Commit 93f92d12 authored by VIGNESHinZONE's avatar VIGNESHinZONE
Browse files

Merge branch 'master' into jax

parents 6d791a50 885b2adb

.github/workflows/jax_setup.yml

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name: Test for DeepChem Jax

on:

  push: # ci work when pushing master branch

    branches:

      - master

  pull_request: # ci work when creating a PR to master branch

    branches:

      - master

jobs:

  build:

    runs-on: ubuntu-latest

    strategy:

      fail-fast: false

      matrix:

        python-version: [3.7]

    steps:

    - uses: actions/checkout@v2

    - name: Cache pip modules for Linux

      uses: actions/cache@v2

      with:

        path: ~/.cache/pip

        key: ${{ runner.os }}-pip-${{ hashFiles('env.*.yml') }}

        restore-keys: |

          ${{ runner.os }}-pip-

    - name: Set up Python ${{ matrix.python-version }}

      uses: actions/setup-python@v2

      with:

        python-version: ${{ matrix.python-version }}

    - name: Build DeepChem

      run: |

        python -m pip install --upgrade pip

        pip install tensorflow==2.4

        pip install -e '.[jax]'

    - name: Import checking

      run: python -c "import deepchem; import jax;"



  test:

    runs-on: ${{ matrix.os }}

    strategy:

      fail-fast: false

      matrix:

        os: [ubuntu-latest, windows-latest]

        python-version: [3.7]

        include:

          - os: ubuntu-latest

            python-version: 3.6

    env:

      OS: ${{ matrix.os }}

      PYTHON_VERSION: ${{ matrix.python-version }}

    steps:

    - uses: actions/checkout@v2

      with:

        fetch-depth: 0

    # https://github.com/galaxyproject/tools-iuc/blob/master/.github/workflows/pr.yaml

    # The range of commits to check for changes is:

    # - for events on the master branch we compare against the sha before the event

    #   (note that this does not work for feature branch events since we want all

    #   commits on the feature branch and not just the commits of the last event)

    # - for pull requests we compare against the 1st ancestor, given the current

    #   HEAD is the merge between the PR branch and the base branch

    - name: Set commit range (push to the master branch, e.g. merge)

      if: github.ref == 'refs/heads/master' && github.event_name == 'push'

      run: echo "COMMIT_RANGE=${{ github.event.before }}.." >> $GITHUB_ENV

    - name: Set commit range (pull request)

      if: github.event_name == 'pull_request'

      run: |

        git fetch origin master

        echo "COMMIT_RANGE=origin/master..." >> $GITHUB_ENV

    - name: Cache pip packages for Linux

      if: runner.os == 'Linux'

      uses: actions/cache@v2

      with:

        path: ~/.cache/pip

        key: ${{ runner.os }}-pip-${{ hashFiles('env.*.yml') }}

        restore-keys: |

          ${{ runner.os }}-pip-

    - name: Cache pip packages for MacOS

      if: runner.os == 'macOS'

      uses: actions/cache@v2

      with:

        path: ~/Library/Caches/pip

        key: ${{ matrix.os }}-pip-${{ hashFiles('env.*.yml') }}

        restore-keys: |

          ${{ runner.os }}-pip-

    - name: Cache pip packages for Windows

      if: runner.os == 'Windows'

      uses: actions/cache@v2

      with:

        path: ~\AppData\Local\pip\Cache

        key: ${{ matrix.os }}-pip-${{ hashFiles('env.*.yml') }}

        restore-keys: |

          ${{ runner.os }}-pip-

    - name: Set up Python ${{ matrix.python-version }}

      uses: actions/setup-python@v2

      with:

        python-version: ${{ matrix.python-version }}

    - name: Create env.yml

      shell: bash

      run: |

        python -m pip install --upgrade pip;

        pip install conda-merge;

        if [ "$(uname)" == 'Darwin' ]; then

          conda-merge env_jax.yml env.test.yml > env.yml

        else

          conda-merge env_jax.yml env.test.yml > env.yml

        fi;

    - name: Install all dependencies

      uses: conda-incubator/setup-miniconda@v2

      with:

        miniconda-version: "latest"

        auto-update-conda: true

        activate-environment: deepchem

        channels: omnia,conda-forge,defaults

        python-version: ${{ matrix.python-version }}

        environment-file: env.yml

    - name: Install DeepChem

      id: install

      shell: bash -l {0}

      run: pip install -e '.[jax]'

    - name: Yapf (version 0.22.0)

      id: yapf

      # on Windows, yapf raise the strange error..., so ignore

      if: runner.os == 'Linux' || runner.os == 'macOS'

      shell: bash -l {0}

      run: |

        CHANGED_FILES=`git diff --name-only $COMMIT_RANGE | grep .py$ | grep -v contrib/ || true`

        if [ -n "$CHANGED_FILES" ]; then

          yapf -d $CHANGED_FILES

        fi

    - name: Flake8

      if: ${{ (success() || failure()) && (steps.install.outcome == 'failure' || steps.install.outcome == 'success') }}

      shell: bash -l {0}

      run: source scripts/flake8_for_ci.sh

    - name: PyTest

      if: ${{ (success() || failure()) && (steps.install.outcome == 'failure' || steps.install.outcome == 'success') }}

      shell: bash -l {0}

      run: pytest -v -m jax deepchem

.github/workflows/main.yml

+1 −1
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@@ -145,7 +145,7 @@ jobs: 
    - name: PyTest

      if: ${{ (success() || failure()) && (steps.install.outcome == 'failure' || steps.install.outcome == 'success') }}

      shell: bash -l {0}

      run: pytest -v -m "not slow" --cov=deepchem --cov-report=xml deepchem

      run: pytest -v -m "not slow and not jax" --cov=deepchem --cov-report=xml deepchem

    - name: Upload coverage to Codecov

      if: ${{ (success() || failure()) && (steps.install.outcome == 'failure' || steps.install.outcome == 'success') }}

      uses: codecov/codecov-action@v1

deepchem/feat/tests/test_smiles_tokenizer.py

+8 −2
Original line number Diff line number Diff line 
# Requirements - transformers, tokenizers

import os

import unittest

from unittest import TestCase

from deepchem.feat.smiles_tokenizer import SmilesTokenizer

try:

  from transformers import RobertaForMaskedLM

  from deepchem.feat.smiles_tokenizer import SmilesTokenizer

  has_transformers = True

except:

  has_transformers = False





class TestSmilesTokenizer(TestCase):

  """Tests the SmilesTokenizer to load the USPTO vocab file and a ChemBERTa Masked LM model with pre-trained weights.."""



  @unittest.skipIf(not has_transformers, 'transformers are not installed')

  def test_tokenize(self):

    current_dir = os.path.dirname(os.path.realpath(__file__))

    vocab_path = os.path.join(current_dir, 'data', 'vocab.txt')

deepchem/models/__init__.py

+1 −3
Original line number Diff line number Diff line
@@ -7,9 +7,6 @@ from deepchem.models.keras_model import KerasModel 
from deepchem.models.multitask import SingletaskToMultitask

from deepchem.models.callbacks import ValidationCallback



from deepchem.models.fcnet import MultitaskRegressor

from deepchem.models.fcnet import MultitaskClassifier

from deepchem.models.fcnet import MultitaskFitTransformRegressor

from deepchem.models.IRV import MultitaskIRVClassifier

from deepchem.models.robust_multitask import RobustMultitaskClassifier

from deepchem.models.robust_multitask import RobustMultitaskRegressor
@@ -38,6 +35,7 @@ try: 
  from deepchem.models.torch_models import GCN, GCNModel

  from deepchem.models.torch_models import LCNN, LCNNModel

  from deepchem.models.torch_models import Pagtn, PagtnModel

  from deepchem.models.fcnet import MultitaskRegressor, MultitaskClassifier, MultitaskFitTransformRegressor

except ModuleNotFoundError:

  pass

deepchem/models/atomic_conv.py

+2 −2
Original line number Diff line number Diff line
@@ -13,7 +13,7 @@ try: 
except:

  from collections import Sequence as SequenceCollection

from typing import Sequence, Union

from deepchem.utils.typing import KerasActivationFn, LossFn, OneOrMany

from deepchem.utils.typing import ActivationFn, LossFn, OneOrMany

from deepchem.utils.data_utils import load_from_disk, save_to_disk



logger = logging.getLogger(__name__)
@@ -56,7 +56,7 @@ class AtomicConvModel(KerasModel): 
      weight_decay_penalty: float = 0.0,

      weight_decay_penalty_type: str = "l2",

      dropouts: OneOrMany[float] = 0.5,

      activation_fns: OneOrMany[KerasActivationFn] = tf.nn.relu,

      activation_fns: OneOrMany[ActivationFn] = tf.nn.relu,

      residual: bool = False,

      learning_rate=0.001,

      **kwargs) -> None:

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