Unverified Commit 311692fd authored by MariBerry's avatar MariBerry Committed by GitHub
Browse files

Merge pull request #1 from deepchem/master 

Update fork
parents 291b5c2f 6860317d

.github/workflows/build.yml

+8 −0
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@@ -3,9 +3,17 @@ on: 
  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 }}

.github/workflows/main.yml

+39 −4
Original line number Diff line number Diff line
@@ -124,8 +124,10 @@ jobs: 
      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
@@ -143,8 +145,8 @@ jobs: 
      with:

        file: ./coverage.xml



  deploy:

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

  pypi-build:

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

    needs: [build]

    runs-on: ubuntu-latest

    steps:
@@ -164,3 +166,36 @@ jobs: 
      run: |

        python setup.py sdist bdist_wheel

        twine upload dist/*



  docker-build:

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

    needs: [build, pypi-build]

    runs-on: ubuntu-latest

    steps:

    - uses: actions/checkout@v2

    - name: Set up Docker Buildx

      id: buildx

      uses: docker/setup-buildx-action@master

    - name: Cache Docker layers

      uses: actions/cache@v2

      with:

        path: /tmp/.buildx-cache

        key: ${{ runner.os }}-buildx-${{ github.sha }}

        restore-keys: ${{ runner.os }}-buildx-

    - name: Login to DockerHub

      uses: docker/login-action@v1 

      with:

        username: ${{ secrets.DOCKER_HUB_USERNAME }}

        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}

    - name: Build and push

      id: docker_build

      uses: docker/build-push-action@v2

      with:

        builder: ${{ steps.buildx.outputs.name }}

        context: ./docker/nightly

        push: true

        tags: deepchemio/deepchem:latest

        cache-from: type=local,src=/tmp/.buildx-cache

        cache-to: type=local,dest=/tmp/.buildx-cache

    - name: Image digest

      run: echo ${{ steps.docker_build.outputs.digest }}

.github/workflows/release.yml

+25 −3
Original line number Diff line number Diff line 
name: Release PyPI packages

name: Release

on:

  push:

    tags:

      - '*' # ci work when pushing a tag

jobs:

  release:

  pypi:

    runs-on: ubuntu-latest

    strategy:

      fail-fast: false

      matrix:

        python-version: [3.7]

    steps:
@@ -41,3 +40,26 @@ jobs: 
      run: |

        python setup.py sdist bdist_wheel --release

        twine upload dist/*



  docker:

    needs: [pypi]

    runs-on: ubuntu-latest

    steps:

    - uses: actions/checkout@v2

    - name: Get the tag version

      id: get_tag_version

      run: echo ::set-output name=VERSION::${GITHUB_REF#refs/tags/}

    - name: Login to DockerHub

      uses: docker/login-action@v1 

      with:

        username: ${{ secrets.DOCKER_HUB_USERNAME }}

        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}

    - name: Build and push

      id: docker_build

      uses: docker/build-push-action@v2

      with:

        context: ./docker/tag

        push: true

        tags: deepchemio/deepchem:${{ steps.get_tag_version.outputs.VERSION }}

    - name: Image digest

      run: echo ${{ steps.docker_build.outputs.digest }}

README.md

+32 −29
Original line number Diff line number Diff line 
# 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)
@@ -36,49 +38,50 @@ DeepChem currently supports Python 3.6 through 3.7 and requires these packages o 
- [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



### Stable version



**Caution!! : The latest stable version was published nearly a year ago. If you are a pip user or you face some errors, we recommend the nightly build version.**



RDKit is a soft requirement package, but many useful methods like molnet depend on it. We recommend installing RDKit with deepchem.

Please install tensorflow v2.3.* before installing deepchem.



```bash

pip install tensorflow==1.14

conda install -y -c conda-forge rdkit deepchem==2.3.0

pip install tensorflow==2.3.*

```



If you want GPU support:

Then, you install deepchem via pip or conda.  



```bash

pip install tensorflow-gpu==1.14

conda install -y -c conda-forge rdkit deepchem==2.3.0

pip install deepchem

```

or 

```

conda install -c conda-forge deepchem

```



### Nightly build version



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

RDKit is a soft requirement package, but many useful methods like molnet depend on it.

We recommend installing RDKit with deepchem if you use conda.



```bash

pip install tensorflow==2.3.0

pip install --pre deepchem

conda install -y -c conda-forge rdkit

```



RDKit is a soft requirement package, but many useful methods like molnet depend on it. We recommend installing RDKit with deepchem if you use conda.

### Nightly build version



The nightly version is built by the HEAD of DeepChem.



```bash

conda install -y -c conda-forge rdkit

pip install tensorflow==2.3.*

pip install --pre deepchem

```



### Docker
@@ -87,18 +90,18 @@ If you want to install deepchem using a docker, you can pull two kinds of images 
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

  - Dockerfile is put in `docker/tag` 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

  - Dockerfile is put in `docker/nightly` directory



You pull the image like this.



```bash

docker pull deepchemio/deepchem:2.3.0

docker pull deepchemio/deepchem:2.4.0

```



If you want to know docker usages with deepchem in more detail, please check [the document](https://deepchem.readthedocs.io/en/latest/installation.html#docker).
@@ -107,7 +110,7 @@ If you want to know docker usages with deepchem in more detail, please check [th 


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

deepchem/__init__.py

+1 −1
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@@ -3,7 +3,7 @@ Imports all submodules 
"""



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

__version__ = '2.4.0.dev'

__version__ = '2.5.0.dev'



import deepchem.data

import deepchem.feat

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