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0.8.0

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

* Pass export_input_data and export_exp_data args around correctly.

* Split split_dict validator into one for initializing and one for checking.

* Add missing args to ds_config.

* Rework kvp splitting function to allow : in the values (needed for e3nn irreps).

* Add eplicit optional to Field annotations.

* Update model building CLI tests.

* Remove visnet tests for now.

* __fields__ -> model_fields

* json -> model_dump_json

* Need to validate defaults for some Fields.

* Need to add general_ds_args decorator.

* Need to add struct_ds_args decorator.

* Update build-and-train CLI tests.

* Capitalize split names automaticall to make plots prettier.

* Filter split datasets for structures with invalid smiles.

* Update jitter CLI testing.

* Only keep floats for target_val.

* Skip tests that won't work yet.

* Update json roundtrip test.

* json -> model_dump_json

* Make sure loss configs are in the same order.

* Remove unused import.

* Add option for date-based filtering.

* bump ci

* test running with multiple env files

* move openeye testing

* use different micromamba command

* fix missing asapdiscovery-modeling install

* Add verbose option for printing info for each pred_tracker file.

* Add handling for trying to parse Nones in pred trackers.

* dict -> model_dump

* Update ML workflow file to include MacOS and latest micromamba version.

* add workflows

* Rename macOS conda-envs directory.

* add workflows

* Environment file for cli ci ubuntu

* Environment file for cli ci macos

* workflow file for CLI CI

* add workflows

* fix workflows for simulation and spectrum

* Remove MacOS from ML workflow.

* add workflows

* install environments for other packages

* Fix pose_predictions format.

* Separate environment files (#9)

* add initial ubuntu and mac latest environments and update data.yaml github workflow to point to it

* add a python script to find imports in files

* add plip dependency

* temporarily fix failing openfe warning catching

* update detect_imports script and add modeling yaml files

* update data and modeling workflows

* update docking CI and add docking yaml

* add dataviz to docking dependencies

* add simulation yamls

* add modeling to simulation dependencies

* add macos to data workflow

* update workflows

* remove unnecessary packages from modeling workflow

* add simulation workflow package

* update simulation deps

* add ml env and update env names

* add torchdata to docking deps

* add openmmtools to deps

* add ml to simulation deps

* remove multiprocessing from ML deps

* remove multiprocessing from simulation deps

* update ml envs

* make mtenn simulation dep

* add modeling to ml deps

* add semver to docking deps

* move cli_args to have lazy imports and add spectrum env files

* also run on the pydantic_2 branch

* bump ci

* test running with multiple env files

* move openeye testing

* use different micromamba command

* fix missing asapdiscovery-modeling install

* Update ML workflow file to include MacOS and latest micromamba version.

* add workflows

* Rename macOS conda-envs directory.

* add workflows

* Environment file for cli ci ubuntu

* Environment file for cli ci macos

* workflow file for CLI CI

* add workflows

* fix workflows for simulation and spectrum

* Remove MacOS from ML workflow.

* add workflows

* install environments for other packages

* adding data missing dependencies

* environment file for alchemy ubuntu-latest

* environment file for alchemy macos-latest

* workflow file update for alchemy

* macos uncapitalized in workflows

* Add pydantic-settings.

* add dataviz env files

* Add mamba installing dependencies in ML workflow file.

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Co-authored-by: kaminow <kaminow@cshl.edu>
Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>
Co-authored-by: Maria Castellanos <castelm3@mskcc.org>
Co-authored-by: kaminow <benjamin.kaminow@choderalab.org>

* make a real workflows env file

* remove workflow deps yaml

* don't run workflows CI on macos

* use bioconda for logomaker

* fix dataviz workflow

* update dataviz workflow install

* rename dataviz env

* fix dataviz env

* remove modeling as a dep for data

* move trim_small_chains to backend

* adapt to str enum update

* fix .schema import

* remove macos-ci workflow

* fix from .backend import

* move prepped structure and docking stuff to modeling and docking envs

* move plip to dataviz

* fix PreppedComplex use in conftests

* most postera api to workflows

* fix imports

* test fintscore in dataviz

* remove other subpackages for data ci workflow

* fix prep tests

* fix imports

* Update ML env.

* Fix env files I messed up.

* Fix env name for installing other drugforge pacakge deps.

* Remove cudatoolkit from macos simulation.yaml.

* Remove unittest dep.

* Make Fields explicitly optional.

* Fix env name

* Fix validator for pose_predictions.

* Add option for random iterating in Dataset class.

* Handle random iter field in build method.

* Add random_iter in DockedDataset builder functions.

* Add test for random iter.

* Add CLI args and handling for dataset random_iter option.

* Add random_iter to the rest of the dataset classes.

* Add CLI test for random iter.

* Add handling in Trainer for CLI args that are passed along with a cache file.

* Fix assigning random_iter so that it works for ds objects build before it was introduced.

* remove cudatoolkit dep from simulation.yaml (#39)

* switch to using the new buckets (#41)

* switch to using the new buckets

* missed a few urls

---------

Co-authored-by: Alexander Matthew Payne <31800806+apayne97@users.noreply.github.com>

* Spectrum struct changes (#10)

* add rmsd-coloring

* Fix chain visualization

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

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* Fix pre-commit-ci

* Add the option to align struct directory and pdb file

* Needed changes on seq_alignment

* Implement fitness-alignment to align wrt fasta

* Add more options to struct-alignment

* changes to fitness-alignment

* Additions to align_seq_match

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

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* precommit ci fixes

* fix seq-align test

* struct-alignment tests

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

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* Add structure alignment tests

* Fix struct-alignment cfold test

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* bump CI

* Added a check for blast.csv file

* Bump CI

* TODO to fix test here with "hidden" error

* Checking subprocess return code, print error

* added mafft dependancy

* add mafft to ubuntu yaml

* remove macOS skips from tests

---------

Co-authored-by: Castellanos Morales <castelm3@iscb007.mskcc.org>
Co-authored-by: Castellanos Morales <castelm3@iscf019.mskcc.org>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Maria Castellanos <castelm3@mskcc.org>
Co-authored-by: hmacdope <hugomacdermott@gmail.com>
Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>

* Dropping bespokefit in codebase (#22)

* Dropping bespokefit in codebase

* using pydantic.v1 instead

* trying to fix CI issues by pinning to torchdata 0.8.0 for compatibility with dgl 2.3

* Fixing env path for alchemy CI

* fixing package name for alchemiscale

* fixing package name for alchemiscale on macos

* pinning openfe versions

* Bump CI

* pinning openfe versions for linux

* pinning compatibility to minor versions

* dropping python pins

* dropping python pins for every package

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Co-authored-by: chrisiacovella <chris.iacovella@gmail.com>

* update cli-ci (#48)

* update cli-ci

* change order of OE license checks

* add simulation to cli deps

* add dataviz and spectrum to deps

* fixing pydantic issues in alchemy (#52)

* FIXING ISSUES with pydantic models to handle ScopedKey (including serialization); fixed issues with passing json files to openfe
---------

Co-authored-by: Alexander Matthew Payne <31800806+apayne97@users.noreply.github.com>

* Add weights_path in model_config.

* Migrate ml.inference to pydantic 2.

* Migrate ml.models to pydantic 2.

* Missed changes.

* Add mtenn pins for model specs.

* Update inference to new mtenn version.

* Add new ML registry to test files.

* Update GAT inference -> LigandOnly inference.

* Handle HttpUrl Fields for urljoin.

Update structure-based model inference tests.

* Track representation types in model specs.

* Update test_models hash.

* Add model selection from representation type.

* Return input_data format from test_data.

* Update structure-based model inference tests.

* Clean up leftover asapdiscovery files.

* Update ML workflow to use the right conda env.

* Update alchemy gufe import.

* Handle label mappings not being passed.

* Add early stopping that checks for loss below a certain threshold.

* Start to add analysis tools.

* Add calc_stats to analysis.

* Add filtering functions.

* Add new stat function to calculate MAE that's adjusted for semi-quantitative values.

* Add GL loss class from book.

* Add PQ loss from book.

* Add progress_quotient es handling to Trainer.

* Add config handling for progress quotient es.

* Missed adding train loss to tr
8000
acked vals.

* Need to add to list every epoch.

* Don't return early.

* Fix training strip math.

* resolving pydantic 2 issues in everything but alchemy. (#108)

* 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 <51923685+kaminow@users.noreply.github.com>

* Handle arbitrary extract epochs.

* Fix how model_weights are assigned when continuing training.

* New analysis method to get training progress.

* Make build_results_dfs a function that can return the dfs if being used not on the CLI.

* Add filter-date for build_results_dfs.

* Return None if no pred trackers could be loaded.

* Fix manual splitting.

* Use existing machinery for manual splitting when continuing training run.

* Only need to make wandb tables if we're not continuing a run.

* Actually need splits for wandb initialization if we're not continuing.

* Add catches for not loading any pred trackers.

* Adding statistical analyses.

* Try running ANOVA on a single thing at a time, but on everything.

* Pass single column to run on instead of doing everything in one.

* Keep backup of pred_tracker during training.

* Check for backup pred_tracker file.

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

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* Remove old comment.

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

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* Rev pydantic2 for alchemy (#132)

* fixing issue in to_rdkit functionality and other minor parts

* Adding env yaml file (all.yaml) that seems to work for creating a single workable environment

* Seems to be an issue with lomap

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

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* Revising code to work with new Gufe that dropped FloatQuantity

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

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* Removing print/debugging that exhausts the file pointer contents

* Need to use raw values instead, because pydantic transforms Quantity to dict

* We force quantities now. Need to review uncertainties.

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

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* Update macos alchemy env

* Remove reference to `pkg_resources`. Using `importlib`

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

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* Remove reference to `pkg_resources`... 2nd iteration :)

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* Using explicit pkg name instead

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

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* fixing some minor pydantic updates

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

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* Using explicit pkg name instead

* Removing unnecessary debug prints

* Making sure we preserve names when creating oe molecules

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

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* Overriding default settings for rdkit to make serialization work properly

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

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* Overriding default settings for rdkit to make serialization work properly; trying putting it in a different spot.

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

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* Overriding default settings for rdkit to make serialization work properly; trying putting it in a different spot.

* Fix some import issues pre-commit found; fixing ml issues.

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* fixing precommit complaints

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* xskip on mac os the test_plan_from_names until we can get the issue resolved on GUFE. Also added in check to ensure we are setting AllProps for pickling in rdkit (things will definitely fail if this is not set, even if this is not sufficient on mac os)

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* addressing precommit formatting complaints

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* use lazy imports for docking score test

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

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* update pin in all.yaml

* addressing comments from Alex.

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

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* A few deprecated pydantic functions were still being used. updating these.

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---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>
Co-authored-by: David Dotson <dotsdl@gmail.com>
Co-authored-by: apayne97 <alex.payne@choderalab.org>

* removing pkg_resources usage in manifold_data_validation.py

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* fixing pre-commit unused/duplicate imports

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* fixing typing issue of conf_tags in ligand.py (needs to be dict)

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* reformatting score.py

* updating pins to be consistent to hopefully speed up CI environment solving.

* to use dask-cuda, it appears we need to use the rapidsai channel for newer versions (they seem to have stopped updating their conda-forge builds)

* mispelled channel in ml.yaml

* trying a different strategy for building environment from multiple yaml files for cli

* trying a different strategy for building environment from multiple yaml files for workflows and dataviz as it worked for cli

* need os dependent yaml file args

* typo in mac os yaml file args

* forgo to remove some additional conda solving in macos on cli.

* accidentally deleted env: tag in cli.yaml (before we set the license.

* fix logomaker error (#141)

* Addressing comments from Ivan and Alex

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

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* Addressing comments from Ivan and Alex

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

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* Addressing comments from Ivan and Alex

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

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* Addressing comments from Ivan and Alex

* reverting quantity encoder changes

* making precommit happy.

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

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* making precommit happy.

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

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* making precommit happy.

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

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* making precommit happy.

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

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* Use Optional typing.

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

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* making precommit happy.

* Add docstring for ML CLI build_ds function.

* Fix early return for build_ds function.

* Adding in some doc strings and adding notes about possible sporadic failure of test_alchemy_prep_run_bad_chemistry.

* Add ml.analysis docstrings.

* Remove unused functions.

* Add ml.cli docstrings.

* Rename es -> early_stopping.

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

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* Remove unused function.

* Remove unused imports.

* Renaming some missed es instances.

* Match CLI args.

* Switch macOS -> macos.

* Rename models from 'drugforge*' back to 'asapdiscovery*' to denote that models were trained on ASAP data.

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Co-authored-by: Alexander Matthew Payne <alexpayne1997@gmail.com>
Co-authored-by: kaminow <kaminow@cshl.edu>
Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>
Co-authored-by: Maria Castellanos <castelm3@mskcc.org>
Co-authored-by: Alexander Matthew Payne <31800806+apayne97@users.noreply.github.com>
Co-authored-by: Alex <alex.payne@choderalab.org>
Co-authored-by: Maria Castellanos <79340102+mariacm12@users.noreply.github.com>
Co-authored-by: Castellanos Morales <castelm3@iscb007.mskcc.org>
Co-authored-by: Castellanos Morales <castelm3@iscf019.mskcc.org>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: hmacdope <hugomacdermott@gmail.com>
Co-authored-by: chrisiacovella <chris.iacovella@gmail.com>
Co-authored-by: David Dotson <dotsdl@gmail.com>

Apr 28, 2026
643e041
zip
tar.gz
Notes

0.7.2

Small improvements to spectrum (#100)

* change toml files

* delete asap- mentions in docstrings

* update documentation on spectrum pt.1

* add all docs building requirements to yaml file

* fix requirements name and docs

* add sphinx reqs back to requirements.yaml

* update docs landing page

* add logo image

* Add files for tutorial to aws

* update spectrum tutorial 2

* add alignment image for tutorial

* changes for tutorial

* corrected mentions of bespoke fit

* show blast score in html

* Add option to calculate bsite similarity

* get rid of mgltool dependency

* add openbabel req to spectrum

* add test for whether file generated by convert_to_pdbqt can be used by vina

---------

Co-authored-by: Maria Castellanos <castelm3@mskcc.org>
Co-authored-by: Alexander Matthew Payne <alexpayne1997@gmail.com>
Co-authored-by: Alex Payne <alex.payne@choderalab.org>
Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alexander Matthew Payne <31800806+apayne97@users.noreply.github.com>

Mar 5, 2026
0a02f4d
zip
tar.gz
Notes

0.7.1

Install instructions for openeye in CLI if openeye not present (#125)

* Warn users of the CLI if openeye oechem triggers import error

* Ignoring F401 not used module rule here from linter

* Freeing up space by removing dotnet from runner

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Jan 14, 2026
4414ac9
zip
tar.gz
Notes

0.7.0

no reason to put an upper bound on the python version AFAIK (#90)

Aug 27, 2025
92d38dd
zip
tar.gz
Notes

v0.0.1

Pydantic 2 (#3)

* change install pin

* normalise imports

* finalise imports

* try bulk replace imports

* Revert "finalise imports"

This reverts commit baad442.

* Revert "Revert "finalise imports""

This reverts commit 840abd5.

* Revert "try bulk replace imports"

This reverts commit 1cb8a82.

* bulk replace again

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

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* Add a shortcut for not training if all epochs have already been trained for.

* Add weight decay handling in Trainer.

* Fix weight_decay math.

* Use torch.no_grad instead of model.eval.

* Add model.eval() and model.train() calls.

* Add Trainer weight decay loss.

* Switch default batch size to be -1.

* Add device Field for DatasetConfig to automatically move data to given device.

* Add option for batch gradient normalization.

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

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* Fix comment.

* Add forgotten optimizer step.

* Remove print statement.

* bump CI

* Add classes for L1Loss and SmoothL1Loss.

* Fix loss calculation for multiple prediction/loss values.

* Add LossFunctionConfig options for new loss classes.

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

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* Add CLI arg for LayerNorm option.

* Fix typo.

* Handle missing column.

* Some plotting improvements.

* Add convenience methods for loading in and formatting groups of TrainingPredictionTrackers.

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* Add multiprocessing capability to TPT loading functions.

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* Add handling for no extract_epochs passed.

* Add a shortcut for not training if all epochs have already been trained for.

* Add weight decay handling in Trainer.

* Fix weight_decay math.

* Use torch.no_grad instead of model.eval.

* Add model.eval() and model.train() calls.

* Add Trainer weight decay loss.

* Switch default batch size to be -1.

* Add device Field for DatasetConfig to automatically move data to given device.

* Add option for batch gradient normalization.

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* Fix comment.

* Add forgotten optimizer step.

* Remove print statement.

* Add classes for L1Loss and SmoothL1Loss.

* Fix loss calculation for multiple prediction/loss values.

* Add LossFunctionConfig options for new loss classes.

* Add CLI arg for LayerNorm option.

* Fix typo.

* Handle missing column.

* Some plotting improvements.

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

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* Add convenience methods for loading in and formatting groups of TrainingPredictionTrackers.

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* Add multiprocessing capability to TPT loading functions.

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* Add handling for no extract_epochs passed.

* Fix minor errors.

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* Update asapdiscovery-ubuntu-latest.yml

* Update asapdiscovery-macOS-latest.yml

* Update asapdiscovery-macOS-12.yml

* Separate environment files (#9)

* add initial ubuntu and mac latest environments and update data.yaml github workflow to point to it

* add a python script to find imports in files

* add plip dependency

* temporarily fix failing openfe warning catching

* update detect_imports script and add modeling yaml files

* update data and modeling workflows

* update docking CI and add docking yaml

* add dataviz to docking dependencies

* add simulation yamls

* add simulation yamls

* add modeling to simulation dependencies

* add modeling to simulation dependencies

* add macos to data workflow

* update workflows

* remove unnecessary packages from modeling workflow

* add simulation workflow package

* update simulation deps

* add ml env and update env names

* add torchdata to docking deps

* add openmmtools to deps

* add ml to simulation deps

* remove multiprocessing from ML deps

* remove multiprocessing from simulation deps

* update ml envs

* make mtenn simulation dep

* add modeling to ml deps

* add semver to docking deps

* move cli_args to have lazy imports and add spectrum env files

* also run on the pydantic_2 branch

* bump ci

* test running with multiple env files

* move openeye testing

* use different micromamba command

* fix missing asapdiscovery-modeling install

* Update ML workflow file to include MacOS and latest micromamba version.

* add workflows

* Rename macOS conda-envs directory.

* add workflows

* Environment file for cli ci ubuntu

* Environment file for cli ci macos

* workflow file for CLI CI

* add workflows

* fix workflows for simulation and spectrum

* Remove MacOS from ML workflow.

* add workflows

* install environments for other packages

* install environments for other packages

* adding data missing dependencies

* environment file for alchemy ubuntu-latest

* environment file for alchemy macos-latest

* workflow file update for alchemy

* macos uncapitalized in workflows

* Add pydantic-settings.

* add dataviz env files

* Add mamba installing dependencies in ML workflow file.

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Co-authored-by: kaminow <kaminow@cshl.edu>
Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>
Co-authored-by: Maria Castellanos <castelm3@mskcc.org>
Co-authored-by: kaminow <benjamin.kaminow@choderalab.org>

* make a real workflows env file

* remove workflow deps yaml

* don't run workflows CI on macos

* use bioconda for logomaker

* fix dataviz workflow

* fix dataviz workflow

* update dataviz workflow install

* rename dataviz env

* fix dataviz env

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Jul 15, 2025
47220a6
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Notes

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Jul 12, 2024
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