Merge branch 'master' into update-data-docs

  push: # ci work when pushing master branch

    branches:

      - master

    paths:

      - "scripts/install_deepchem_conda.ps1"

      - "scripts/install_deepchem_conda.sh"

      - "env.*.yml"

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

    branches:

      - master

    paths:

      - "scripts/install_deepchem_conda.ps1"

      - "scripts/install_deepchem_conda.sh"

      - "env.*.yml"

jobs:

  bash-build:

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

      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/`

        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

      shell: bash -l {0}

      run: source scripts/flake8_for_ci.sh

        file: ./coverage.xml

  deploy:

    if: ${{ github.ref == 'master' }}

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

    needs: [build]

    runs-on: ubuntu-latest

    steps:

# DeepChem

[![Build Status](https://travis-ci.org/deepchem/deepchem.svg?branch=master)](https://travis-ci.org/deepchem/deepchem)

[![Coverage Status](https://coveralls.io/repos/github/deepchem/deepchem/badge.svg?branch=master)](https://coveralls.io/github/deepchem/deepchem?branch=master)

[![Documentation Status](https://readthedocs.org/projects/deepchem/badge/?version=latest)](https://deepchem.readthedocs.io/en/latest/?badge=latest)

[![Anaconda-Server Badge](https://anaconda.org/conda-forge/deepchem/badges/version.svg)](https://anaconda.org/conda-forge/deepchem)

[![PyPI version](https://badge.fury.io/py/deepchem.svg)](https://badge.fury.io/py/deepchem)

[![PyPI version](https://badge.fury.io/py/deepchem.svg)](https://pypi.org/project/deepchem/)

[![Documentation Status](https://readthedocs.org/projects/deepchem/badge/?version=latest)](https://deepchem.readthedocs.io/en/latest/?badge=latest)  

[![Test for DeepChem Core](https://github.com/deepchem/deepchem/workflows/Test%20for%20DeepChem%20Core/badge.svg)](https://github.com/deepchem/deepchem/actions?query=workflow%3A%22Test+for+DeepChem+Core%22)

[![Test for documents](https://github.com/deepchem/deepchem/workflows/Test%20for%20documents/badge.svg)](https://github.com/deepchem/deepchem/actions?query=workflow%3A%22Test+for+documents%22)

[![Test for build scripts](https://github.com/deepchem/deepchem/workflows/Test%20for%20build%20scripts/badge.svg)](https://github.com/deepchem/deepchem/actions?query=workflow%3A%22Test+for+build+scripts%22)

[![codecov](https://codecov.io/gh/deepchem/deepchem/branch/master/graph/badge.svg?token=5rOZB2BY3h)](https://codecov.io/gh/deepchem/deepchem)  

[Website](https://deepchem.io/) | [Documentation](https://deepchem.readthedocs.io/en/latest/) | [Colab Tutorial](https://github.com/deepchem/deepchem/tree/master/examples/tutorials) | [Discussion Forum](https://forum.deepchem.io/) | [Gitter](https://gitter.im/deepchem/Lobby)

- [scikit-learn](https://scikit-learn.org/stable/)

- [SciPy](https://www.scipy.org/)

- [TensorFlow](https://www.tensorflow.org/)

  - `deepchem>=2.4.0` requires tensorflow v2

  - `deepchem<2.4.0` requires tensorflow v1

  - `deepchem>=2.4.0` depends on TensorFlow v2

  - `deepchem<2.4.0` depends on TensorFlow v1

### Soft Requirements

DeepChem has a number of "soft" requirements.

If you face some errors like `ImportError: This class requires XXXX`, you may need to install some packages.

Please check [the document](https://deepchem.readthedocs.io/en/latest/requirements.html##soft-requirements) about soft requirements.

Please check [the document](https://deepchem.readthedocs.io/en/latest/requirements.html#soft-requirements) about soft requirements.

## Installation

You install the nightly build version via pip. The nightly version is built by the HEAD of DeepChem.

```bash

pip install tensorflow==2.3.0

pip install tensorflow==2.3.*

pip install --pre deepchem

```

DockerHub : https://hub.docker.com/repository/docker/deepchemio/deepchem

- `deepchemio/deepchem:x.x.x`

  - Image built by using a conda package manager (x.x.x is a version of deepchem)

  - Image built by using a conda (x.x.x is a version of deepchem)

  - The x.x.x image is built when we push x.x.x. tag

  - Dockerfile is put in `docker/conda-forge` directory

- `deepchemio/deepchem:latest`

  - Image built by the master branch of deepchem source codes

  - Image built from source codes

  - The latest image is built every time we commit to the master branch

  - Dockerfile is put in `docker/master` directory

If you try install all soft dependencies at once or contribute to deepchem, we recommend you should install deepchem from source.

Please check [this introduction](https://deepchem.readthedocs.io/en/latest/installation.html#from-source).

Please check [this introduction](https://deepchem.readthedocs.io/en/latest/installation.html#from-source-with-conda).

## Getting Started

"""

# If you push the tag, please remove `.dev`

__version__ = '2.4.0.dev'

__version__ = '2.4.0-rc1.dev'

import deepchem.data

import deepchem.feat

  def _compute_tf_loss(self, output, labels):

    import tensorflow as tf

    if len(labels.shape) == len(output.shape):

      labels = tf.squeeze(labels, axis=-1)

    labels = tf.cast(labels, tf.int32)

    return tf.nn.sparse_softmax_cross_entropy_with_logits(labels, output)

  def _create_pytorch_loss(self):

      # This is for API consistency

      if len(output.shape) == 3:

        output = output.permute(0, 2, 1)

      if len(labels.shape) == len(output.shape):

        labels = labels.squeeze(-1)

      return ce_loss(output, labels.long())

    return loss