Implement ViSNet #41

fyng · 2024-01-26T20:37:23Z

Description

Implement VisNet from pytorch geometric

Fixes #40

TODO

import PyG-nightly from pip
try importing ViSNet, add flag for successful import
implement tests for VisNet

Status

Ready to go

codecov-commenter · 2024-01-26T21:55:47Z

Codecov Report

Merging #41 (3924d3f) into main (3cae786) will increase coverage by 1.22%.
Report is 22 commits behind head on main.
The diff coverage is 83.70%.

Additional details and impacted files

hmacdope · 2024-01-29T16:51:36Z

@fyng ping myself and @kaminow when you want review 😄

fyng · 2024-01-29T18:44:15Z

@hmacdope @kaminow ready for review!

hmacdope

You also need to add a CI runner that uses nightly and one that doesn't, I or Ben can show you how to do that.

devtools/conda-envs/test_env.yaml

mtenn/conversion_utils/visnet.py

mtenn/tests/test_model_config.py

.github/workflows/CI.yaml

mtenn/config.py

mtenn/conversion_utils/visnet.py

…to add-conversion-utils

mtenn/conversion_utils/visnet.py

Co-authored-by: kaminow <51923685+kaminow@users.noreply.github.com>

kaminow · 2024-02-05T19:43:06Z

@fyng is this ready for another review?

kaminow

one more quick change but then I think we're good to go!

mtenn/tests/test_model_config.py

kaminow

I think the test is actually not at all doing what we think it should be (see comments). should've caught this earlier, sorry

mtenn/tests/test_model_config.py

kaminow

two more super quick things but the new test looks good!

kaminow · 2024-02-08T17:41:26Z

mtenn/tests/test_model_config.py

+    }
+
+    pyg_model = PyVisNet(**kwargs)
+    visnet_model = ViSNet(pyg_model)


Suggested change

visnet_model = ViSNet(pyg_model)

visnet_model = ViSNet(model=pyg_model)

Great catch @kaminow, thanks! I almost snuck in a bug 🤧

mtenn/tests/test_model_config.py

Co-authored-by: kaminow <51923685+kaminow@users.noreply.github.com>

kaminow

code looks good! just a couple small docstring changes and then we should be good to go

mtenn/conversion_utils/visnet.py

kaminow

looks good, I think we're finally there!

fyng added 7 commits January 23, 2024 15:15

add visnet template

de57eda

ViSNet outputs vector embedding

eadb44c

add visnet to ModelType

f61d2d1

standardize naming for visnet

bdcadfb

add visnet to init

6a0d111

fix typo

9c9d96a

fix last layer of model

14864db

fyng requested review from kaminow and hmacdope January 26, 2024 20:42

fyng self-assigned this Jan 26, 2024

fyng added 2 commits January 26, 2024 16:27

install packages from pytorch-nightly

81f8818

pip install pytorch geometric nightly instead

be05591

fyng added 2 commits January 26, 2024 17:14

try importing visnet, implement has_visnet_flag

7be95b7

add test for visnet

f78ed8c

VisNet import error handling for older PyG version

4f8975f

hmacdope requested changes Jan 29, 2024

View reviewed changes

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mtenn/conversion_utils/visnet.py Outdated Show resolved Hide resolved

mtenn/tests/test_model_config.py Show resolved Hide resolved

fyng added 6 commits January 29, 2024 14:06

change variable name

6c15f04

add import guard to VisNet test

549e8f7

create two test environment files

efad5c3

update CI to test stable and nightly builds

25be213

fix CI

73765c4

add pytest import

f92491c

hmacdope requested changes Jan 29, 2024

View reviewed changes

.github/workflows/CI.yaml Outdated Show resolved Hide resolved

mtenn/config.py Outdated Show resolved Hide resolved

mtenn/conversion_utils/visnet.py Outdated Show resolved Hide resolved

mtenn/conversion_utils/visnet.py Outdated Show resolved Hide resolved

fyng added 4 commits January 29, 2024 16:05

fix typo and style

eb81626

Comments for Issue 42

176fccc

comments for issue #42

a277bee

fix a typo

c083277

fyng added 2 commits January 31, 2024 10:03

Merge branch 'add-conversion-utils' of github.com:choderalab/mtenn in…

e8fe374

…to add-conversion-utils

clean up todo

48721fb

kaminow reviewed Jan 31, 2024

View reviewed changes

mtenn/conversion_utils/visnet.py Show resolved Hide resolved

fyng and others added 5 commits January 31, 2024 15:23

bring in prior_model from PyG visnet

ffa571c

Co-authored-by: kaminow <51923685+kaminow@users.noreply.github.com>

fix indentation

ec3c0c2

add a visnet test

34c8ace

add import warning to visnet import guard

ba91938

fix typo

a406012

kaminow requested changes Feb 5, 2024

View reviewed changes

mtenn/tests/test_model_config.py Outdated Show resolved Hide resolved

remove redundant visnet set_config test

5f161a3

fyng requested a review from kaminow February 5, 2024 21:30

kaminow requested changes Feb 5, 2024

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fyng added 2 commits February 7, 2024 13:41

fix typo in docstring

d14f65d

fix visnet instantiation from pyg test

60aa245

fyng requested a review from kaminow February 7, 2024 19:17

kaminow requested changes Feb 8, 2024

View reviewed changes

fyng and others added 5 commits February 9, 2024 00:43

Update mtenn/tests/test_model_config.py

c85b995

Co-authored-by: kaminow <51923685+kaminow@users.noreply.github.com>

minor changes

ec8b6c2

update visnet instantiation of pyg and test

4a53919

fix mtenn visnet instantiation from pyg visnet

3458514

guard import

cd2086b

fyng requested a review from kaminow February 9, 2024 20:18

kaminow requested changes Feb 12, 2024

View reviewed changes

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mtenn/conversion_utils/visnet.py Outdated Show resolved Hide resolved

mtenn/conversion_utils/visnet.py Outdated Show resolved Hide resolved

mtenn/conversion_utils/visnet.py Outdated Show resolved Hide resolved

fyng added 2 commits February 12, 2024 14:54

update docstrings

d5c1b46

update doc strings

3924d3f

fyng requested a review from kaminow February 13, 2024 15:26

kaminow approved these changes Feb 13, 2024

View reviewed changes

kaminow merged commit 3b08d3e into main Feb 13, 2024
8 of 9 checks passed

kaminow deleted the add-conversion-utils branch February 13, 2024 20:00

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Implement ViSNet #41

Implement ViSNet #41

fyng commented Jan 26, 2024 •

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	visnet_model = ViSNet(pyg_model)
	visnet_model = ViSNet(model=pyg_model)

Implement ViSNet #41

Implement ViSNet #41

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fyng commented Jan 26, 2024 • edited Loading

Description

TODO

Status

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fyng commented Jan 26, 2024 •

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