Merge pull request #1658 from peastman/python

language: python

python:

- '2.7'

- '3.5'

- '3.7'

sudo: required

dist: trusty

dist: xenial

install:

- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O anaconda.sh;

- export python_version=$TRAVIS_PYTHON_VERSION

script:

- nosetests -q --with-flaky -a '!slow' --with-coverage --cover-package=deepchem

  -v deepchem --nologcapture

- if [ $TRAVIS_PYTHON_VERSION == '3.5' ]; then

- if [ $TRAVIS_PYTHON_VERSION == '3.7' ]; then

      find ./deepchem | grep .py$ |xargs python -m doctest -v;

  fi

- bash devtools/travis-ci/test_format_code.sh

from deepchem.utils.genomics import encode_fasta_sequence

from deepchem.feat import UserDefinedFeaturizer

from deepchem.data import DiskDataset, NumpyDataset, ImageDataset

from scipy import misc

import zipfile

from PIL import Image

      _, extension = os.path.splitext(image_file)

      extension = extension.lower()

      if extension == ".png":

        image = misc.imread(image_file)

        image = np.array(Image.open(image_file))

        images.append(image)

      elif extension == ".tif":

        im = Image.open(image_file)

import unittest

import tempfile

from scipy import misc

from PIL import Image

import deepchem as dc

import zipfile

    self.data_dir = tempfile.mkdtemp()

    self.face = misc.face()

    self.face_path = os.path.join(self.data_dir, "face.png")

    misc.imsave(self.face_path, self.face)

    Image.fromarray(self.face).save(self.face_path)

    self.face_copy_path = os.path.join(self.data_dir, "face_copy.png")

    misc.imsave(self.face_copy_path, self.face)

    Image.fromarray(self.face).save(self.face_copy_path)

    # Create zip of image file

    #self.zip_path = "/home/rbharath/misc/cells.zip"

    # Create image directory

    self.image_dir = tempfile.mkdtemp()

    face_path = os.path.join(self.image_dir, "face.png")

    misc.imsave(face_path, self.face)

    Image.fromarray(self.face).save(face_path)

    face_copy_path = os.path.join(self.image_dir, "face_copy.png")

    misc.imsave(face_copy_path, self.face)

    Image.fromarray(self.face).save(face_copy_path)

  def test_png_simple_load(self):

    loader = dc.data.ImageLoader()

    value = np.random.uniform(size=(2, 3)).astype(np.float32)

    with self.session() as sess:

      result = Exp()(value).eval()

      assert np.array_equal(np.exp(value), result)

      assert np.allclose(np.exp(value), result)

  def test_interatomic_distances(self):

    """Test that the interatomic distance calculation works."""

  """Load clintox datasets."""

  if data_dir is None:

    data_dir = DEFAULT_DIR

  else:

  if save_dir is None:

    save_dir = DEFAULT_DIR

  if reload: