<gh_stars>1-10
import itertools

from joblib import Parallel, delayed
import numpy as np
from scipy.spatial.distance import squareform

from . import jaccard_utils


def _compare_serial(siglist, iterator):
    n = len(siglist)
    values = np.ones((n, n))

    for i, j in iterator:
        jaccard = jaccard_utils.jaccard_sigs(i, j, siglist)

        values[i, j] = jaccard
        values[j, i] = jaccard

    return values


def compare_all_pairs(siglist, n_jobs=None):
    n = len(siglist)
    iterator = itertools.combinations(range(n), 2)

    if n_jobs is None:
        values = _compare_serial(siglist, iterator)
    else:
        # This creates a condensed distance matrix
        condensed = Parallel(n_jobs=n_jobs)(
            delayed(jaccard_utils.jaccard_sigs)(i, j, siglist) for i, j in iterator
        )
        values = squareform(condensed)

    return values


def get_similarity_difference(similarity, groupby=("ksize", "alphabet", "num_hashes")):
    """Calculate difference in similarity from "true" aka maximum sampling
    similarity

    Parameters
    ----------
    similiarity : pandas.DataFrame
        tidy dataframe with "cell1", "cell2", "similarity" columns,
        plus groupby columns

    """
    CELL_INDEX = ["cell1", "cell2"]

    # flake8 can't detect that the variable is used by pandas dataframe
    # querying so ignore with #noqa
    max_num_hashes = similarity.num_hashes.max()  # noqa
    true_similarity = similarity.query("num_hashes == @max_num_hashes")
    true_similarity = true_similarity.set_index(CELL_INDEX).sort_index()

    test_similarity = similarity.query("num_hashes != @max_num_hashes")
    test_similarity = test_similarity.set_index(CELL_INDEX).sort_index()

    similarity_difference = test_similarity.groupby(groupby).apply(
        lambda x: x["similarity"].subtract(true_similarity["similarity"])
    )
    similarity_difference = similarity_difference.unstack(level=[0, 1, 2]).reset_index()
    similarity_difference = similarity_difference.rename(
        columns={0: "similarity_difference"}
    )

    return similarity_difference

import itertools

from joblib import Parallel, delayed
import numpy as np
from scipy.spatial.distance import squareform

from . import jaccard_utils


def _compare_serial(siglist, iterator):
    n = len(siglist)
    values = np.ones((n, n))

    for i, j in iterator:
        jaccard = jaccard_utils.jaccard_sigs(i, j, siglist)

        values[i, j] = jaccard
        values[j, i] = jaccard

    return values


def compare_all_pairs(siglist, n_jobs=None):
    n = len(siglist)
    iterator = itertools.combinations(range(n), 2)

    if n_jobs is None:
        values = _compare_serial(siglist, iterator)
    else:
        # This creates a condensed distance matrix
        condensed = Parallel(n_jobs=n_jobs)(
            delayed(jaccard_utils.jaccard_sigs)(i, j, siglist) for i, j in iterator
        )
        values = squareform(condensed)

    return values


def get_similarity_difference(similarity, groupby=("ksize", "alphabet", "num_hashes")):
    """Calculate difference in similarity from "true" aka maximum sampling
    similarity

    Parameters
    ----------
    similiarity : pandas.DataFrame
        tidy dataframe with "cell1", "cell2", "similarity" columns,
        plus groupby columns

    """
    CELL_INDEX = ["cell1", "cell2"]

    # flake8 can't detect that the variable is used by pandas dataframe
    # querying so ignore with #noqa
    max_num_hashes = similarity.num_hashes.max()  # noqa
    true_similarity = similarity.query("num_hashes == @max_num_hashes")
    true_similarity = true_similarity.set_index(CELL_INDEX).sort_index()

    test_similarity = similarity.query("num_hashes != @max_num_hashes")
    test_similarity = test_similarity.set_index(CELL_INDEX).sort_index()

    similarity_difference = test_similarity.groupby(groupby).apply(
        lambda x: x["similarity"].subtract(true_similarity["similarity"])
    )
    similarity_difference = similarity_difference.unstack(level=[0, 1, 2]).reset_index()
    similarity_difference = similarity_difference.rename(
        columns={0: "similarity_difference"}
    )

    return similarity_difference
# This creates a condensed distance matrix Calculate difference in similarity from "true" aka maximum sampling     similarity      Parameters     ----------     similiarity : pandas.DataFrame         tidy dataframe with "cell1", "cell2", "similarity" columns,         plus groupby columns # flake8 can't detect that the variable is used by pandas dataframe # querying so ignore with #noqa # noqa