Merge pull request #72 from rbharath/travis

language: python

python:

  # We don't actually use the Travis Python, but this keeps it organized.

  - "2.7"

- '2.7'

install:

  - sudo apt-get update

  - wget http://repo.continuum.io/archive/Anaconda2-2.4.1-Linux-x86_64.sh -O anaconda.sh;

  - export PATH="$HOME/anaconda/bin:$PATH"

  - hash -r

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

  - conda config --add channels http://conda.binstar.org/omnia

  - conda update -q conda

  # Useful for debugging any issues with conda

  - conda info -a

  # Replace dep1 dep2 ... with your dependencies

  #- conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION dep1 dep2 ...

  - conda install pandas

  - conda install -c omnia rdkit

  - conda install -c omnia openbabel

  - conda install joblib

  - pip install --upgrade --no-deps git+git://github.com/Theano/Theano.git

  - pushd .

  - cd ~/

  - git clone https://github.com/pandegroup/keras.git

  - cd keras/

  - conda install -c omnia theano

  - conda install -c omnia keras

  - python setup.py install

  - popd

  - python setup.py develop

script:

- nosetests -v deepchem

env:

  global:

  # encrypted AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY to push documentation to S3

  - secure: "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"

  - secure: "Qu0HJwAAzxcavXcDn7mIczNc3sv3xZNYs0LPoCEsJ4azjewFAC9KwI9tptqdbnEkcRJ3cyHde2n+CLg67+m3KTg9s6hoJ+lUSb+jW97zSVXusF4p3vprak+i2dqnH8JAwMD2mOktmSC+FKsQEUzm0gwwCg1BPzxJTsTngWKjYqRk5aAddSMGrVojV+D3mQoyZhqI+eCg7YRb3bl43aPwrcy11yDLhmEbP/8zEuabu02IG3Eix7qJghALbTaRi2amNSmS900y70Jm6uvIX+cUnkXJImUQathwrbIUJfQLTTQN6Rs5prR5MRd2a9Dtcp1ZtnQykNpfZ6bn847jdDtBx3emovvj4CQMEoxhTSUgePjYhU3rU7lVa5tIt2ZITL638MnZUHXVj36bZXzYJpmKZK9tUFQAp7RdjCf8twdfxaQYaVj6buZrJtD0EYDCyLtSA2KHkY48Z6+8z6idxL3vPACnuREsBpRc9I/oyJ9ygrXR9ghUdS0Pt+0YQwzkBvW3dREDdQL/ibWoI3WTXEY0y7TO/LfAAkk51MBE79xdq4EilzVrMEzGlsihPI6dGbYvF2V8+jBGN1XPayHPFIL4QBJuCo1sk7lXf55siAyMElq1uTmKTF3qn1BXs7p8DSyQQ5+S/CeWokOPNYZTpvWgM0B/BvMt2wJwcVQoOtlQM9o="

after_success:

  - source devtools/travis-ci/after_sucess.sh

    """

    Compute Binana fingerprint for complex.

    """

    ### OPEN TEMPDIR

    tempdir = tempfile.mkdtemp()

    mol_pdb_file = os.path.join(tempdir, "mol.pdb")

    with open(mol_pdb_file, "w") as mol_f:

    mol_pdb_file = tempfile.NamedTemporaryFile(suffix="pdb")

    with open(mol_pdb_file.name, "w") as mol_f:

      mol_f.writelines(mol_pdb)

    protein_pdb_file = os.path.join(tempdir, "protein.pdb")

    with open(protein_pdb_file, "w") as protein_f:

    protein_pdb_file = tempfile.NamedTemporaryFile(suffix="pdb")

    with open(protein_pdb_file.name, "w") as protein_f:

      protein_f.writelines(protein_pdb)

    mol_hyd_file = os.path.join(tempdir, "mol_hyd.pdb")

    mol_pdbqt_file = os.path.join(tempdir, "mol_hyd.pdbqt")

    mol_hyd_file = tempfile.NamedTemporaryFile(suffix="pdb")

    mol_pdbqt_file = tempfile.NamedTemporaryFile(suffix="pdbqt")

    hydrogenate_and_compute_partial_charges(

        mol_pdb_file, "pdb", tempdir, mol_hyd_file, mol_pdbqt_file)

        mol_pdb_file.name, "pdb", mol_hyd_file.name,

        mol_pdbqt_file.name)

    protein_hyd_file = os.path.join(tempdir, "protein_hyd.pdb")

    protein_pdbqt_file = os.path.join(tempdir, "protein_hyd.pdbqt")

    protein_hyd_file = tempfile.NamedTemporaryFile(suffix="pdb")

    protein_pdbqt_file = tempfile.NamedTemporaryFile(suffix="pdbqt")

    hydrogenate_and_compute_partial_charges(

        protein_pdb_file, "pdb", tempdir, protein_hyd_file, protein_pdbqt_file)

        protein_pdb_file.name, "pdb", protein_hyd_file.name,

        protein_pdbqt_file.name)

    mol_pdb_obj = PDB()

    mol_pdb_obj.load_from_files(mol_pdb_file, mol_pdbqt_file)

    mol_pdb_obj.load_from_files(mol_pdb_file.name, mol_pdbqt_file.name)

    protein_pdb_obj = PDB()

    protein_pdb_obj.load_from_files(protein_pdb_file, protein_pdbqt_file)

    protein_pdb_obj.load_from_files(

        protein_pdb_file.name, protein_pdbqt_file.name)

    features = self.binana.compute_input_vector(mol_pdb_obj, protein_pdb_obj)

    ### CLOSE TEMPDIR

    shutil.rmtree(tempdir)

    return features

  """

  basename = os.path.basename(input_file).split(".")[0]

  pdb_output = os.path.join(output_directory, basename + ".pdb")

  print "About to write to"

  print pdb_output

  with open(pdb_output, "wb") as outfile:

    obabel_command = ["obabel", "-ipdbqt", input_file, "-opdb"]

    subprocess.Popen(obabel_command, stdout=outfile).wait()

def hydrogenate_and_compute_partial_charges(input_file, input_format,

                                            output_directory,

                                            hyd_output=None,

                                            pdbqt_output=None,

                                            verbose=False):

    Path to input file.

  input_format: String

    Name of input format.

  output_directory: String

    Path to desired output directory.

  """

  basename = os.path.basename(input_file).split(".")[0]

  if hyd_output is None:

    hyd_output = os.path.join(output_directory, basename + "_hyd.pdb")

  if pdbqt_output is None:

    pdbqt_output = os.path.join(output_directory, basename + "_hyd.pdbqt")

  if verbose:

    print "Create pdb with hydrogens added"

  hyd_conversion = openbabel.OBConversion()

This is a recipe for building the current development package into a conda

binary.

The installation on travis-ci is done by building the conda package,

installing it, running the tests, and then if successful pushing the

docs to AWS S3.

#!/bin/bash

pip install .