Commit d57e4de9 authored by Ninad Bhat's avatar Ninad Bhat
Browse files

yapf updates

parent 61967fc1

deepchem/data/data_loader.py

+20 −23
Original line number Diff line number Diff line
@@ -488,8 +488,8 @@ class UserCSVLoader(CSVLoader): 
    shard[feature_fields] = shard[feature_fields].apply(pd.to_numeric)

    X_shard = shard[feature_fields].to_numpy()

    time2 = time.time()

    logger.info(

        "TIMING: user specified processing took %0.3f s" % (time2 - time1))

    logger.info("TIMING: user specified processing took %0.3f s" %

                (time2 - time1))

    return (X_shard, np.ones(len(X_shard), dtype=bool))
@@ -768,7 +768,6 @@ class SDFLoader(DataLoader): 
    if not isinstance(inputs, list):

      inputs = [inputs]





    processed_files = []

    for input_file in inputs:

      filename, extension = os.path.splitext(input_file)
@@ -780,16 +779,14 @@ class SDFLoader(DataLoader): 
        zip_ref = zipfile.ZipFile(input_file, 'r')

        zip_ref.extractall(path=zip_dir)

        zip_ref.close()

        zip_files = [

            os.path.join(zip_dir, name) for name in zip_ref.namelist()

        ]

        zip_files = [os.path.join(zip_dir, name) for name in zip_ref.namelist()]

        for zip_file in zip_files:

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

          extension = extension.lower()

          if extension in [".sdf"]:

            processed_files.append(zip_file)

      else:

          raise ValueError("unsupported file format")

        raise ValueError("Unsupported file format")



    inputs = processed_files
@@ -834,8 +831,7 @@ class SDFLoader(DataLoader): 
    Iterator[pd.DataFrame]

      Iterator over shards

    """

    return load_sdf_files(

        input_files=input_files,

    return load_sdf_files(input_files=input_files,

                          clean_mols=self.sanitize,

                          tasks=self.tasks,

                          shard_size=shard_size)
@@ -1035,11 +1031,12 @@ class ImageLoader(DataLoader): 


    if in_memory:

      if data_dir is None:

        return NumpyDataset(

            load_image_files(image_files), y=labels, w=weights, ids=image_files)

        return NumpyDataset(load_image_files(image_files),

                            y=labels,

                            w=weights,

                            ids=image_files)

      else:

        dataset = DiskDataset.from_numpy(

            load_image_files(image_files),

        dataset = DiskDataset.from_numpy(load_image_files(image_files),

                                         y=labels,

                                         w=weights,

                                         ids=image_files,
@@ -1188,8 +1185,8 @@ class InMemoryLoader(DataLoader): 


  # FIXME: Signature of "_featurize_shard" incompatible with supertype "DataLoader"

  def _featurize_shard(  # type: ignore[override]

      self, shard: List, global_index: int

  ) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:

      self, shard: List, global_index: int) -> Tuple[np.ndarray, np.ndarray,

                                                     np.ndarray, np.ndarray]:

    """Featurizes a shard of an input data.



    Parameters

deepchem/data/tests/test_sdf_loader.py

+32 −19
Original line number Diff line number Diff line
@@ -5,8 +5,9 @@ import deepchem as dc 
def test_sdf_load():

  current_dir = os.path.dirname(os.path.realpath(__file__))

  featurizer = dc.feat.CircularFingerprint(size=16)

  loader = dc.data.SDFLoader(

      ["LogP(RRCK)"], featurizer=featurizer, sanitize=True)

  loader = dc.data.SDFLoader(["LogP(RRCK)"],

                             featurizer=featurizer,

                             sanitize=True)

  dataset = loader.create_dataset(

      os.path.join(current_dir, "membrane_permeability.sdf"))

  assert len(dataset) == 2
@@ -15,26 +16,32 @@ def test_sdf_load(): 
def test_singleton_sdf_load():

  current_dir = os.path.dirname(os.path.realpath(__file__))

  featurizer = dc.feat.CircularFingerprint(size=16)

  loader = dc.data.SDFLoader(

      ["LogP(RRCK)"], featurizer=featurizer, sanitize=True)

  loader = dc.data.SDFLoader(["LogP(RRCK)"],

                             featurizer=featurizer,

                             sanitize=True)

  dataset = loader.create_dataset(os.path.join(current_dir, "singleton.sdf"))

  assert len(dataset) == 1





def test_singleton_sdf_zip_load():

  current_dir = os.path.dirname(os.path.realpath(__file__))

  featurizer = dc.feat.CircularFingerprint(size=16)

  loader = dc.data.SDFLoader(

      ["LogP(RRCK)"], featurizer=featurizer, sanitize=True)

  loader = dc.data.SDFLoader(["LogP(RRCK)"],

                             featurizer=featurizer,

                             sanitize=True)

  dataset = loader.create_dataset(os.path.join(current_dir, "singleton.zip"))

  assert len(dataset) == 1





def test_sharded_sdf_load():

  current_dir = os.path.dirname(os.path.realpath(__file__))

  featurizer = dc.feat.CircularFingerprint(size=16)

  loader = dc.data.SDFLoader(

      ["LogP(RRCK)"], featurizer=featurizer, sanitize=True)

  dataset = loader.create_dataset(

      os.path.join(current_dir, "membrane_permeability.sdf"), shard_size=1)

  loader = dc.data.SDFLoader(["LogP(RRCK)"],

                             featurizer=featurizer,

                             sanitize=True)

  dataset = loader.create_dataset(os.path.join(current_dir,

                                               "membrane_permeability.sdf"),

                                  shard_size=1)

  assert dataset.get_number_shards() == 2

  assert len(dataset) == 2
@@ -42,8 +49,9 @@ def test_sharded_sdf_load(): 
def test_sharded_multi_file_sdf_load():

  current_dir = os.path.dirname(os.path.realpath(__file__))

  featurizer = dc.feat.CircularFingerprint(size=16)

  loader = dc.data.SDFLoader(

      ["LogP(RRCK)"], featurizer=featurizer, sanitize=True)

  loader = dc.data.SDFLoader(["LogP(RRCK)"],

                             featurizer=featurizer,

                             sanitize=True)

  input_files = [

      os.path.join(current_dir, "membrane_permeability.sdf"),

      os.path.join(current_dir, "singleton.sdf")
@@ -52,23 +60,28 @@ def test_sharded_multi_file_sdf_load(): 
  assert dataset.get_number_shards() == 3

  assert len(dataset) == 3





def test_sharded_multi_file_sdf_zip_load():

  current_dir = os.path.dirname(os.path.realpath(__file__))

  featurizer = dc.feat.CircularFingerprint(size=16)

  loader = dc.data.SDFLoader(

      ["LogP(RRCK)"], featurizer=featurizer, sanitize=True)

  dataset = loader.create_dataset(os.path.join(current_dir, "multiple_sdf.zip"), shard_size=1)

  loader = dc.data.SDFLoader(["LogP(RRCK)"],

                             featurizer=featurizer,

                             sanitize=True)

  dataset = loader.create_dataset(os.path.join(current_dir, "multiple_sdf.zip"),

                                  shard_size=1)

  assert dataset.get_number_shards() == 3

  assert len(dataset) == 3





def test_sdf_load_with_csv():

  """Test a case where SDF labels are in associated csv file"""

  current_dir = os.path.dirname(os.path.realpath(__file__))

  featurizer = dc.feat.CircularFingerprint(size=16)

  loader = dc.data.SDFLoader(

      ["atomization_energy"], featurizer=featurizer, sanitize=True)

  dataset = loader.create_dataset(

      os.path.join(current_dir, "water.sdf"), shard_size=1)

  loader = dc.data.SDFLoader(["atomization_energy"],

                             featurizer=featurizer,

                             sanitize=True)

  dataset = loader.create_dataset(os.path.join(current_dir, "water.sdf"),

                                  shard_size=1)

  assert len(dataset) == 10

  assert dataset.get_number_shards() == 10

  assert dataset.get_task_names() == ["atomization_energy"]

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