Specialize diffexp for tiledb (#1384)

* Specialize diffexp for tiledb

This patch adds a new diffexp algorithm which is tuned for tiledb.
This algorithm was written by Bruce and is adapted here to plug into the
current framework.  The anndata_adaptor still calls the original
algotithm (which was move from diffexp.py to diffexp_generic.py).
The cxg_adaptor now calls the new diffexp_tiledb version.  Some
code is shared between the two.

This is part 1 of the diffexp for tiledb.  Further tuning and
global throttles are still needed.

A script to run and time diffexp with various options is also
added: test/run_diffexp.py.

server/data_cxg/cxg_util.py

@@ -0,0 +1,37 @@
+import numpy as np
+
+
+def pack_selector_from_mask(boolarray):
+    """
+    pack all contiguous selectors into slices.  Remember that
+    tiledb multi_index requires INCLUSIVE indices.
+    """
+
+    if boolarray is None:
+        return slice(None)
+
+    assert type(boolarray) == np.ndarray
+    assert boolarray.dtype == bool
+
+    selector = np.nonzero(boolarray)[0]
+    return pack_selector_from_indices(selector)
+
+
+def pack_selector_from_indices(selector):
+
+    if len(selector) == 0:
+        return slice(None)
+
+    result = []
+    current = slice(selector[0], selector[0])
+    for sel in selector[1:]:
+        if sel == current.stop + 1:
+            current = slice(current.start, sel)
+        else:
+            result.append(current if current.start != current.stop else current.start)
+            current = slice(sel, sel)
+
+    if len(result) == 0 or result[-1] != current:
+        result.append(current if current.start != current.stop else current.start)
+
+    return result