def client_context(dask_client=None, dask_scheduler=None):
'''client_context creates a dask distributed or threadpool client or None
Parameters:
dask_client: str from choices ("DISTRIBUTED", 'THREAD_POOL', 'SERIAL')
or None to take DASK_CLIENT from environment
dask_scheduler: Distributed scheduler url or None to take
DASK_SCHEDULER from environment
'''
env = parse_env_vars()
dask_client = dask_client or env.get('DASK_CLIENT', 'SERIAL')
dask_scheduler = dask_scheduler or env.get('DASK_SCHEDULER')
if dask_client == 'DISTRIBUTED':
if Executor is None:
raise ValueError('distributed is not installed - "conda install distributed"')
client = Executor(dask_scheduler)
elif dask_client == 'THREAD_POOL':
client = ThreadPool(env.get('DASK_THREADS'))
elif dask_client == 'SERIAL':
client = None
else:
raise ValueError('Did not expect DASK_CLIENT to be {}'.format(dask_client))
get_func = _find_get_func_for_client(client)
with da.set_options(pool=dask_client):
yield client
import dask.array as da
import dask. async
from nose.tools import assert_raises, eq_ as eq
from allel.model.ndarray import GenotypeArray, HaplotypeArray, \
AlleleCountsArray
from allel.test.tools import assert_array_equal as aeq
from allel.test.test_model_api import GenotypeArrayInterface, \
diploid_genotype_data, triploid_genotype_data, HaplotypeArrayInterface, \
haplotype_data, allele_counts_data, AlleleCountsArrayInterface
from allel.model.dask import GenotypeDaskArray, HaplotypeDaskArray, \
AlleleCountsDaskArray
# use synchronous scheduler because getting random hangs with default
da.set_options(get=dask. async .get_sync)
class GenotypeDaskArrayTests(GenotypeArrayInterface, unittest.TestCase):
_class = GenotypeDaskArray
def setup_instance(self, data):
return GenotypeDaskArray.from_array(data, chunks=(2, 2, None))
def test_constructor(self):
# missing data arg
with assert_raises(TypeError):
# noinspection PyArgumentList
GenotypeDaskArray.from_array()
import dask.async
from nose.tools import assert_raises, eq_ as eq
from allel.model.ndarray import GenotypeArray, HaplotypeArray, \
AlleleCountsArray
from allel.test.tools import assert_array_equal as aeq
from allel.test.test_model_api import GenotypeArrayInterface, \
diploid_genotype_data, triploid_genotype_data, HaplotypeArrayInterface, \
haplotype_data, allele_counts_data, AlleleCountsArrayInterface
from allel.model.dask import GenotypeDaskArray, HaplotypeDaskArray, \
AlleleCountsDaskArray
# use synchronous scheduler because getting random hangs with default
da.set_options(get=dask.async.get_sync)
class GenotypeDaskArrayTests(GenotypeArrayInterface, unittest.TestCase):
_class = GenotypeDaskArray
def setup_instance(self, data):
return GenotypeDaskArray.from_array(data, chunks=(2, 2, None))
def test_constructor(self):
# missing data arg
with assert_raises(TypeError):
# noinspection PyArgumentList
GenotypeDaskArray.from_array()
import numpy as np
import dask.array as da
import dask.local
from nose.tools import assert_raises, eq_ as eq
import zarr
from allel import GenotypeArray, HaplotypeArray, AlleleCountsArray, GenotypeVector
from allel import GenotypeDaskArray, HaplotypeDaskArray, AlleleCountsDaskArray, \
GenotypeDaskVector
from allel.test.tools import assert_array_equal as aeq
from allel.test.model.test_api import GenotypeArrayInterface, \
diploid_genotype_data, triploid_genotype_data, HaplotypeArrayInterface, \
haplotype_data, allele_counts_data, AlleleCountsArrayInterface
# use synchronous scheduler because getting random hangs with default
da.set_options(get=dask.local.get_sync)
class GenotypeDaskArrayTests(GenotypeArrayInterface, unittest.TestCase):
_class = GenotypeDaskArray
def setup_instance(self, data, dtype=None):
return GenotypeDaskArray(np.asarray(data, dtype=dtype),
chunks=(2, 2, None))
def test_constructor(self):
# missing data arg
with assert_raises(TypeError):
# noinspection PyArgumentList