refactor hail context management in tests

hail-is · Oct 21, 2022 · d5bf722 · d5bf722
1 parent 76dfaec
commit d5bf722
Show file tree

Hide file tree

Showing 37 changed files with 26 additions and 149 deletions.
diff --git a/hail/python/hail/conftest.py b/hail/python/hail/conftest.py
@@ -44,6 +44,11 @@ def init(doctest_namespace):
         os.chdir(olddir)
 
 
+@pytest.fixture(autouse=True)
+def reset_randomness(init):
+    hl.reset_global_randomness()
+
+
 def generate_datasets(doctest_namespace):
     doctest_namespace['hl'] = hl
     doctest_namespace['np'] = np

diff --git a/hail/python/test/hail/conftest.py b/hail/python/test/hail/conftest.py
@@ -4,8 +4,9 @@
 
 import pytest
 
-from hail import current_backend
+from hail import current_backend, init
 from hail.backend.service_backend import ServiceBackend
+from .helpers import startTestHailContext, stopTestHailContext
 
 
 def pytest_collection_modifyitems(config, items):
@@ -33,8 +34,15 @@ def ensure_event_loop_is_initialized_in_test_thread():
         asyncio.set_event_loop(asyncio.new_event_loop())
 
 
+@pytest.fixture(scope="session", autouse=True)
+def init_hail():
+    startTestHailContext()
+    yield
+    stopTestHailContext()
+
+
 @pytest.fixture(autouse=True)
-def set_query_name(request):
+def set_query_name(init_hail, request):
     backend = current_backend()
     if isinstance(backend, ServiceBackend):
         backend.batch_attributes = dict(name=request.node.name)

diff --git a/hail/python/test/hail/experimental/test_codec.py b/hail/python/test/hail/experimental/test_codec.py
@@ -1,9 +1,6 @@
 import hail as hl
 from test.hail.helpers import *
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 UNBLOCKED_UNBUFFERED_SPEC = '{"name":"StreamBufferSpec"}'
 
 

diff --git a/hail/python/test/hail/experimental/test_experimental.py b/hail/python/test/hail/experimental/test_experimental.py
@@ -5,9 +5,6 @@
 from ..helpers import *
 from hail.utils import new_temp_file
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 
 class Tests(unittest.TestCase):
     @fails_service_backend()

diff --git a/hail/python/test/hail/experimental/test_vcf_combiner.py b/hail/python/test/hail/experimental/test_vcf_combiner.py
@@ -4,10 +4,7 @@
 from hail.experimental.vcf_combiner import vcf_combiner as vc
 from hail.utils.java import Env
 from hail.utils.misc import new_temp_file
-from ..helpers import resource, startTestHailContext, stopTestHailContext, fails_local_backend, fails_service_backend
-
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
+from ..helpers import resource, fails_local_backend, fails_service_backend
 
 
 all_samples = ['HG00308', 'HG00592', 'HG02230', 'NA18534', 'NA20760',

diff --git a/hail/python/test/hail/expr/test_expr.py b/hail/python/test/hail/expr/test_expr.py
@@ -11,9 +11,6 @@
 import hail.ir as ir
 from ..helpers import *
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 
 def _test_many_equal(test_cases):
     expressions = [t[0] for t in test_cases]

diff --git a/hail/python/test/hail/expr/test_ndarrays.py b/hail/python/test/hail/expr/test_ndarrays.py
@@ -4,9 +4,6 @@
 
 from hail.utils.java import FatalError, HailUserError
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 def assert_ndarrays(asserter, exprs_and_expecteds):
     exprs, expecteds = zip(*exprs_and_expecteds)
 

diff --git a/hail/python/test/hail/expr/test_show.py b/hail/python/test/hail/expr/test_show.py
@@ -1,11 +1,7 @@
-from ..helpers import startTestHailContext, stopTestHailContext
 import unittest
 
 import hail as hl
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 
 class Tests(unittest.TestCase):
     def test(self):

diff --git a/hail/python/test/hail/expr/test_types.py b/hail/python/test/hail/expr/test_types.py
@@ -5,9 +5,6 @@
 from ..helpers import *
 from hail.utils.java import Env
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 
 class Tests(unittest.TestCase):
     def types_to_test(self):

diff --git a/hail/python/test/hail/fs/test_worker_driver_fs.py b/hail/python/test/hail/fs/test_worker_driver_fs.py
@@ -1,11 +1,7 @@
 import hail as hl
-from ..helpers import startTestHailContext, stopTestHailContext
 from hailtop.utils import secret_alnum_string
 from hailtop.test_utils import skip_in_azure
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 
 @skip_in_azure
 def test_requester_pays_no_settings():

diff --git a/hail/python/test/hail/genetics/test_call.py b/hail/python/test/hail/genetics/test_call.py
@@ -3,9 +3,6 @@
 from hail.genetics import *
 from ..helpers import *
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 
 class Tests(unittest.TestCase):
     def test_hom_ref(self):

diff --git a/hail/python/test/hail/genetics/test_locus.py b/hail/python/test/hail/genetics/test_locus.py
@@ -4,9 +4,6 @@
 from hail.genetics import *
 from ..helpers import *
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 class Tests(unittest.TestCase):
 
     def test_constructor(self):

diff --git a/hail/python/test/hail/genetics/test_pedigree.py b/hail/python/test/hail/genetics/test_pedigree.py
@@ -4,9 +4,6 @@
 from ..helpers import *
 from hail.utils.java import FatalError
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 
 class Tests(unittest.TestCase):
 

diff --git a/hail/python/test/hail/genetics/test_reference_genome.py b/hail/python/test/hail/genetics/test_reference_genome.py
@@ -5,9 +5,6 @@
 from ..helpers import *
 from hail.utils import FatalError
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 
 class Tests(unittest.TestCase):
 

diff --git a/hail/python/test/hail/linalg/test_linalg.py b/hail/python/test/hail/linalg/test_linalg.py
@@ -8,9 +8,6 @@
 import math
 from hail.expr.expressions import ExpressionException
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 
 def sparsify_numpy(np_mat, block_size, blocks_to_sparsify):
     n_rows, n_cols = np_mat.shape

diff --git a/hail/python/test/hail/matrixtable/test_file_formats.py b/hail/python/test/hail/matrixtable/test_file_formats.py
@@ -5,9 +5,6 @@
 from hail.utils.java import Env, scala_object
 from ..helpers import *
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 
 def create_backward_compatibility_files():
     import os
@@ -39,12 +36,12 @@ def test_write():
 
 
 @pytest.fixture(scope="module")
-def all_values_matrix_table_fixture():
+def all_values_matrix_table_fixture(init_hail):
     return create_all_values_matrix_table()
 
 
 @pytest.fixture(scope="module")
-def all_values_table_fixture():
+def all_values_table_fixture(init_hail):
     return create_all_values_table()
 
 

diff --git a/hail/python/test/hail/matrixtable/test_grouped_matrix_table.py b/hail/python/test/hail/matrixtable/test_grouped_matrix_table.py
@@ -3,9 +3,6 @@
 import hail as hl
 from ..helpers import *
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 
 class Tests(unittest.TestCase):
 

diff --git a/hail/python/test/hail/matrixtable/test_matrix_table.py b/hail/python/test/hail/matrixtable/test_matrix_table.py
@@ -10,9 +10,6 @@
 from hail.utils.misc import new_temp_file
 from ..helpers import *
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 
 class Tests(unittest.TestCase):
     def get_mt(self, min_partitions=None) -> hl.MatrixTable:

diff --git a/hail/python/test/hail/methods/relatedness/test_identity_by_descent.py b/hail/python/test/hail/methods/relatedness/test_identity_by_descent.py
@@ -4,11 +4,7 @@
 
 import hail as hl
 import hail.utils as utils
-from ...helpers import (startTestHailContext, stopTestHailContext, get_dataset,
-                        fails_service_backend, fails_local_backend)
-
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
+from ...helpers import get_dataset, fails_service_backend, fails_local_backend
 
 
 class Tests(unittest.TestCase):

diff --git a/hail/python/test/hail/methods/relatedness/test_pc_relate.py b/hail/python/test/hail/methods/relatedness/test_pc_relate.py
@@ -1,10 +1,7 @@
 import hail as hl
 import hail.utils as utils
 
-from ...helpers import (resource, startTestHailContext, stopTestHailContext, skip_when_service_backend)
-
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
+from ...helpers import resource, skip_when_service_backend
 
 
 def test_pc_relate_against_R_truth():

diff --git a/hail/python/test/hail/methods/test_family_methods.py b/hail/python/test/hail/methods/test_family_methods.py
@@ -3,9 +3,6 @@
 import hail as hl
 from ..helpers import *
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 
 class Tests(unittest.TestCase):
     def test_trio_matrix(self):

diff --git a/hail/python/test/hail/methods/test_impex.py b/hail/python/test/hail/methods/test_impex.py
@@ -14,9 +14,6 @@
 from ..helpers import *
 from hail.utils import new_temp_file, FatalError, run_command, uri_path, HailUserError
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 _FLOAT_INFO_FIELDS = [
     'BaseQRankSum',
     'ClippingRankSum',

diff --git a/hail/python/test/hail/methods/test_king.py b/hail/python/test/hail/methods/test_king.py
@@ -1,10 +1,7 @@
 import pytest
 
 import hail as hl
-from ..helpers import resource, startTestHailContext, stopTestHailContext, fails_local_backend, fails_service_backend
-
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
+from ..helpers import resource, fails_local_backend, fails_service_backend
 
 
 def assert_c_king_same_as_hail_king(c_king_path, hail_king_mt):

diff --git a/hail/python/test/hail/methods/test_misc.py b/hail/python/test/hail/methods/test_misc.py
@@ -3,9 +3,6 @@
 import hail as hl
 from ..helpers import *
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 
 class Tests(unittest.TestCase):
     def test_rename_duplicates(self):

diff --git a/hail/python/test/hail/methods/test_pca.py b/hail/python/test/hail/methods/test_pca.py
@@ -4,12 +4,7 @@
 
 import hail as hl
 from hail.methods.pca import _make_tsm
-from ..helpers import (resource, startTestHailContext, stopTestHailContext, fails_local_backend,
-                       fails_service_backend, skip_when_service_backend)
-
-
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
+from ..helpers import resource, fails_local_backend, fails_service_backend, skip_when_service_backend
 
 
 @fails_service_backend()

diff --git a/hail/python/test/hail/methods/test_qc.py b/hail/python/test/hail/methods/test_qc.py
@@ -4,9 +4,6 @@
 import hail.expr.aggregators as agg
 from ..helpers import *
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 
 class Tests(unittest.TestCase):
     def test_sample_qc(self):

diff --git a/hail/python/test/hail/methods/test_statgen.py b/hail/python/test/hail/methods/test_statgen.py
@@ -10,11 +10,7 @@
 from hail.linalg import BlockMatrix
 from hail.utils import FatalError
 from hail.utils.java import choose_backend
-from ..helpers import (startTestHailContext, stopTestHailContext, resource,
-                       fails_local_backend, fails_service_backend)
-
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
+from ..helpers import resource, fails_local_backend, fails_service_backend
 
 
 class Tests(unittest.TestCase):

diff --git a/hail/python/test/hail/table/test_grouped_table.py b/hail/python/test/hail/table/test_grouped_table.py
@@ -1,10 +1,6 @@
 import unittest
 
 import hail as hl
-from ..helpers import *
-
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
 
 
 class GroupedTableTests(unittest.TestCase):

diff --git a/hail/python/test/hail/table/test_table.py b/hail/python/test/hail/table/test_table.py
@@ -16,9 +16,6 @@
 from ..helpers import *
 from test.hail.matrixtable.test_file_formats import create_all_values_datasets
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 
 class Tests(unittest.TestCase):
     def test_annotate(self):

diff --git a/hail/python/test/hail/test_context.py b/hail/python/test/hail/test_context.py
@@ -1,12 +1,8 @@
 import unittest
 
 import hail as hl
-from .helpers import startTestHailContext, stopTestHailContext, skip_unless_spark_backend, fails_local_backend, fails_service_backend
 from hail.utils.java import Env
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 
 class Tests(unittest.TestCase):
     def test_init_hail_context_twice(self):

diff --git a/hail/python/test/hail/test_ir.py b/hail/python/test/hail/test_ir.py
@@ -8,9 +8,6 @@
 from hail.utils import new_temp_file
 from .helpers import *
 
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
-
 
 class ValueIRTests(unittest.TestCase):
     def value_irs_env(self):

diff --git a/hail/python/test/hail/utils/test_google_fs_utils.py b/hail/python/test/hail/utils/test_google_fs_utils.py
@@ -11,11 +11,6 @@
 from hailtop.utils import secret_alnum_string
 from hailtop.config import get_remote_tmpdir
 from hail.utils.java import FatalError
-from ..helpers import startTestHailContext, stopTestHailContext, _initialized
-
-
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
 
 
 class Tests(unittest.TestCase):

diff --git a/hail/python/test/hail/utils/test_placement_tree.py b/hail/python/test/hail/utils/test_placement_tree.py
@@ -3,10 +3,6 @@
 import hail as hl
 
 from hail.utils.placement_tree import PlacementTree
-from ..helpers import startTestHailContext, stopTestHailContext
-
-setUpModule = startTestHailContext
-tearDownModule = stopTestHailContext
 
 
 class Tests(unittest.TestCase):