Commit 3a9ebac9 authored by nd-02110114's avatar nd-02110114
Browse files

🐛 fix bug

parent 637ec7ab

.github/workflows/build.yml

+0 −27
Original line number Diff line number Diff line
@@ -7,33 +7,6 @@ on: 
    branches:

      - master

jobs:

  minimum-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==2.3.0

        pip install -e .

    - name: Import checking

      run: python -c "import deepchem"



  bash-build:

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

    strategy:

.github/workflows/test.yml→.github/workflows/main.yml

+57 −12
Original line number Diff line number Diff line 
name: Test for DeepChem core modules

name: Test for DeepChem Core

on:

  push: # ci work when pushing master branch

    branches:
@@ -7,6 +7,33 @@ on: 
    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==2.3.0

        pip install -e .

    - name: Import checking

      run: python -c "import deepchem"



  test:

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

    strategy:
@@ -24,25 +51,21 @@ jobs: 
    - uses: actions/checkout@v2

      with:

        fetch-depth: 0

    # This 

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

    # The range of commits to check for changes is:

    # - `origin/master...` for all events happening on a feature branch

    # - 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 feature branch)

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

      run: |

        git fetch origin master

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

    - 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: echo "COMMIT_RANGE=HEAD~.." >> $GITHUB_ENV

      run: |

        git fetch origin master

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

    - name: Cache pip packages for Linux

      if: startsWith(runner.os, 'Linux')

      uses: actions/cache@v2
@@ -96,9 +119,11 @@ jobs: 
    - name: Install DeepChem

      shell: bash -l {0}

      run: pip install -e .

    - name: Yapf

    - name: Yapf (version 0.22.0)

      shell: bash -l {0}

      run: source scripts/yapf_for_ci.sh

      run: |

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

        yapf -d $CHANGED_FILES

    - name: Flake8

      shell: bash -l {0}

      run: source scripts/flake8_for_ci.sh
@@ -119,4 +144,24 @@ jobs: 
        fail_ci_if_error: true

        verbose: true



  deploy:

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

    needs: [build, test]

    runs-on: ubuntu-latest

    steps:

    - uses: actions/checkout@v2

    - name: Set up Python

      uses: actions/setup-python@v1

      with:

        python-version: '3.7'

    - name: Install dependencies

      run: |

        python -m pip install --upgrade pip

        pip install setuptools wheel twine

    - name: Publish (Nightly)

      env:

        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}

        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}

      run: |

        python setup.py sdist bdist_wheel

        twine upload dist/*

.github/workflows/release.yml

0 → 100644
+43 −0
Original line number Diff line number Diff line 
name: Release PyPI packages

on:

  push:

    tags:

      - '*'

jobs:

  release:

    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==2.3.0

        pip install -e .

    - name: Import checking

      run: python -c "import deepchem"

    - name: Prepare for publishing

      run: |

        rm -rf ./build ./dist ./*egg-info

        pip install setuptools wheel twine

    - name: Publish (Stable)

      env:

        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}

        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}

      run: |

        python setup.py sdist bdist_wheel --release

        twine upload dist/*

deepchem/dock/pose_generation.py

+0 −2
Original line number Diff line number Diff line
@@ -8,7 +8,6 @@ import tempfile 
import tarfile

import numpy as np

from subprocess import call

from subprocess import check_output

from typing import List, Optional, Tuple, Union



from deepchem.dock.binding_pocket import BindingPocketFinder
@@ -151,7 +150,6 @@ class VinaPoseGenerator(PoseGenerator): 
            "Check how to install from this link : http://vina.scripps.edu/manual.html#windows."

        )





  def generate_poses(self,

                     molecular_complex: Tuple[str, str],

                     centroid: Optional[np.ndarray] = None,

deepchem/dock/tests/test_pose_generation.py

+1 −0
Original line number Diff line number Diff line
@@ -14,6 +14,7 @@ class TestPoseGeneration(unittest.TestCase): 
  """

  Does sanity checks on pose generation.

  """



  def test_vina_initialization(self):

    """Test that VinaPoseGenerator can be initialized."""

    dc.dock.VinaPoseGenerator()

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