Skip to content

Full Pydantic V2 support & latest MTENN (0.7.8) support #2

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Open
kaminow wants to merge 322 commits into
base: main
Choose a base branch
from
Open

Full Pydantic V2 support & latest MTENN (0.7.8) support #2

kaminow wants to merge 322 commits into from

Conversation

@kaminow
Copy link
Contributor

@kaminow kaminow commented Apr 2, 2025

mtenn is updating to allow separate treatment of the complex, protein, and ligand, so need to update here for compatibility.

kaminow added 26 commits April 2, 2025 14:51
@kaminow
Start to rewrite CLI to be more unified and match mtenn split model.
68197bd
@kaminow
Add representation CLI args.
fb72fa3
@kaminow
Import stuff.
9e02d18
@kaminow
Update mtenn.ModelTypes.
c2ae60c
@kaminow
Add warning if config cache is passed but doesn't exist.
f452bbd
@kaminow
Rename Trainer.model_config -> mtenn_model_config to avoid clash with…
fc2ffcc 
… pydantic v2.
@kaminow
Replace Config class with m odel_config.
3f5e737
@kaminow
Pydantic v1 -> v2.
9fb938d
@kaminow
Pydantic v1 -> v2.
140ea8e
@kaminow
Pydantic v1 -> v2.
0c5cf2d
@kaminow
Fix model_validators.
53219fe
@kaminow
Handle list types.
3705d6e
@kaminow
Pydantic v1 -> v2.
b602821
@kaminow
Pydantic v1 -> v2.
4f24acf
@kaminow
Add function to build and train.
c307c95
@kaminow
Add dataset class for split data representations.
5a499b2
@kaminow
Add handling for split dataset in DatasetConfig.
9811e5b
@kaminow
Handle split data in Trainer.
e1f61f1
@kaminow
Update e3nn label fixing for split datasets.
50bfb11
@kaminow
Can't call other click methods apparently.
2ab80eb
@kaminow
Fix validator signature.
8d00f2b
@kaminow
Validate default for pred tracker.
6664587
@kaminow
Allow missing values.
ae11ce8
@kaminow
Handle updating of nested dicts.
71b1127
@kaminow
Switch pred_tracker validator to before.
f81744e
@kaminow
Start to add dataset building back in to ML CLI.
0a94e08
@kaminow kaminow changed the base branch from main to pydantic_2 April 7, 2025 20:50
kaminow and others added 5 commits October 7, 2025 11:28
@kaminow
Need to add to list every epoch.
cc925a0
@kaminow
Don't return early.
c46f12c
@kaminow
Fix training strip math.
65c70dd
@chrisiacovella @kaminow
resolving pydantic 2 issues in everything but alchemy. (#108)
d790eae 
* updated pydantic v1 models to v2
* updating all Config classes to ConfigDict.  
* I  had to remove the multimethod overloading for dispatch function and just put in logic to switch in the dispatch function, as the multi method decorator does not seem to work with pydantic2
* skip mac os pip install of drugforge ml in cli.yaml
* pinning openmmforcefields to  >=0.15.0 to resolve issues with openmmforcefields system setup on macOS.

---------

Co-authored-by: kaminow <[email protected]>
@kaminow
Merge branch 'main' into add-split-model
7e558f8
@ijpulidos
Copy link
Contributor

ijpulidos commented Oct 14, 2025

We want to use this branch as the feature branch for all the pydantic v2 support. So we should fork off this branch to fix the alchemy pydantic v2 support.

@ijpulidos ijpulidos changed the title Add compatibility for split models in mtenn Full Pydantic V2 support & latest MTENN (0.7.8) support Oct 14, 2025
@ijpulidos ijpulidos mentioned this pull request Oct 14, 2025
Open
kaminow and others added 20 commits October 14, 2025 17:07
@kaminow
Handle arbitrary extract epochs.
a2eda9b
@kaminow
Fix how model_weights are assigned when continuing training.
99bd36c
@kaminow
New analysis method to get training progress.
013b3ba
@kaminow
Make build_results_dfs a function that can return the dfs if being us…
6fc36a8 
…ed not on the CLI.
@kaminow
Add filter-date for build_results_dfs.
3a65eeb
@kaminow
Return None if no pred trackers could be loaded.
2a04cc3
@kaminow
Fix manual splitting.
5e4e3ee
@kaminow
Use existing machinery for manual splitting when continuing training …
33bf84e 
…run.
@kaminow
Only need to make wandb tables if we're not continuing a run.
6b48643
@kaminow
Actually need splits for wandb initialization if we're not continuing.
d90475b
@kaminow
Add catches for not loading any pred trackers.
a9774d3
@kaminow
Adding statistical analyses.
1996e06
@kaminow
Try running ANOVA on a single thing at a time, but on everything.
5993a68
@kaminow
Pass single column to run on instead of doing everything in one.
92149dc
@kaminow
Keep backup of pred_tracker during training.
b416d42
@kaminow
Check for backup pred_tracker file.
2bd16d8
@kaminow
Merge branch 'main' into add-split-model
e5493a6
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
e6d1829 
for more information, see https://pre-commit.ci
@kaminow
Remove old comment.
28f3ca3
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
b85ba4a 
for more information, see https://pre-commit.ci
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@ijpulidos ijpulidos Awaiting requested review from ijpulidos

@mikemhenry mikemhenry Awaiting requested review from mikemhenry

@apayne97 apayne97 Awaiting requested review from apayne97

@mariacm12 mariacm12 Awaiting requested review from mariacm12

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

release 0.8

Development

Successfully merging this pull request may close these issues.

8 participants

@kaminow @codecov-commenter @ijpulidos @mariacm12 @apayne97 @mikemhenry @chrisiacovella