fix for incorrect stats computation in diff exp t-test (#2318)

* 2211 fixes

* lint

* lint

* add missing test and bug found by test

* change terminology for count distribution

* update scanpy requirement

* update scanpy requirement

backend/test/test_server/unit/common/config/__init__.py

@@ -103,6 +103,7 @@ class ConfigTests(unittest.TestCase):
         environment=None,
         aws_secrets_manager_region=None,
         aws_secrets_manager_secrets=[],
+        X_approx_distribution="auto",
         config_file_name="app_config.yml",
     ):
         random_num = random.randrange(999999)
@@ -150,6 +151,7 @@ class ConfigTests(unittest.TestCase):
             enable_difexp=enable_difexp,
             lfc_cutoff=lfc_cutoff,
             top_n=top_n,
+            X_approx_distribution=X_approx_distribution,
             config_file_name=f"temp_dataset_config_{random_num}.yml",
         )
         external_config = self.custom_external_config(
@@ -185,6 +187,7 @@ class ConfigTests(unittest.TestCase):
         enable_difexp="true",
         lfc_cutoff=0.01,
         top_n=10,
+        X_approx_distribution="auto",
         config_file_name="dataset_config.yml",
     ):
         configfile = os.path.join(self.tmp_fixtures_directory, config_file_name)

backend/test/test_server/unit/common/config/test_dataset_config.py

@@ -7,7 +7,7 @@ from unittest.mock import patch
 from backend.server.common.annotations.local_file_csv import AnnotationsLocalFile
 from backend.server.common.config.app_config import AppConfig
 from backend.server.common.config.base_config import BaseConfig
-from backend.test import FIXTURES_ROOT, H5AD_FIXTURE
+from backend.test import H5AD_FIXTURE
 
 from backend.common.errors import ConfigurationError
 from backend.test.test_server.unit.common.config import ConfigTests
@@ -46,7 +46,7 @@ class TestDatasetConfig(ConfigTests):
         mock_check_attrs.side_effect = BaseConfig.validate_correct_type_of_configuration_attribute()
         self.dataset_config.complete_config(self.context)
         self.assertIsNotNone(self.config.server_config.data_adaptor)
-        self.assertEqual(mock_check_attrs.call_count, 16)
+        self.assertEqual(mock_check_attrs.call_count, 17)
 
     def test_app_sets_script_vars(self):
         config = self.get_config(scripts=["path/to/script"])