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/app/scanpy_engine/matrix_proxy.py

@@ -0,0 +1,42 @@
+
+from server.app.util.matrix_proxy import MatrixProxyView, ArrayProxyView
+
+"""
+AnnData/h5py are inconsistent in the API supported by various types of
+X matrices.  Sometimes you get a fully ndarray, sometims a Scipy sparse
+matrix, sometimes h5py proxies with a subset of our needed interfaces.
+
+This glue code paves over all of that, providing the core set of methods
+that the cellxgene ScanPy driver assumes are in existance.  Put another
+way, all of the non-portable assumptions are here.
+"""
+
+
+class ArrayProxyView_anndata_h5py(ArrayProxyView):
+    """
+    override to handle sparse getitem semantics, which differ
+    from numpy.
+    """
+    def toarray(self):
+        """ sadly, sparse indexing doesn't drop dimensions like numpy! """
+        arr = self.m[self._index[0], self._index[1]]
+        if self._vdim == 0:
+            arr = arr.transpose()
+        return arr.toarray()[0]
+
+
+class MatrixProxy_anndata_h5py(MatrixProxyView):
+    """
+    AnnData sparse array stored in H5AD, or proxies for backed data.
+    None of these handle indexing very well, so we plop a proxy on top.
+    """
+    @classmethod
+    def __supports__(cls):
+        return ("anndata.h5py.h5sparse.SparseDataset",
+                "anndata.h5py.h5sparse.backed_csc_matrix",
+                "anndata.h5py.h5sparse.backed_csr_matrix",
+                "h5py._hl.dataset.Dataset")
+
+    @classmethod
+    def create_array(cls, *args, **kwargs):
+        return ArrayProxyView_anndata_h5py(*args, **kwargs)