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import functools
from pyensembl import genome_for_reference_name, cached_release
import pytest
grch37 = genome_for_reference_name("GRCh37")
grch38 = genome_for_reference_name("GRCh38")
major_releases = [grch37, grch38]
contigs = [str(c) for c in range(1, 23)] + ["X", "Y", "M"]
def run_multiple_genomes(*versions):
if len(versions) == 1 and callable(versions[0]):
return pytest.mark.parametrize("genome", major_releases)(versions[0])
if not versions:
genomes = major_releases
else:
genomes = [cached_release(v) for v in versions]
return lambda fn: pytest.mark.parametrize("genome", genomes)(fn)
# TemporaryDirectory only got added to Python in version 3.2
try:
# pylint: disable=no-name-in-module
from tempfile import TemporaryDirectory
except ImportError:
# only added in Python 3.2
from tempfile import mkdtemp
from shutil import rmtree
class TemporaryDirectory(object):
def __init__(self):
self.name = mkdtemp()
def __enter__(self, *args, **kwargs):
return self.name
def __exit__(self, type, value, traceback):
rmtree(self.name)
# don't suppress exceptions
return False
def ok_(b):
assert b
def eq_(x, y, msg=None):
if msg is None:
assert x == y
else:
assert x == y, msg
def neq_(x, y, msg=None):
if msg is None:
assert x != y
else:
assert x != y, msg
def gt_(x, y, msg=None):
if msg is None:
assert x > y
else:
assert x > y, msg
def gte_(x, y, msg=None):
if msg is None:
assert x >= y
else:
assert x >= y, msg
def lt_(x, y, msg=None):
if msg is None:
assert x < y
else:
assert x < y, msg
def lte_(x, y, msg=None):
if msg is None:
assert x <= y
else:
assert x <= y, msg
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