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Models:
Amanda Davis
Amanda-D/
oddt
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[d6730e]: / azure-pipelines.yml

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# Python package

# Create and test a Python package on multiple Python versions.

# Add steps that analyze code, save the dist with the build record, publish to a PyPI-compatible index, and more:

# https://docs.microsoft.com/azure/devops/pipelines/languages/python



trigger:

- main



pool:

  vmImage: 'ubuntu-latest'

strategy:

  matrix:

    Python_min_ob:

      python.version: '3.6'

      ODDT_TOOLKIT: 'ob'

      MINIMAL_REQ: '1'

    Python_min_rdk:

      python.version: '3.6'

      ODDT_TOOLKIT: 'rdk'

      MINIMAL_REQ: '1'

    Python36_ob:

      python.version: '3.6'

      ODDT_TOOLKIT: 'ob'

    Python36_rdk:

      python.version: '3.6'

      ODDT_TOOLKIT: 'rdk'

    Python37_ob:

      python.version: '3.7'

      ODDT_TOOLKIT: 'ob'

    Python37_rdk:

      python.version: '3.7'

      ODDT_TOOLKIT: 'rdk'

    Python38_ob:

      python.version: '3.8'

      ODDT_TOOLKIT: 'ob'

    Python38_rdk:

      python.version: '3.8'

      ODDT_TOOLKIT: 'rdk'

steps:

- bash: echo "##vso[task.prependpath]$CONDA/bin"

  displayName: Add conda to PATH



- bash: |

    conda config --set always_yes yes --set changeps1 no

    conda install -q -c conda-forge mamba

    mamba create -q -n testenv python=$(python.version)

    source activate /usr/share/miniconda/envs/testenv

    if [[ "$MINIMAL_REQ" == "1" ]]; then

      mamba install -q -c conda-forge numpy=1.12 scipy=0.19 joblib=0.10.3 scikit-image=0.12.3 xlsxwriter \

        scikit-learn=0.18 pandas=0.19.2;

      if [[ "$ODDT_TOOLKIT" == "ob" ]]; then

        mamba install -q -c conda-forge openbabel=3.0.0;

      elif [[ "$ODDT_TOOLKIT" == "rdk" ]]; then

        mamba install -q -c conda-forge rdkit=2018.03 boost=1.68;

      fi

    else

      mamba install -q -c anaconda numpy scikit-learn joblib pandas scikit-image xlsxwriter six

      if [[ "$ODDT_TOOLKIT" == "ob" ]]; then

        mamba install -q -c conda-forge openbabel;

      elif [[ "$ODDT_TOOLKIT" == "rdk" ]]; then

        mamba install -q -c conda-forge rdkit;

      fi

    fi

    mamba install -q -c bioconda autodock-vina

    mamba install -q -c conda-forge pytest pytest-cov pytest-xdist

    pip install coveralls

    python setup.py install

    echo "Using toolkit: ${ODDT_TOOLKIT}"

    pytest --cov=oddt -n 2 -v -s --durations=0 tests/

    oddt_cli --help

    oddt_cli tests/data/dude/xiap/crystal_ligand.sdf -osmi

    oddt_cli tests/data/dude/xiap/actives_docked.sdf --similarity ifp --query tests/data/dude/xiap/crystal_ligand.sdf --cutoff 0.9 --receptor tests/data/dude/xiap/receptor_rdkit.pdb -ocsv

    oddt_cli tests/data/dude/xiap/actives_docked.sdf --similarity sifp --query tests/data/dude/xiap/crystal_ligand.sdf --cutoff 0.9 --receptor tests/data/dude/xiap/receptor_rdkit.pdb -ocsv

    oddt_cli tests/data/dude/xiap/actives_docked.sdf --similarity usr --query tests/data/dude/xiap/crystal_ligand.sdf --cutoff 0.3 -ocsv

    oddt_cli tests/data/dude/xiap/actives_docked.sdf --similarity usr_cat --query tests/data/dude/xiap/crystal_ligand.sdf --cutoff 0.3 -ocsv

    oddt_cli tests/data/dude/xiap/actives_docked.sdf --similarity electroshape --query tests/data/dude/xiap/crystal_ligand.sdf --cutoff 0.3 -ocsv

    oddt_cli tests/data/dude/xiap/actives_docked.sdf --score pleclinear --receptor tests/data/dude/xiap/receptor_rdkit.pdb -ocsv

  displayName: 'pytest'