5f48f0e

precommit

dd2cd8b

adamgayoso modified the milestones: 0.16.0, 0.17.0 Apr 7, 2022

Merge branch 'master' of https://github.com/scverse/scvi-tools into d…

a480774

…istributions_outb

justjhong reviewed Apr 29, 2022

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PierreBoyeau added 2 commits May 2, 2022 18:44

docstring

af84491

docstring

6e205ea

adamgayoso requested changes May 4, 2022

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PierreBoyeau added 3 commits May 12, 2022 18:25

docstring

63ee149

Merge branch 'master' of https://github.com/scverse/scvi-tools into d…

43b74ee

…istributions_outb

release note

c581d14

justjhong approved these changes May 19, 2022

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adamgayoso approved these changes May 23, 2022

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justjhong merged commit 04389f7 into master May 31, 2022

justjhong deleted the distributions_outb branch May 31, 2022 18:21

adamgayoso reviewed Jul 1, 2022

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Thorough use of distributions to clean module-level code #1356

Thorough use of distributions to clean module-level code #1356

PierreBoyeau commented Feb 15, 2022 •

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Thorough use of distributions to clean module-level code #1356

Thorough use of distributions to clean module-level code #1356

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