Revert

szhan · Sep 13, 2023 · 2799ad3 · 2799ad3
1 parent 641a121
commit 2799ad3
Showing 1 changed file with 3 additions and 47 deletions.
diff --git a/python/tests/test_imputation.py b/python/tests/test_imputation.py
@@ -492,9 +492,9 @@ def test_compare_imputed_alleles(input_ref, input_query, expected):
     "input_ref,input_query,expected",
     [
         (toy_ref_0, toy_query_0, toy_query_0_beagle_allele_probs),
-        (toy_ref_1, toy_query_1, toy_query_1_beagle_allele_probs),
-        (toy_ref_2, toy_query_2, toy_query_2_beagle_allele_probs),
-        (toy_ref_3, toy_query_3, toy_query_3_beagle_allele_probs),
+        # (toy_ref_1, toy_query_1, toy_query_1_beagle_allele_probs),
+        # (toy_ref_2, toy_query_2, toy_query_2_beagle_allele_probs),
+        # (toy_ref_3, toy_query_3, toy_query_3_beagle_allele_probs),
         # (toy_ref_4, toy_query_4, toy_query_4_beagle_allele_probs),
         # (toy_ref_5, toy_query_5, toy_query_5_beagle_allele_probs),
         # (toy_ref_6, toy_query_6, toy_query_6_beagle_allele_probs),
@@ -513,50 +513,6 @@ def test_compare_allele_probabilities(input_ref, input_query, expected):
         assert np.allclose(allele_probs.T, expected[i], atol=1e-04)
 
 
-@pytest.mark.parametrize(
-    "input_ref,input_query",
-    [
-        (toy_ref_0, toy_query_0),
-    ],
-)
-def test_beagle_numba(input_ref, input_query):
-    pos = (np.arange(9) + 1) * 1e4
-    num_query_haps = input_query.shape[0]
-    for i in np.arange(num_query_haps):
-        imputed_alleles, allele_probs = tests.beagle.run_beagle(
-            input_ref, input_query[i], pos, miscall_rate=0.0001, ne=10.0
-        )
-        imputed_alleles_numba, allele_probs_numba = tests.beagle_numba.run_beagle(
-            input_ref, input_query[i], pos, miscall_rate=0.0001, ne=10.0
-        )
-        assert np.array_equal(imputed_alleles, imputed_alleles_numba)
-        assert np.allclose(allele_probs, allele_probs_numba)
-
-
-@pytest.mark.parametrize(
-    "input_ref,input_query",
-    [
-        (toy_ref_0, toy_query_0),
-    ],
-)
-def test_tsimpute(input_ref, input_query):
-    pos = (np.arange(9) + 1) * 1e4
-    num_query_haps = input_query.shape[0]
-    for i in np.arange(num_query_haps):
-        imputed_alleles, allele_probs = tests.beagle.run_beagle(
-            input_ref, input_query[i], pos, miscall_rate=0.0001, ne=10.0
-        )
-        # Note that parametrization of BEAGLE and tsinfer
-        mu = tests.beagle_numba.get_mismatch_prob(pos, miscall_rate=1e-8)
-        rho = tests.beagle_numba.get_switch_prob(pos, input_ref.shape[0], ne=10_000.0)
-        rho /= 1e5
-        imputed_alleles_ts, allele_probs_ts = tests.beagle_numba.run_tsimpute(
-            input_ref, input_query[i], pos, mu, rho
-        )
-        assert np.array_equal(imputed_alleles, imputed_alleles_ts)
-        assert np.allclose(allele_probs, allele_probs_ts)
-
-
 # Below is toy data set case 7 in tree sequence format.
 toy_ts_nodes_text = """\
 id      is_sample       time    population      individual      metadata