Unverified Commit 3345a5d4 authored by Ashwin Murali's avatar Ashwin Murali Committed by GitHub
Browse files

Merge branch 'deepchem:master' into flake8fix

parents 91a76eae 275a0827

.github/workflows/jax_setup.yml

+1 −1
Original line number Diff line number Diff line
@@ -39,7 +39,7 @@ jobs: 
    strategy:

      fail-fast: false

      matrix:

        os: [ubuntu-latest, windows-latest]

        os: [ubuntu-latest]

        python-version: [3.7]

        include:

          - os: ubuntu-latest

.gitignore

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@@ -67,6 +67,9 @@ target/ 
# Vim swap

*.swp



# Weights & Biases

wandb/



# Dataset files

datasets/2008-2011_USPTO_reactionSmiles_filtered.zip

datasets/2008-2011_USPTO_reactionSmiles_filtered/

deepchem/feat/smiles_tokenizer.py

+1 −2
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@@ -22,8 +22,7 @@ References 
        1572-1583 DOI: 10.1021/acscentsci.9b00576

"""



SMI_REGEX_PATTERN = r"""(\[[^\]]+]|Br?|Cl?|N|O|S|P|F|I|b|c|n|o|s|p|\(|\)|\.|=|

#|-|\+|\\|\/|:|~|@|\?|>>?|\*|\$|\%[0-9]{2}|[0-9])"""

SMI_REGEX_PATTERN = r"""(\[[^\]]+]|Br?|Cl?|N|O|S|P|F|I|b|c|n|o|s|p|\(|\)|\.|=|#|-|\+|\\|\/|:|~|@|\?|>>?|\*|\$|\%[0-9]{2}|[0-9])"""



# add vocab_file dict

VOCAB_FILES_NAMES = {"vocab_file": "vocab.txt"}

deepchem/models/__init__.py

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@@ -6,6 +6,7 @@ from deepchem.models.models import Model 
from deepchem.models.keras_model import KerasModel

from deepchem.models.multitask import SingletaskToMultitask

from deepchem.models.callbacks import ValidationCallback

from deepchem.models.wandblogger import WandbLogger



from deepchem.models.IRV import MultitaskIRVClassifier

from deepchem.models.robust_multitask import RobustMultitaskClassifier

deepchem/models/callbacks.py

+4 −3
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@@ -80,9 +80,6 @@ class ValidationCallback(object): 
      for key in scores:

        model._log_scalar_to_tensorboard(key, scores[key],

                                         model.get_global_step())

    if model.wandb:

      import wandb

      wandb.log(scores, step=step)

    if self.save_dir is not None:

      score = scores[self.metrics[self.save_metric].name]

      if not self.save_on_minimum:
@@ -90,3 +87,7 @@ class ValidationCallback(object): 
      if self._best_score is None or score < self._best_score:

        model.save_checkpoint(model_dir=self.save_dir)

        self._best_score = score

    if model.wandb or (model.wandb_logger is not None):

      # Log data to Wandb

      data = {'eval/' + k: v for k, v in scores.items()}

      model.wandb_logger.log_data(data, step)

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