azure-pipelines.yml

# 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'