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.travis.yml
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.travis.yml
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sudo: false
language: python
cache: pip
env:
matrix:
# Minimal required package versions
- ODDT_TOOLKIT=ob CONDA_PY=3.6 MINIMAL_REQ=1
- ODDT_TOOLKIT=rdk CONDA_PY=3.6 MINIMAL_REQ=1
# Recent versions
- ODDT_TOOLKIT=ob CONDA_PY=3.6
- ODDT_TOOLKIT=ob CONDA_PY=3.7
- ODDT_TOOLKIT=ob CONDA_PY=3.8
- ODDT_TOOLKIT=rdk CONDA_PY=3.6
- ODDT_TOOLKIT=rdk CONDA_PY=3.7
- ODDT_TOOLKIT=rdk CONDA_PY=3.8
global:
secure: "XOHub9EE1aj4xDWvws5Ej1oGvb5Dw2vVnDRKpU9ZP5Ko9yJ6AYvy3zDeHBb83htp2JSxdciIB5voBb3LF+o0YliBpHdgrub8CgV8VH3Lpl+f0X14yBsnP/swwY0Lde/Xyq2lq6FcP3siNx8OpaSFFTDIZnAqt/kKzUzBknd9wgA="
deploy:
# pypi
- provider: pypi
user: __token__
password:
secure: "PVENDt0UDwftDGLKwd6iFSxra9x95txpE//gfqThhYV36EZyw1KxKmIKfWjZzjok7jI60s3pIwhFFjToErHj4zaE7F+OdS/qflZGMCisV4jl7lNZhIV2LW/9VZ5V2x1Ow+NG28DqWNPpWyd2C4FIqUk9FeO+sslgLkqaAZZW4rU="
distributions: sdist
on:
tags: true
repo: oddt/oddt
branch: master
# deploy once to prevent conflicting names on PyPi
python: '3.6'
condition: $ODDT_TOOLKIT = ob
# conda
- provider: script
script: conda/deploy.sh
on:
tags: true
repo: oddt/oddt
branch: master
# deploy once to prevent conflicting names on Anaconda.org
python: '3.6'
condition: $ODDT_TOOLKIT = ob
skip_cleanup: true
install:
# Install Miniconda.
- wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; bash miniconda.sh -b -f -p $HOME/miniconda;
- export PATH="$HOME/miniconda/bin:$PATH"
- conda config --set always_yes yes --set changeps1 no
- conda update -q conda
- conda install -q conda-build anaconda-client
- conda info -a
- if [ -d $HOME/miniconda/envs/test-environment ]; then rm -rf $HOME/miniconda/envs/test-environment; fi
- conda create -q -n test-environment python=$CONDA_PY numpydoc six pillow
- source activate test-environment
- |
if [[ "$MINIMAL_REQ" == "1" ]]; then
conda install -q -c conda-forge numpy=1.12 scipy=0.19 joblib=0.10.3 scikit-image=0.12.3 xlsxwriter \
scikit-learn=0.18 pandas=0.19.2;
if [[ "$ODDT_TOOLKIT" == "ob" ]]; then
conda install -q -c conda-forge openbabel=3.0.0;
elif [[ "$ODDT_TOOLKIT" == "rdk" ]]; then
conda install -q -c conda-forge rdkit=2018.03 boost=1.68;
fi
else
conda install -q -c anaconda numpy scikit-learn joblib pandas scikit-image xlsxwriter;
if [[ "$ODDT_TOOLKIT" == "ob" ]]; then
conda install -q -c conda-forge openbabel;
elif [[ "$ODDT_TOOLKIT" == "rdk" ]]; then
conda install -q -c conda-forge rdkit=2019.09;
fi
fi
conda install -q -c bioconda autodock-vina
conda install -q pytest pytest-cov pytest-xdist
pip install coveralls
- python setup.py install
script:
- 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
after_success:
- coveralls