Add support for anndata backed mode (#943)

* initial cut at backed mode

* make flask multithreading conditional on debug flag

* update X access to support backed mode

* lint

* improve help message for backed mode

* fix tests

* add MatrixProxy to normalize supported matrix types

* add FAQ entry for --backed

* remove use of matrix.T

* clean up

* add ability to disable diffexp from CLI; add hueristic to detect likely slow diffexp calculation, and warn user

* fix tests

* do not print diffexp speed warning if diffexp is disabled

* tweak wording of diffexp speed messages

* add FAQ entry on --disable-diffexp

* revise heuristic for warning about slow diffexp

* use quick tooltip delay on diffexp button

server/test/test_scanpy_engine.py

@@ -18,10 +18,14 @@ Test the scanpy engine using the pbmc3k data set.
 """
 
 
-@parameterized_class(("data_locator",), [
-    ("example-dataset/pbmc3k.h5ad",),
-    ("server/test/test_datasets/pbmc3k-CSC-gz.h5ad",),
-    ("server/test/test_datasets/pbmc3k-CSR-gz.h5ad",)
+@parameterized_class(("data_locator", "backed"), [
+    ("example-dataset/pbmc3k.h5ad", False),
+    ("server/test/test_datasets/pbmc3k-CSC-gz.h5ad", False),
+    ("server/test/test_datasets/pbmc3k-CSR-gz.h5ad", False),
+
+    ("example-dataset/pbmc3k.h5ad", True),
+    ("server/test/test_datasets/pbmc3k-CSC-gz.h5ad", True),
+    ("server/test/test_datasets/pbmc3k-CSR-gz.h5ad", True),
 ])
 class EngineTest(unittest.TestCase):
     def setUp(self):
@@ -31,7 +35,8 @@ class EngineTest(unittest.TestCase):
             "obs_names": None,
             "var_names": None,
             "diffexp_lfc_cutoff": 0.01,
-            "layout_file": None
+            "layout_file": None,
+            "backed": self.backed
         }
         self.data = ScanpyEngine(DataLocator(self.data_locator), args)
 
@@ -51,9 +56,12 @@ class EngineTest(unittest.TestCase):
 
     @pytest.mark.filterwarnings("ignore:Scanpy data matrix")
     def test_data_type(self):
-        self.data.data.X = self.data.data.X.astype("float64")
-        with self.assertWarns(UserWarning):
-            self.data._validate_data_types()
+        # don't run the test on the more exotic data types, as they don't
+        # support the astype() interface (used by this test, but not underlying app)
+        if isinstance(self.data.data.X, np.ndarray):
+            self.data.data.X = self.data.data.X.astype("float64")
+            with self.assertWarns(UserWarning):
+                self.data._validate_data_types()
 
     def test_filter_idx(self):
         filter_ = {
@@ -159,10 +167,11 @@ class EngineTest(unittest.TestCase):
         self.assertEqual(len(result), 20)
 
     def test_data_frame(self):
-        fbs = self.data.data_frame_to_fbs_matrix(None, "var")
+        f1 = {"var": {"index": [[0, 10]]}}
+        fbs = self.data.data_frame_to_fbs_matrix(f1, "var")
         data = decode_fbs.decode_matrix_FBS(fbs)
         self.assertEqual(data["n_rows"], 2638)
-        self.assertEqual(data["n_cols"], 1838)
+        self.assertEqual(data["n_cols"], 10)
 
         with self.assertRaises(ValueError):
             self.data.data_frame_to_fbs_matrix(None, "obs")