Commit 7f636811 authored by VIGNESHinZONE's avatar VIGNESHinZONE
Browse files

new setup

parent 75a2d8bb

.github/workflows/common_setup.yml

0 → 100644
+136 −0
Original line number Diff line number Diff line 
name: Test for DeepChem Torch

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 -e .

    - name: Import checking

      run: python -c "import deepchem"



  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: 3.8

    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 requirements/env_common.yml env.test.yml > env.yml

        else

          conda-merge requirements/env_common.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 '.[torch]'

    - 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 "not slow and not jax and not torch and not tensorflow" deepchem

.github/workflows/tensorflow_setup.yml

0 → 100644
+136 −0
Original line number Diff line number Diff line 
name: Test for DeepChem Torch

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 -e '.[tensorflow]'

    - name: Import checking

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



  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 requirements/tensorflow/env_tensorflow.yml env.test.yml > env.yml

        else

          conda-merge requirements/tensorflow/env_tensorflow.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 '.[tensorflow]'

    - 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 torch deepchem

requirements/env_common.yml

0 → 100644
+26 −0
Original line number Diff line number Diff line 
name: deepchem

channels:

  - omnia

  - conda-forge

  - defaults

dependencies:

  - openmm

  - pdbfixer

  - rdkit

  - mdtraj

  - numpy==1.21.*

  - pip==20.2.*

  - pip:

    - biopython

    - lightgbm==3.*

    - matminer==0.6.5

    - mordred

    - networkx

    - pillow

    - pubchempy

    - pyGPGO

    - pymatgen==2020.12.31

    - simdna

    - transformers==4.6.*

    - xgboost==1.*

    - git+https://github.com/samoturk/mol2vec

requirements/tensorflow/env_tensorflow.yml

0 → 100644
+24 −0
Original line number Diff line number Diff line 
name: deepchem

channels:

  - omnia

  - conda-forge

  - defaults

dependencies:

  - openmm

  - pdbfixer

  - rdkit

  - mdtraj

  - numpy==1.19.*

  - pip==20.2.*

  - pip:

    - biopython

    - dgllife==0.2.8

    - lightgbm==3.*

    - mordred

    - networkx

    - pillow

    - pubchempy

    - pyGPGO

    - simdna

    - transformers==4.6.*

    - git+https://github.com/samoturk/mol2vec

setup.py

+5 −1
Original line number Diff line number Diff line
@@ -12,7 +12,11 @@ else: 
# Environment-specific dependencies.

extras = {

    'jax': ['jax==0.2.14', 'jaxlib==0.1.67', 'dm-haiku==0.0.4', 'optax==0.0.8'],

    'torch': ['torch', 'torchvision', 'dgl', 'dgllife']

    'torch': ['torch', 'torchvision', 'dgl', 'dgllife'],

    'tensorflow': [

        'tensorflow==2.4.*', 'tensorflow_probability==0.12.*',

        'tensorflow_addons==0.12.*'

    ],

}

CRA Git | Maintained and supported by SUSTech CRA and CCSE