dmyersturnbull

# Douglas Myers-Turnbull wrote this for the Kokel Lab, which has released it under the Apache Software License, Version 2.0
# See the license file here: https://gist.github.com/dmyersturnbull/bfa1c3371e7449db553aaa1e7cd3cac1
# The list of copyright owners is unknown

import pymysql
import contextlib
from typing import Tuple, List, Dict, Iterator

@contextlib.contextmanager
def connected(connection: pymysql.connections.Connection):

dmyersturnbull

# Douglas Myers-Turnbull wrote this for the Kokel Lab, which has released it under the Apache Software License, Version 2.0
# See the license file here: https://gist.github.com/dmyersturnbull/bfa1c3371e7449db553aaa1e7cd3cac1
# The list of copyright owners is unknown

import numpy as np
from matplotlib import pyplot as plt
import seaborn as sns
import matplotlib
import pandas as pd
from typing import Callable, Tuple, Dict, Optional, Union

dmyersturnbull

# Douglas Myers-Turnbull wrote this for the Kokel Lab, which has released it under the Apache Software License, Version 2.0
# See the license file here: https://gist.github.com/dmyersturnbull/bfa1c3371e7449db553aaa1e7cd3cac1
# The list of copyright owners is unknown

import pandas as pd
import itertools
from typing import Iterator

def marker_iterator(df: pd.DataFrame, class_column: str='class') -> Iterator[str]:
    """Returns an iterator of decent marker shapes. The order is such that similar markers aren't used unless they're needed."""

dmyersturnbull

# Douglas Myers-Turnbull wrote this for the Kokel Lab, which has released it under the Apache Software License, Version 2.0
# See the license file here: https://gist.github.com/dmyersturnbull/bfa1c3371e7449db553aaa1e7cd3cac1
# The list of copyright owners is unknown

import pandas as pd
import seaborn as sns
from scipy.spatial.distance import squareform
from sklearn import manifold
from scipy.spatial.distance import pdist
from sklearn.decomposition import PCA

dmyersturnbull

# Douglas Myers-Turnbull wrote this for the Kokel Lab, which has released it under the Apache Software License, Version 2.0
# See the license file here: https://gist.github.com/dmyersturnbull/bfa1c3371e7449db553aaa1e7cd3cac1
# The list of copyright owners is unknown

import matplotlib.pyplot as plt
import numpy as np
from typing import Optional, Tuple

def colored_barplot(x: np.ndarray, y: np.ndarray, colors: np.ndarray, y_ticks: Optional[np.ndarray]=None, fig_size: Tuple[float, float]=(10.0, 10.0), label_rotation: float=75):
    index = np.arange(0, len(x))

dmyersturnbull

import java.io.Closeable
import scala.util.control.NonFatal
import scala.util.{Failure, Try}

/**
 * Taken from user Morgen on StackOverflow with no substantive modifications:
 * https://codereview.stackexchange.com/questions/79267/scala-trywith-that-closes-resources-automatically
 * Which is licensed under cc-wiki with attribution required.
 */
object TryWith {

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def zip_strict(*args):
    """Same as zip(), but raises a ValueError if the lengths don't match."""
    iters = [iter(axis) for axis in args]
    n_elements = 0
    failures = []
    while len(failures) == 0:
        n_elements += 1
        values = []
        failures = []

dmyersturnbull

import pandas as pd
import itertools
import time
import multiprocessing
from typing import Callable, Tuple, Union

def groupby_parallel(
  groupby_df: pd.core.groupby.DataFrameGroupBy,
  func: Callable[[Tuple[str, pd.DataFrame]], Union[pd.DataFrame, pd.Series]],
  num_cpus: int = multiprocessing.cpu_count() - 1,

dmyersturnbull

# coding=utf-8
# Douglas Myers-Turnbull wrote this for the Kokel Lab, which has released it under the Apache Software License, Version 2.0
# See the license file here: https://gist.github.com/dmyersturnbull/bfa1c3371e7449db553aaa1e7cd3cac1
# The list of copyright owners is unknown

import warnings
import numpy as np
from typing import List, Optional, Tuple, Callable, Dict, Any
from collections import OrderedDict

dmyersturnbull

# Douglas Myers-Turnbull wrote this for the Kokel Lab, which has released it under the Apache Software License, Version 2.0
# See the license file here: https://gist.github.com/dmyersturnbull/bfa1c3371e7449db553aaa1e7cd3cac1
# The list of copyright owners is unknown

from .scan_for_files import scan_for_files  # see https://gist.github.com/dmyersturnbull/80845ba9ebab2da83963
from typing import Callable, Iterator

def find_only_file_matching(directory: str, matcher: Callable[[str], bool], file_iterator: Callable[[str], Iterator[str]]=scan_for_files) -> str:
    """Returns the full path of the matching file and raises an exception if none are found or more than 1 is found."""
    file = None