Deepchem

New Contributors
* maithili232 made their first contribution in https://github.com/deepchem/deepchem/pull/3178
* brianpzaide made their first contribution in https://github.com/deepchem/deepchem/pull/3210
* GreatRSingh made their first contribution in https://github.com/deepchem/deepchem/pull/3207
* vsaravind01 made their first contribution in https://github.com/deepchem/deepchem/pull/3249
* gauthamk02 made their first contribution in https://github.com/deepchem/deepchem/pull/3276
* shoaib6174 made their first contribution in https://github.com/deepchem/deepchem/pull/3324
* anoushka2000 made their first contribution in https://github.com/deepchem/deepchem/pull/3371
* Yukino2002 made their first contribution in https://github.com/deepchem/deepchem/pull/3384
* riya-singh28 made their first contribution in https://github.com/deepchem/deepchem/pull/3430
* shreyasvinaya made their first contribution in https://github.com/deepchem/deepchem/pull/3331
* NimishaDey made their first contribution in https://github.com/deepchem/deepchem/pull/3428
* mgyigit made their first contribution in https://github.com/deepchem/deepchem/pull/3477
* Ash-29 made their first contribution in https://github.com/deepchem/deepchem/pull/3519
* piyushkanadje made their first contribution in https://github.com/deepchem/deepchem/pull/3481
* vmm221313 made their first contribution in https://github.com/deepchem/deepchem/pull/3531
* CurtisColwell made their first contribution in https://github.com/deepchem/deepchem/pull/3570
* KitVB made their first contribution in https://github.com/deepchem/deepchem/pull/3585
* aaronrockmenezes made their first contribution in https://github.com/deepchem/deepchem/pull/3595
* MarcS18 made their first contribution in https://github.com/deepchem/deepchem/pull/3632
* soulpower007 made their first contribution in https://github.com/deepchem/deepchem/pull/3574
* P-Kelley made their first contribution in https://github.com/deepchem/deepchem/pull/3705
* naseehasalam made their first contribution in https://github.com/deepchem/deepchem/pull/3723
* HridayM25 made their first contribution in https://github.com/deepchem/deepchem/pull/3726
* Shiva-sankaran made their first contribution in https://github.com/deepchem/deepchem/pull/3801
* quincylin1 made their first contribution in https://github.com/deepchem/deepchem/pull/3820
* Dragonwagon18 made their first contribution in https://github.com/deepchem/deepchem/pull/3837
* karannb made their first contribution in https://github.com/deepchem/deepchem/pull/3832

**Full Changelog**: https://github.com/deepchem/deepchem/compare/2.7.1...2.8.0

Pre-release for 2.8.0. If tests look stable, will release 2.8.0 shortly

- Update to release workflow for publishing package in pypi

Highlights
- DeepChem adds support for new models including DMPNNs, and MEGNet
- We have ported NormalizingFlows to PyTorch
- Added support for multi-gpu training via pytorch lightning.
- Utilities to run hhsearch multisequence alignment search on a dataset
- We have ported several layers to pytorch

Porting Models to PyTorch
The following models/layers have been ported to pytorch: GRU, InterAtomicL2Distance, WeightedLinearCombo, CombineMeanStd, AtomicConvolution layer, NeighborList, CNN, LSTMStep

New Features
- Fake graph data generator to generate random graphs
- FASTQ Loader to load biological sequences of data
- Added top_k_accuracy_score metric for evaluating model performances
- Extracting molecular coordinates from QM9 dataset
- Support for Random hyperparameter tuning

Featurizers
- DMPNN Featurizer
- Sparse matrix one hot featurizer
- Position Frequency Matrix Featurizer implements a featurizer for position frequency matrices on a list of multisequence alignments to return a list of position frequency matrices.

New Layers
- MEGNet Layer

Deprecations
- dc.evaluate.utils.relative_difference is being deprecated. A deprecation warning to use `math.isclose`, `np.isclose`, `np.allclose` has been put in place.

Examples and Tutorials
- Using hydra config system with pytorch-lightning system
- New tutorial have been added to DeepQMC, SCVI and ScanPy, HierVAE, molGAN, hyper-parameter optimization, neural ODE, gaussian process, pytorch lightning, training a normalising flow on qm9 model, grover.

Documentation
- Documentation has been improved with wider examples, using deepchem with docker, model cheat sheets.
- Citations have been added to some of the tutorials to make them citable.

Improvements
- Speed up in atomic convolution model
- Utilities in deepchem disk dataset to convert it to a csv file.
- Added file storage of validation and train scores during hyperparameter optimization.
- Modified GraphData to support kwargs for storing additional attributes
- Made it possible to run DeepChem in offline mode by removing default download call from CGCNN

Refactors
- Mol2vec_fingerprints to directly use method from gensim library rather than mol2vec sub-package.

Bug Fixes
- Retrieving shape of disk dataset when task names are not specified
- Improvements in k-fold split when the number of data points is not exactly divisible by k
- Fix a bug in SmilesToSeq featurizer when the padding length is 0.
- A bug in which LogTransformer fails on data without an explicit task dimension has been fixed.

Maintenance
- Adding type hints.
- CI pipeline to consume less time

What's Changed
* Bump to dev version by rbharath in https://github.com/deepchem/deepchem/pull/2825
* add top_k_accuracy metric by tonydavis629 in https://github.com/deepchem/deepchem/pull/2818
* Update models.rst by neerajanand321 in https://github.com/deepchem/deepchem/pull/2828
* adding Docker tutorial by shaipranesh2 in https://github.com/deepchem/deepchem/pull/2814
* Added Graph Networks by arunppsg in https://github.com/deepchem/deepchem/pull/2843
* added molGAN tutorial by saithat in https://github.com/deepchem/deepchem/pull/2773
* adding hyperopt tutorials by shaipranesh2 in https://github.com/deepchem/deepchem/pull/2851
* Improvements to GraphData by arunppsg in https://github.com/deepchem/deepchem/pull/2860
* Update to Documentation for Using DeepChem in Jupyter Notebook by iherath in https://github.com/deepchem/deepchem/pull/2856
* Removing some obsolete code by arunppsg in https://github.com/deepchem/deepchem/pull/2855
* Removing package pins by arunppsg in https://github.com/deepchem/deepchem/pull/2783
* Fake graph data generator by arunppsg in https://github.com/deepchem/deepchem/pull/2865
* removing package pin by arunppsg in https://github.com/deepchem/deepchem/pull/2873
* adding jax dependencies by arunppsg in https://github.com/deepchem/deepchem/pull/2877
* Sparse matrix one hot featurizer by davidRFB in https://github.com/deepchem/deepchem/pull/2870
* added neural ode tutorial :books: by shivance in https://github.com/deepchem/deepchem/pull/2859
* Fixing Colab Links by rbharath in https://github.com/deepchem/deepchem/pull/2883
* Adding batch processing to GraphNet layer by arunppsg in https://github.com/deepchem/deepchem/pull/2874
* MEGNet layer implementation by arunppsg in https://github.com/deepchem/deepchem/pull/2837
* Fixing broken CI on windows - Jax and Vina by arunppsg in https://github.com/deepchem/deepchem/pull/2886
* Fresh gp tutorial by TheRealSalmon in https://github.com/deepchem/deepchem/pull/2864
* Fix to log transformer by rbharath in https://github.com/deepchem/deepchem/pull/2887
* Best score callback by TheRealSalmon in https://github.com/deepchem/deepchem/pull/2866
* fix for bug(issue 2106) by shaipranesh2 in https://github.com/deepchem/deepchem/pull/2857
* deepchem pytorch lightning tutorial by Chahalprincy in https://github.com/deepchem/deepchem/pull/2826
* sequence_utils for sequence homology search by tonydavis629 in https://github.com/deepchem/deepchem/pull/2890
* Speed up AtomicConv model, improvements to AtomicConv tutorial by juliusgeo in https://github.com/deepchem/deepchem/pull/2888
* Update Training_a_Normalizing_Flow_on_QM9.ipynb by JoseAntonioSiguenza in https://github.com/deepchem/deepchem/pull/2885
* Resolve the bug issue of loading the .sdf files by JoseAntonioSiguenza in https://github.com/deepchem/deepchem/pull/2795
* Position Frequency Matrix Featurizer by tonydavis629 in https://github.com/deepchem/deepchem/pull/2896
* Adding a tutorial for GROVER. by atreyamaj in https://github.com/deepchem/deepchem/pull/2901
* Update tutorials.rst by BalajiAI in https://github.com/deepchem/deepchem/pull/2902
* Adding FutureWarning to depreciate deepchem.utils.evaluate.relative_difference by arunppsg in https://github.com/deepchem/deepchem/pull/2909
* Module dl dependancies by Nozziel in https://github.com/deepchem/deepchem/pull/2908
* Extracting molecular coordinates for QM9 dataset from sdf files by arunppsg in https://github.com/deepchem/deepchem/pull/2903
* Add bibtex citation to first tutorial by paupaiz in https://github.com/deepchem/deepchem/pull/2912
* Update torchvision version requirement by Matthew-Hostetler in https://github.com/deepchem/deepchem/pull/2916
* add citation tutorial 4 by paupaiz in https://github.com/deepchem/deepchem/pull/2921
* add citation tutorial 5 by paupaiz in https://github.com/deepchem/deepchem/pull/2922
* Fixing CI errors by arunppsg in https://github.com/deepchem/deepchem/pull/2931
* Update scientists.rst by shivance in https://github.com/deepchem/deepchem/pull/2932
* resolved deprecation warning by ARY2260 in https://github.com/deepchem/deepchem/pull/2937
* atom features function and helper functions for DMPNN Featurizer by ARY2260 in https://github.com/deepchem/deepchem/pull/2929
* NormalizingFlow class and Affine transformation created using Pytorch by JoseAntonioSiguenza in https://github.com/deepchem/deepchem/pull/2918
* add bond_features and reaction mapping with suitable tests for DMPNN by ARY2260 in https://github.com/deepchem/deepchem/pull/2942
* Adding DeepQMC tutorial by shaipranesh2 in https://github.com/deepchem/deepchem/pull/2914
* Intro8 bibtex by paupaiz in https://github.com/deepchem/deepchem/pull/2925
* add bibtex tutorial 7 by paupaiz in https://github.com/deepchem/deepchem/pull/2924
* Update model cheatsheet by j-frie in https://github.com/deepchem/deepchem/pull/2947
* first steps in fixing docker build by Nozziel in https://github.com/deepchem/deepchem/pull/2949
* Added torch equivalent of InterAtomicL2Distances in torch_layers.py + YAPF changes by atreyamaj in https://github.com/deepchem/deepchem/pull/2934
* added HierVAE tutorial by saithat in https://github.com/deepchem/deepchem/pull/2904
* modify molecular featurizer base class and suitable tests by ARY2260 in https://github.com/deepchem/deepchem/pull/2960
* added _MapperDMPNN class and suitable tests by ARY2260 in https://github.com/deepchem/deepchem/pull/2962
* implement DCLightningModule by Chahalprincy in https://github.com/deepchem/deepchem/pull/2945
* Normalizing Flow Torch Model by JoseAntonioSiguenza in https://github.com/deepchem/deepchem/pull/2944
* Adding Metropolis Hasting sampler by shaipranesh2 in https://github.com/deepchem/deepchem/pull/2935
* Minor fix for utils.rst by shaipranesh2 in https://github.com/deepchem/deepchem/pull/2973
* add global feature generator and suitable unit tests by ARY2260 in https://github.com/deepchem/deepchem/pull/2971
* Updated Tutorial File with TorchModel example by allesrebel in https://github.com/deepchem/deepchem/pull/2977
* :octocat: Fixed potential bug in deepchem's CNN implementation by shivance in https://github.com/deepchem/deepchem/pull/2964
* fix bug in GraphData class and add suitable unit test by ARY2260 in https://github.com/deepchem/deepchem/pull/2979
* Gcn by Chahalprincy in https://github.com/deepchem/deepchem/pull/2958
* python v3.8 in readthedocs.yml by arunppsg in https://github.com/deepchem/deepchem/pull/2984
* Pinning sphinx version in docs/requirements.txt by arunppsg in https://github.com/deepchem/deepchem/pull/2985
* Fixing 2986 by shivance in https://github.com/deepchem/deepchem/pull/2988
* PEP-008 style corrections for electron sampler by shaipranesh2 in https://github.com/deepchem/deepchem/pull/2987
* add count-based morgan fingerprint featurizer and suitable unit tests by ARY2260 in https://github.com/deepchem/deepchem/pull/2980
* removed css theme by arunppsg in https://github.com/deepchem/deepchem/pull/2991
* modify RDKitDescriptors class for normalized features by ARY2260 in https://github.com/deepchem/deepchem/pull/2983
* Add Trident Chemwidgets tutorial to `examples/tutorials by TShimko126 in https://github.com/deepchem/deepchem/pull/2965
* add DMPNN featurizer class and suitable unit tests by ARY2260 in https://github.com/deepchem/deepchem/pull/2995
* add new global feature generators and units tests for DMPNN featurizer by ARY2260 in https://github.com/deepchem/deepchem/pull/3005
* bibtex tutorial 9 by paupaiz in https://github.com/deepchem/deepchem/pull/2926
* implement dc lightning dataset module by Chahalprincy in https://github.com/deepchem/deepchem/pull/2993
* update unit tests with DC Lightning dataset module by Chahalprincy in https://github.com/deepchem/deepchem/pull/2994
* Added pytorch-lightning in mac requirements by ojeda-e in https://github.com/deepchem/deepchem/pull/3008
* modify PositionwiseFeedForward class and add unit tests by ARY2260 in https://github.com/deepchem/deepchem/pull/3009
* add mapper class for dmpnn model and suitable unit tests by ARY2260 in https://github.com/deepchem/deepchem/pull/3001
* :octocat: Porting CNN, TF ➡️ PyTorch by shivance in https://github.com/deepchem/deepchem/pull/2963
* Adding KFAC by shaipranesh2 in https://github.com/deepchem/deepchem/pull/2972
* ScanPy tutorial by paupaiz in https://github.com/deepchem/deepchem/pull/3018
* Adding to_csv method to DiskDataset by arunppsg in https://github.com/deepchem/deepchem/pull/3007
* bibtex tutorial 10 by paupaiz in https://github.com/deepchem/deepchem/pull/2927
* Port of WeightedLinearCombo from Keras to Torch by subzjee in https://github.com/deepchem/deepchem/pull/3022
* add dmpnn encoder layer and suitable unit test by ARY2260 in https://github.com/deepchem/deepchem/pull/3023
* Port of CombineMeanStd from Keras to Torch by subzjee in https://github.com/deepchem/deepchem/pull/3021
* Port of AtomicConvolution to Torch by subzjee in https://github.com/deepchem/deepchem/pull/3026
* Port of NeighborList from Keras to Torch by subzjee in https://github.com/deepchem/deepchem/pull/3020
* add dmpnn class and suitable unit tests by ARY2260 in https://github.com/deepchem/deepchem/pull/3028
* Scvi tools tutorial by paupaiz in https://github.com/deepchem/deepchem/pull/3025
* Adding electron input streams for Ferminet by shaipranesh2 in https://github.com/deepchem/deepchem/pull/2997
* add torch model wrapper for DMPNN model class by ARY2260 in https://github.com/deepchem/deepchem/pull/3034
* Real NVP Transformation Layer for Normalizing Flows by JoseAntonioSiguenza in https://github.com/deepchem/deepchem/pull/2996
* Fixes to k-fold fingerprint splitting by chertianser in https://github.com/deepchem/deepchem/pull/3038
* GCNModel benchmark script for gpu by Chahalprincy in https://github.com/deepchem/deepchem/pull/3016
* Update pytorch-lightning version by Chahalprincy in https://github.com/deepchem/deepchem/pull/3042
* FASTQ loader by paupaiz in https://github.com/deepchem/deepchem/pull/3036
* pinning scipy to fix torch build in ci by arunppsg in https://github.com/deepchem/deepchem/pull/3051
* Using github actions v3 in workflows by arunppsg in https://github.com/deepchem/deepchem/pull/3053
* Removing mol2vec dependency by arunppsg in https://github.com/deepchem/deepchem/pull/3052
* Refactoring CI by arunppsg in https://github.com/deepchem/deepchem/pull/3055
* Fix issue 3057 (update _Mapper class for dmpnn) by ARY2260 in https://github.com/deepchem/deepchem/pull/3058
* Hydra by Chahalprincy in https://github.com/deepchem/deepchem/pull/3030
* Improving CI by arunppsg in https://github.com/deepchem/deepchem/pull/3056
* Assigning task names when they are not specified by arunppsg in https://github.com/deepchem/deepchem/pull/3047
* Update __init__.py by ARY2260 in https://github.com/deepchem/deepchem/pull/3063
* Correctly import lightning to avoid import errors by abhiskk in https://github.com/deepchem/deepchem/pull/3065
* Ported Tensorflow LSTMStep to PyTorch by vinay-hebb in https://github.com/deepchem/deepchem/pull/3072
* Add random hyperparameter search by Manas2030 in https://github.com/deepchem/deepchem/pull/2897
* added file output of validation and train scores by arunppsg in https://github.com/deepchem/deepchem/pull/3073
* Adding CI tests for python 3.10 by arunppsg in https://github.com/deepchem/deepchem/pull/2846
* Fix broken typehint in SparseMatrixOneHotFeaturizer.untransform by AcylSilane in https://github.com/deepchem/deepchem/pull/3080
* Substract padding from list length when slicing by xerus in https://github.com/deepchem/deepchem/pull/3079
* Ported Tensorflow GRU to PyTorch by vinay-hebb in https://github.com/deepchem/deepchem/pull/3076
* implementation of batching for DMPNN model by ARY2260 in https://github.com/deepchem/deepchem/pull/3040
* Minor Patch by arunppsg in https://github.com/deepchem/deepchem/pull/3101
* Minor patches by arunppsg in https://github.com/deepchem/deepchem/pull/3105
* adding batch size argument to lightning module by arunppsg in https://github.com/deepchem/deepchem/pull/3106
* updated mdtraj requirement by arunppsg in https://github.com/deepchem/deepchem/pull/3112
* Deepchem 2.7.0 by arunppsg in https://github.com/deepchem/deepchem/pull/3099

New Contributors
* shaipranesh2 made their first contribution in https://github.com/deepchem/deepchem/pull/2814
* saithat made their first contribution in https://github.com/deepchem/deepchem/pull/2773
* iherath made their first contribution in https://github.com/deepchem/deepchem/pull/2856
* shivance made their first contribution in https://github.com/deepchem/deepchem/pull/2859
* TheRealSalmon made their first contribution in https://github.com/deepchem/deepchem/pull/2864
* juliusgeo made their first contribution in https://github.com/deepchem/deepchem/pull/2888
* JoseAntonioSiguenza made their first contribution in https://github.com/deepchem/deepchem/pull/2885
* BalajiAI made their first contribution in https://github.com/deepchem/deepchem/pull/2902
* Nozziel made their first contribution in https://github.com/deepchem/deepchem/pull/2908
* paupaiz made their first contribution in https://github.com/deepchem/deepchem/pull/2912
* Matthew-Hostetler made their first contribution in https://github.com/deepchem/deepchem/pull/2916
* ARY2260 made their first contribution in https://github.com/deepchem/deepchem/pull/2937
* j-frie made their first contribution in https://github.com/deepchem/deepchem/pull/2947
* allesrebel made their first contribution in https://github.com/deepchem/deepchem/pull/2977
* TShimko126 made their first contribution in https://github.com/deepchem/deepchem/pull/2965
* ojeda-e made their first contribution in https://github.com/deepchem/deepchem/pull/3008
* subzjee made their first contribution in https://github.com/deepchem/deepchem/pull/3022
* chertianser made their first contribution in https://github.com/deepchem/deepchem/pull/3038
* abhiskk made their first contribution in https://github.com/deepchem/deepchem/pull/3065
* vinay-hebb made their first contribution in https://github.com/deepchem/deepchem/pull/3072
* Manas2030 made their first contribution in https://github.com/deepchem/deepchem/pull/2897
* AcylSilane made their first contribution in https://github.com/deepchem/deepchem/pull/3080
* xerus made their first contribution in https://github.com/deepchem/deepchem/pull/3079

**Full Changelog**: https://github.com/deepchem/deepchem/compare/2.6.1...2.7.0

This release is a minor version bump that increases the required version of numpy.

What's Changed
* fix gpu installation by Chahalprincy in https://github.com/deepchem/deepchem/pull/2806

What's Changed
* Version bump to 2.6.0.dev by rbharath in https://github.com/deepchem/deepchem/pull/2447
* Revised first tutorial by Suzukazole in https://github.com/deepchem/deepchem/pull/2435
* Add save reload to atomicconv by ncfrey in https://github.com/deepchem/deepchem/pull/2450
* Fix import issue in 22:Chemberta tutorial by seyonechithrananda in https://github.com/deepchem/deepchem/pull/2445
* Fixed error in computing Pearson correlation coefficient by peastman in https://github.com/deepchem/deepchem/pull/2463
* [WIP] Generalize OneHotFeaturizer to Support Arbitrary Strings by alat-rights in https://github.com/deepchem/deepchem/pull/2458
* Run all tests even if some fail by peastman in https://github.com/deepchem/deepchem/pull/2461
* Adds zip handling to SDFLoader by NinadBhat in https://github.com/deepchem/deepchem/pull/2446
* Use Log Transform for Clearance and HPPB by mufeili in https://github.com/deepchem/deepchem/pull/2462
* Improve SmilesToImage Error Message for long molecules by PascalIversen in https://github.com/deepchem/deepchem/pull/2442
* Added updating website to release instructions by alat-rights in https://github.com/deepchem/deepchem/pull/2469
* Fix pymatgen subclasses import error by JainSamyak8840 in https://github.com/deepchem/deepchem/pull/2460
* Update issues.rst by alat-rights in https://github.com/deepchem/deepchem/pull/2471
* Fixed Documentation for Graph Convolution Featurizers - MolGanFeaturizer by atreyamaj in https://github.com/deepchem/deepchem/pull/2473
* Add img_size parameter to ChemCeption by PascalIversen in https://github.com/deepchem/deepchem/pull/2466
* Fixing the failing test case - test_mol2vec_fingerprint by VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2486
* MEGNET model and evaluate the design by VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2485
* Update infra.rst by alat-rights in https://github.com/deepchem/deepchem/pull/2491
* Update release.md to reflect migration of deepchem.io repo by alat-rights in https://github.com/deepchem/deepchem/pull/2492
* Fix String Comparison to use POSIX standard 2481 by peterskipper in https://github.com/deepchem/deepchem/pull/2482
* Adding essential Molecular Utils by VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2484
* Basic MolGAN model by MiloszGrabski in https://github.com/deepchem/deepchem/pull/2426
* Adding the Huber Loss function by atreyamaj in https://github.com/deepchem/deepchem/pull/2479
* Update moleculenet.rst by ncfrey in https://github.com/deepchem/deepchem/pull/2503
* PAGTN featurisation support for Molecular Graph Conv by VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2496
* Added Sparse/Lazy Adam optimizer by atreyamaj in https://github.com/deepchem/deepchem/pull/2493
* Adding the AdamW optimizer by atreyamaj in https://github.com/deepchem/deepchem/pull/2488
* n_classes made variable(fixed to 2 classes) by OmerOzgur271 in https://github.com/deepchem/deepchem/pull/2506
* Added Squared Hinge loss by atreyamaj in https://github.com/deepchem/deepchem/pull/2497
* Fix DGL Dependency by mufeili in https://github.com/deepchem/deepchem/pull/2516
* Wrapper function for Pagtn Model by VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2508
* Tokenizer fix by schithranandanurix in https://github.com/deepchem/deepchem/pull/2524
* Adding Pytorch dependency into deepchem by VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2541
* added paper reference to tutorial 28 by MariBerry in https://github.com/deepchem/deepchem/pull/2535
* Fix typo in class name by alat-rights in https://github.com/deepchem/deepchem/pull/2539
* correct link of flake8 by autodataming in https://github.com/deepchem/deepchem/pull/2522
* Converted MultitaskRegressor and MultitaskClassifier to PyTorch by peastman in https://github.com/deepchem/deepchem/pull/2559
* Fixed errors in training models with uncertainty by peastman in https://github.com/deepchem/deepchem/pull/2538
* Setup for Jax dependency by VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2560
* [WIP] Adding the MAT Featurizer by atreyamaj in https://github.com/deepchem/deepchem/pull/2544
* Weights & Biases Basic Integration by kshen3778 in https://github.com/deepchem/deepchem/pull/2520
* Fix failing test cases by peastman in https://github.com/deepchem/deepchem/pull/2568
* Fix: Tokenizer is not able to encode triple bonds by niklashoelter in https://github.com/deepchem/deepchem/pull/2566
* Flake8 fix for molnet directory by Suzukazole in https://github.com/deepchem/deepchem/pull/2525
* Tensorflow independent environment by VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2567
* deepchem-Torch environment by VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2563
* Add DummyFeaturizer by Suzukazole in https://github.com/deepchem/deepchem/pull/2570
* Corrected Test Case for Smiles Tokenizer (adding to 2572) by seyonechithrananda in https://github.com/deepchem/deepchem/pull/2578
* Update FASTA Loader to accept arbitrary featurizers by alat-rights in https://github.com/deepchem/deepchem/pull/2565
* [WIP] Added examples for featurizers in documentation by arunppsg in https://github.com/deepchem/deepchem/pull/2571
* Fix full CI by VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2573
* Add section on setting up symbolic link by Suzukazole in https://github.com/deepchem/deepchem/pull/2587
* Added 'transformers' argument to ValidationCallback by kshen3778 in https://github.com/deepchem/deepchem/pull/2584
* USPTO Loader by Suzukazole in https://github.com/deepchem/deepchem/pull/2546
* Updates docs to Material Featurizers by arunppsg in https://github.com/deepchem/deepchem/pull/2585
* Adding the Freesolv dataset by atreyamaj in https://github.com/deepchem/deepchem/pull/2576
* Remove pin for matminer by peastman in https://github.com/deepchem/deepchem/pull/2590
* JaxModel (For integerating Jax into deepchem) by VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2549
* Adding Docs for New CI by VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2591
* Improved handling of classification_handling_mode in Metric by peastman in https://github.com/deepchem/deepchem/pull/2595
* Added MATFeaturizer to website by atreyamaj in https://github.com/deepchem/deepchem/pull/2599
* Fixed errors caused by new Pandas version by peastman in https://github.com/deepchem/deepchem/pull/2605
* WandbLogger fixes: removed finish() from Model fit(), ValidationCallbacks fixes by kshen3778 in https://github.com/deepchem/deepchem/pull/2586
* Added ScaleNorm as the first MAT layer by atreyamaj in https://github.com/deepchem/deepchem/pull/2601
* Fixed ScaleNorm Test by atreyamaj in https://github.com/deepchem/deepchem/pull/2610
* Added ToC and Getting Started section in CONTRIBUTING.md by arunppsg in https://github.com/deepchem/deepchem/pull/2592
* Changed return type to np.ndarray in a few files by atreyamaj in https://github.com/deepchem/deepchem/pull/2607
* Made behavior of GaussianProcessHyperparamOpt more consistent by peastman in https://github.com/deepchem/deepchem/pull/2620
* Added defaults for precision_recall_curve by peastman in https://github.com/deepchem/deepchem/pull/2614
* FirstDraftTutorial30 by davidRFB in https://github.com/deepchem/deepchem/pull/2483
* Fixed examples for loading perovskite dataset by arunppsg in https://github.com/deepchem/deepchem/pull/2621
* Reaction Split Transformer by Suzukazole in https://github.com/deepchem/deepchem/pull/2597
* Update loader to include transformer by Suzukazole in https://github.com/deepchem/deepchem/pull/2628
* Evaluation stage of JaxModel by VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2604
* Tutorial 31 - Introduction to material science by arunppsg in https://github.com/deepchem/deepchem/pull/2626
* [WIP] MAT: Attention Module by atreyamaj in https://github.com/deepchem/deepchem/pull/2622
* Adding bash-script for lightweight installs by VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2618
* Fixes to robertafeaturizer by seyonechithrananda in https://github.com/deepchem/deepchem/pull/2581
* pass featurizer kwargs by walid0925 in https://github.com/deepchem/deepchem/pull/2507
* RobertaFeaturizer by walid0925 in https://github.com/deepchem/deepchem/pull/2523
* First linear layer from AlphaFold by rbharath in https://github.com/deepchem/deepchem/pull/2634
* Minor fixes to examples in torch models by arunppsg in https://github.com/deepchem/deepchem/pull/2630
* [WIP] MAT Layers: Encoder by atreyamaj in https://github.com/deepchem/deepchem/pull/2623
* Fix doctest error in RxnSplitTransform by Suzukazole in https://github.com/deepchem/deepchem/pull/2643
* Made a test less flaky by peastman in https://github.com/deepchem/deepchem/pull/2645
* [WIP] MAT Layers: Embedding + Generator by atreyamaj in https://github.com/deepchem/deepchem/pull/2624
* Add integrations section to README by kshen3778 in https://github.com/deepchem/deepchem/pull/2649
* Init parameter modifications for WandbLogger by kshen3778 in https://github.com/deepchem/deepchem/pull/2648
* Update PR template and docs with doctest, pytest by Suzukazole in https://github.com/deepchem/deepchem/pull/2651
* Fix splitter errors for datasets without labels by Suzukazole in https://github.com/deepchem/deepchem/pull/2641
* installation clarification for zsh [skip ci] by arunppsg in https://github.com/deepchem/deepchem/pull/2664
* fixes attribute error from sklearn in print model by arunppsg in https://github.com/deepchem/deepchem/pull/2671
* BertFeaturizer (Replaces 2608) by alat-rights in https://github.com/deepchem/deepchem/pull/2642
* Fixes to tutorial section by arunppsg in https://github.com/deepchem/deepchem/pull/2637
* Fixes to MATFeaturizer and Tests by atreyamaj in https://github.com/deepchem/deepchem/pull/2652
* Reaction Featurizer by Suzukazole in https://github.com/deepchem/deepchem/pull/2656
* adding PINNs class by VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2658
* Adding Optimizers in Jax by VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2695
* Fix doctest - assign featurize to variable by seyonechithrananda in https://github.com/deepchem/deepchem/pull/2696
* Pinns Tutorial using PINN_Model/Jax_Model by VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2682
* MATModel: Wrapper MATModel class by atreyamaj in https://github.com/deepchem/deepchem/pull/2691
* Docs ScaffoldSplitter by davidRFB in https://github.com/deepchem/deepchem/pull/2698
* Bug fix to_json method by arunppsg in https://github.com/deepchem/deepchem/pull/2694
* Merge datasets preserves shard sizes by EvanKomp in https://github.com/deepchem/deepchem/pull/2654
* Updates to documentation by arunppsg in https://github.com/deepchem/deepchem/pull/2712
* Changes to CI by arunppsg in https://github.com/deepchem/deepchem/pull/2715
* Documenting CI by arunppsg in https://github.com/deepchem/deepchem/pull/2713
* Mypy fix by arunppsg in https://github.com/deepchem/deepchem/pull/2720
* Diffrential Physics in Deepchem with Jax by VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2711
* Tutorial Notebook for MAT by atreyamaj in https://github.com/deepchem/deepchem/pull/2708
* Minor fix to CI template by arunppsg in https://github.com/deepchem/deepchem/pull/2722
* modify tutorial 1 text to include log(solubility) by deloragaskins in https://github.com/deepchem/deepchem/pull/2729
* Remove omnia channel when installing dependencies by peastman in https://github.com/deepchem/deepchem/pull/2732
* Improvements to Grid Hyperparameter logging by arunppsg in https://github.com/deepchem/deepchem/pull/2725
* Pinned torch scatter to 2.0.8 by arunppsg in https://github.com/deepchem/deepchem/pull/2733
* Added rdkit-pypi to install requires in setup.py by arunppsg in https://github.com/deepchem/deepchem/pull/2740
* Reshard with no labels. by davidRFB in https://github.com/deepchem/deepchem/pull/2707
* Integrating with Autodock Vina's Python API by arunppsg in https://github.com/deepchem/deepchem/pull/2741
* Minor fixes by arunppsg in https://github.com/deepchem/deepchem/pull/2742
* Recommendations Ext File by davidRFB in https://github.com/deepchem/deepchem/pull/2752
* Fixed documentation by tonydavis629 in https://github.com/deepchem/deepchem/pull/2751
* PAINS filtering for Large_Scale_Chemical_Screens.ipynb1355 by puaykaipoh in https://github.com/deepchem/deepchem/pull/2746
* Very small quick fix by VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2759
* Fixes to MAT model testing by arunppsg in https://github.com/deepchem/deepchem/pull/2757
* added assertion for number of atoms in MolGraphConvFeaturizer by arunppsg in https://github.com/deepchem/deepchem/pull/2766
* Removal of dc.feat.graph_features.AtomicConvFeaturizer by arunppsg in https://github.com/deepchem/deepchem/pull/2769
* Doc fixes by arunppsg in https://github.com/deepchem/deepchem/pull/2768
* Changes to remove_missing_entries by arunppsg in https://github.com/deepchem/deepchem/pull/2774
* Temporary fix to low r2-scores on benchmarking QM7 dataset by arunppsg in https://github.com/deepchem/deepchem/pull/2777
* Minor fixes by arunppsg in https://github.com/deepchem/deepchem/pull/2767
* updated tensorflow to 2.7 by arunppsg in https://github.com/deepchem/deepchem/pull/2789
* Add precommit by SauravMaheshkar in https://github.com/deepchem/deepchem/pull/2790
* removed Model being an sklearn BaseEstimator by arunppsg in https://github.com/deepchem/deepchem/pull/2724
* Minor fixes by arunppsg in https://github.com/deepchem/deepchem/pull/2799
* Consolidating installation yml files and github workflows by arunppsg in https://github.com/deepchem/deepchem/pull/2793
* Multi-gpu distributed training for deepchem by ncfrey in https://github.com/deepchem/deepchem/pull/2786
* Multisequence alignment tutorial by tonydavis629 in https://github.com/deepchem/deepchem/pull/2805
* Fix bug for dataset.get_shape() after dataset.set_shard() by DingQK in https://github.com/deepchem/deepchem/pull/2802
* Updated type annotations to work with numpy 1.20 by peastman in https://github.com/deepchem/deepchem/pull/2545
* Minor fixes by arunppsg in https://github.com/deepchem/deepchem/pull/2807

New Contributors
* Suzukazole made their first contribution in https://github.com/deepchem/deepchem/pull/2435
* NinadBhat made their first contribution in https://github.com/deepchem/deepchem/pull/2446
* PascalIversen made their first contribution in https://github.com/deepchem/deepchem/pull/2442
* JainSamyak8840 made their first contribution in https://github.com/deepchem/deepchem/pull/2460
* atreyamaj made their first contribution in https://github.com/deepchem/deepchem/pull/2473
* peterskipper made their first contribution in https://github.com/deepchem/deepchem/pull/2482
* OmerOzgur271 made their first contribution in https://github.com/deepchem/deepchem/pull/2506
* schithranandanurix made their first contribution in https://github.com/deepchem/deepchem/pull/2524
* autodataming made their first contribution in https://github.com/deepchem/deepchem/pull/2522
* kshen3778 made their first contribution in https://github.com/deepchem/deepchem/pull/2520
* niklashoelter made their first contribution in https://github.com/deepchem/deepchem/pull/2566
* arunppsg made their first contribution in https://github.com/deepchem/deepchem/pull/2571
* davidRFB made their first contribution in https://github.com/deepchem/deepchem/pull/2483
* walid0925 made their first contribution in https://github.com/deepchem/deepchem/pull/2507
* EvanKomp made their first contribution in https://github.com/deepchem/deepchem/pull/2654
* deloragaskins made their first contribution in https://github.com/deepchem/deepchem/pull/2729
* tonydavis629 made their first contribution in https://github.com/deepchem/deepchem/pull/2751
* puaykaipoh made their first contribution in https://github.com/deepchem/deepchem/pull/2746
* SauravMaheshkar made their first contribution in https://github.com/deepchem/deepchem/pull/2790
* DingQK made their first contribution in https://github.com/deepchem/deepchem/pull/2802

**Full Changelog**: https://github.com/deepchem/deepchem/compare/2.5.0...2.6.0