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import contextlib
import os
import shutil
import tempfile
import numpy as np
from pandas.api.types import is_numeric_dtype
import cooler
@contextlib.contextmanager
def isolated_filesystem():
"""A context manager that creates a temporary folder and changes
the current working directory to it for isolated filesystem tests.
"""
cwd = os.getcwd()
t = tempfile.mkdtemp()
os.chdir(t)
try:
yield t
finally:
os.chdir(cwd)
try:
shutil.rmtree(t)
except OSError:
pass
def cooler_cmp(uri1, uri2):
c1 = cooler.Cooler(uri1)
c2 = cooler.Cooler(uri2)
with c1.open("r") as f1, c2.open("r") as f2:
for path in (
"chroms/name",
"chroms/length",
"bins/chrom",
"bins/start",
"bins/end",
"pixels/bin1_id",
"pixels/bin2_id",
"pixels/count",
):
dset1, dset2 = f1[path], f2[path]
dtype1 = dset1.dtype
dtype2 = dset2.dtype
if dtype1.kind == "S":
# Null padding of ascii arrays is not guaranteed to be
# preserved so we only check the kind.
assert dtype2.kind == "S"
else:
assert dtype1 == dtype2
if is_numeric_dtype(dtype1):
assert np.allclose(dset1[:], dset2[:])
else:
assert np.all(dset1[:] == dset2[:])
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