remove experimental reembedding support (#2301)

* 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

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

@@ -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

@@ -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)

backend/test/test_server/unit/common/test_api.py

@@ -73,34 +73,6 @@ class EndPoints(object):
         self.assertIsNone(df["row_idx"])
         self.assertEqual(len(df["columns"]), df["n_cols"])
 
-    def test_put_layout_fbs(self):
-        # first check that re-embedding is turned on
-        result = self.session.get(f"{self.URL_BASE}config")
-        config_data = result.json()
-        re_embed = config_data["config"]["parameters"]["enable-reembedding"]
-        if not re_embed:
-            return
-        # attempt to reembed with umap over 100 cells.
-        endpoint = "layout/obs"
-        url = f"{self.URL_BASE}{endpoint}"
-        data = {}
-        data["filter"] = {}
-        data["filter"]["obs"] = {}
-        data["filter"]["obs"]["index"] = list(range(100))
-        data["method"] = "umap"
-        result = self.session.put(url, json=data)
-
-        self.assertEqual(result.status_code, HTTPStatus.OK)
-        result_data = result.json()
-        self.assertIsInstance(result_data, dict)
-        self.assertEqual(result_data["type"], "float32")
-        self.assertTrue(result_data["name"].startswith("reembed:umap_"))
-        self.assertIsInstance(result_data["dims"], list)
-        self.assertEqual(len(result_data["dims"]), 2)
-        dims = result_data["dims"]
-        self.assertTrue(dims[0].startswith("reembed:umap_") and dims[0].endswith("_0"))
-        self.assertTrue(dims[1].startswith("reembed:umap_") and dims[1].endswith("_1"))
-
     def test_bad_filter(self):
         endpoint = "data/var"
         url = f"{self.URL_BASE}{endpoint}"
@@ -389,7 +361,6 @@ class EndPointsAnndata(unittest.TestCase, EndPoints):
                 f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad",
                 "--disable-annotations",
                 "--disable-gene-sets-save",
-                "--experimental-enable-reembedding",
             ],
         )