Commit 8a36634e authored by nd-02110114's avatar nd-02110114
Browse files

Merge branch 'master' into update-feat-docs

parents af0e3ed7 6860317d
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@@ -145,7 +145,7 @@ jobs:
      with:
        file: ./coverage.xml

  deploy:
  pypi-build:
    if: github.event_name == 'push' && github.ref == 'refs/heads/master'
    needs: [build]
    runs-on: ubuntu-latest
@@ -166,3 +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 }}
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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 }}
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@@ -52,37 +52,38 @@ Please check [the document](https://deepchem.readthedocs.io/en/latest/requiremen

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

RDKit is a soft requirement package, but many useful methods like molnet depend on it. We recommend installing RDKit with deepchem.
```bash
pip install tensorflow==2.3.*
```

Then, you install deepchem via pip or conda.  

```bash
pip install tensorflow==1.14
conda install -y -c conda-forge rdkit deepchem==2.3.0
pip install deepchem
```
or 
```
conda install -c conda-forge deepchem
```

If you want GPU support:
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-gpu==1.14
conda install -y -c conda-forge rdkit deepchem==2.3.0
conda install -y -c conda-forge rdkit
```

### Nightly build version

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

```bash
pip install tensorflow==2.3.*
pip install --pre 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
conda install -y -c conda-forge rdkit
```

### Docker

If you want to install deepchem using a docker, you can pull two kinds of images.  
@@ -91,16 +92,16 @@ DockerHub : https://hub.docker.com/repository/docker/deepchemio/deepchem
- `deepchemio/deepchem:x.x.x`
  - 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 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).
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@@ -3,7 +3,7 @@ Imports all submodules
"""

# If you push the tag, please remove `.dev`
__version__ = '2.4.0-rc1.dev'
__version__ = '2.5.0.dev'

import deepchem.data
import deepchem.feat
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@@ -45,7 +45,7 @@ class GridHyperparamOpt(HyperparamOpt):
  (in this case, `n_tasks` and `n_features` which are properties of a
  dataset and not hyperparameters to search over.)

  >>> def model_builder(**model_params):
  >>> def model_builder(model_dir, **model_params):
  ...   n_layers = model_params['layers']
  ...   layer_width = model_params['width']
  ...   dropout = model_params['dropout']
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