fixes

hail-is · Oct 21, 2022 · 116548b · 116548b
1 parent 47a8e22
commit 116548b
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Showing 4 changed files with 17 additions and 19 deletions.
diff --git a/hail/python/hail/docs/scans.rst b/hail/python/hail/docs/scans.rst
@@ -45,6 +45,8 @@ along the genome:
     +---------------+------------+-----------+---------------+
     | locus<GRCh37> | array<str> |     int64 |         int64 |
     +---------------+------------+-----------+---------------+
+    | 20:10579373   | ["C","T"]  |         1 |             0 |
+    | 20:10579398   | ["C","T"]  |         1 |             1 |
     | 20:10627772   | ["C","T"]  |         2 |             2 |
     | 20:10633237   | ["G","A"]  |        69 |             4 |
     | 20:10636995   | ["C","T"]  |         2 |            73 |

diff --git a/hail/python/hail/expr/aggregators/aggregators.py b/hail/python/hail/expr/aggregators/aggregators.py
@@ -1219,7 +1219,7 @@ def call_stats(call, alleles) -> StructExpression:
     +---------------+--------------+---------------------+-------------+---------------------------+
     | 20:10579373   | [199,1]      | [9.95e-01,5.00e-03] |         200 | [99,0]                    |
     | 20:10579398   | [198,2]      | [9.90e-01,1.00e-02] |         200 | [99,1]                    |
-    | 20:10627772   | [198,2]      | [9.90e-01,1.00e-02] |         200 | [98,0]
+    | 20:10627772   | [198,2]      | [9.90e-01,1.00e-02] |         200 | [98,0]                    |
     | 20:10633237   | [108,92]     | [5.40e-01,4.60e-01] |         200 | [31,23]                   |
     | 20:10636995   | [198,2]      | [9.90e-01,1.00e-02] |         200 | [98,0]                    |
     | 20:10639222   | [175,25]     | [8.75e-01,1.25e-01] |         200 | [78,3]                    |

diff --git a/hail/python/test/hail/experimental/test_annotation_db.py b/hail/python/test/hail/experimental/test_annotation_db.py
@@ -1,27 +1,25 @@
-import unittest
+import pytest
 
 import hail as hl
 from hail.backend.service_backend import ServiceBackend
-from ..helpers import startTestHailContext, stopTestHailContext
 
 
-class AnnotationDBTests(unittest.TestCase):
-    @classmethod
-    def setupAnnotationDBTests(cls):
-        startTestHailContext()
+class TestAnnotationDB:
+    @pytest.fixture(scope="class")
+    def db_json(init_hail):
         backend = hl.current_backend()
         if isinstance(backend, ServiceBackend):
             backend.batch_attributes = dict(name='setupAnnotationDBTests')
         t = hl.utils.range_table(10)
         t = t.key_by(locus=hl.locus('1', t.idx + 1))
         t = t.annotate(annotation=hl.str(t.idx))
-        cls.tempdir_manager = hl.TemporaryDirectory()
-        d = cls.tempdir_manager.__enter__()
+        tempdir_manager = hl.TemporaryDirectory()
+        d = tempdir_manager.__enter__()
         fname = d + '/f.mt'
         t.write(fname)
         if isinstance(backend, ServiceBackend):
             backend.batch_attributes = dict()
-        cls.db_json = {
+        db_json = {
             'unique_dataset': {
                 'description': 'now with unique rows!',
                 'url': 'https://example.com',
@@ -46,16 +44,12 @@ def setupAnnotationDBTests(cls):
             }
         }
 
-    @classmethod
-    def tearDownAnnotationDBTests(cls):
-        stopTestHailContext()
-        cls.tempdir_manager.__exit__(None, None, None)
+        yield db_json
 
-    setUpClass = setupAnnotationDBTests
-    tearDownClass = tearDownAnnotationDBTests
+        tempdir_manager.__exit__(None, None, None)
 
-    def test_uniqueness(self):
-        db = hl.experimental.DB(region='us', cloud='gcp', config=AnnotationDBTests.db_json)
+    def test_uniqueness(self, db_json):
+        db = hl.experimental.DB(region='us', cloud='gcp', config=db_json)
         t = hl.utils.range_table(10)
         t = t.key_by(locus=hl.locus('1', t.idx + 1))
         t = db.annotate_rows_db(t, 'unique_dataset', 'nonunique_dataset')

diff --git a/hail/python/test/hail/methods/test_statgen.py b/hail/python/test/hail/methods/test_statgen.py
@@ -9,7 +9,7 @@
 import hail.utils as utils
 from hail.linalg import BlockMatrix
 from hail.utils import FatalError
-from hail.utils.java import choose_backend
+from hail.utils.java import choose_backend, Env
 from ..helpers import resource, fails_local_backend, fails_service_backend
 
 
@@ -1626,6 +1626,8 @@ def variance(expr):
         test_stat(40, 400, 20, 12)
 
     def test_balding_nichols_model_phased(self):
+        print(f'current static uid: {Env._static_rng_uid}')
+        print(f"rng_nonce: {hl._get_flags('rng_nonce')['rng_nonce']}")
         bn_ds = hl.balding_nichols_model(1, 5, 5, phased=True)
         assert bn_ds.aggregate_entries(hl.agg.all(bn_ds.GT.phased)) == True
         actual = bn_ds.GT.collect()