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remove experimental reembedding support (#2301)

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* remove experimental reembedding support

* lint

* lint

* add prepare requirements to requirements-dev

* oops, revert accidental deletion of import

* more test modifications

* remove obsolete unit tests
This commit is contained in:
Bruce Martin
2021-07-15 13:55:26 -07:00
committed by GitHub
parent e334fbe96e
commit 0667ad0274
46 changed files with 12 additions and 661 deletions
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backend/test/test_server/unit/common/config/__init__.py
-3
View File
@@ -97,7 +97,6 @@ class ConfigTests(unittest.TestCase):
local_file_csv_gene_sets_file="null",
gene_sets_readonly="false",
embedding_names=[],
enable_reembedding="false",
enable_difexp="true",
lfc_cutoff=0.01,
top_n=10,
@@ -148,7 +147,6 @@ class ConfigTests(unittest.TestCase):
local_file_csv_gene_sets_file=local_file_csv_gene_sets_file,
gene_sets_readonly=gene_sets_readonly,
embedding_names=embedding_names,
enable_reembedding=enable_reembedding,
enable_difexp=enable_difexp,
lfc_cutoff=lfc_cutoff,
top_n=top_n,
@@ -184,7 +182,6 @@ class ConfigTests(unittest.TestCase):
local_file_csv_gene_sets_file="null",
gene_sets_readonly="false",
embedding_names=[],
enable_reembedding="false",
enable_difexp="true",
lfc_cutoff=0.01,
top_n=10,
backend/test/test_server/unit/common/config/test_dataset_config.py
+1 -15
View File
@@ -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, 17)
self.assertEqual(mock_check_attrs.call_count, 16)
def test_app_sets_script_vars(self):
config = self.get_config(scripts=["path/to/script"])
@@ -106,20 +106,6 @@ class TestDatasetConfig(ConfigTests):
cwd = os.getcwd()
self.assertEqual(config.dataset_config.user_annotations._get_output_dir(), cwd)
def test_handle_embeddings__checks_data_file_types(self):
file_name = self.custom_app_config(
embedding_names=["name1", "name2"],
enable_reembedding="true",
dataset_datapath=f"{FIXTURES_ROOT}/pbmc3k-CSC-gz.h5ad",
anndata_backed="true",
config_file_name=self.config_file_name,
)
config = AppConfig()
config.update_from_config_file(file_name)
config.server_config.complete_config(self.context)
with self.assertRaises(ConfigurationError):
config.dataset_config.handle_embeddings()
def test_handle_diffexp__raises_warning_for_large_datasets(self):
config = self.get_config(lfc_cutoff=0.02, enable_difexp="true", top_n=15)
config.server_config.complete_config(self.context)