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import numpy as np
import pytest as pytest
from numba import njit
from umap import UMAP
@pytest.fixture(scope="session")
def all_finite_data():
return np.arange(100.0).reshape(25, 4)
@pytest.fixture(scope="session")
def inverse_data():
return np.arange(50).reshape(25, 2)
@njit
def nan_dist(a: np.ndarray, b: np.ndarray):
a[0] = np.nan
a[1] = np.inf
return 0, a
def test_check_input_data(all_finite_data, inverse_data):
"""
Data input to UMAP gets checked for liability.
This tests checks the if data input is dismissed/accepted
according to the "force_all_finite" keyword as used by
sklearn.
Parameters
----------
all_finite_data
inverse_data
-------
"""
inf_data = all_finite_data.copy()
inf_data[0] = np.inf
nan_data = all_finite_data.copy()
nan_data[0] = np.nan
inf_nan_data = all_finite_data.copy()
inf_nan_data[0] = np.nan
inf_nan_data[1] = np.inf
# wrapper to call each data handling function of UMAP in a convenient way
def call_umap_functions(data, force_all_finite):
u = UMAP(metric=nan_dist)
if force_all_finite is None:
u.fit_transform(data)
u.fit(data)
u.transform(data)
u.update(data)
u.inverse_transform(inverse_data)
else:
u.fit_transform(data, force_all_finite=force_all_finite)
u.fit(data, force_all_finite=force_all_finite)
u.transform(data, force_all_finite=force_all_finite)
u.update(data, force_all_finite=force_all_finite)
u.inverse_transform(inverse_data)
# Check whether correct data input is accepted
call_umap_functions(all_finite_data, None)
call_umap_functions(all_finite_data, True)
call_umap_functions(nan_data, 'allow-nan')
call_umap_functions(all_finite_data, 'allow-nan')
call_umap_functions(inf_data, False)
call_umap_functions(inf_nan_data, False)
call_umap_functions(nan_data, False)
call_umap_functions(all_finite_data, False)
# Check whether illegal data raises a ValueError
with pytest.raises(ValueError):
call_umap_functions(nan_data, None)
call_umap_functions(inf_data, None)
call_umap_functions(inf_nan_data, None)
call_umap_functions(nan_data, True)
call_umap_functions(inf_data, True)
call_umap_functions(inf_nan_data, True)
call_umap_functions(inf_data, 'allow-nan')
call_umap_functions(inf_nan_data, 'allow-nan')
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