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/common/app_config.py

@@ -84,6 +84,7 @@ class AppConfig(object):
 
             self.diffexp__enable = dc["diffexp"]["enable"]
             self.diffexp__lfc_cutoff = dc["diffexp"]["lfc_cutoff"]
+            self.diffexp__top_n = dc["diffexp"]["top_n"]
 
             self.data_locator__s3__region_name = dc["data_locator"]["s3"]["region_name"]
 
@@ -189,6 +190,7 @@ class AppConfig(object):
         context = dict(messagefn=messagefn)
 
         self.handle_server(context)
+        self.handle_adaptor(context)
         self.handle_data_locator(context)
         self.handle_adaptor(context)  # may depend on data_locator
         self.handle_presentation(context)
@@ -430,6 +432,7 @@ class AppConfig(object):
     def handle_diffexp(self, context):
         self.__check_attr("diffexp__enable", bool)
         self.__check_attr("diffexp__lfc_cutoff", float)
+        self.__check_attr("diffexp__top_n", int)
 
         if self.single_dataset__datapath:
             with self.matrix_data_cache_manager.data_adaptor(self.single_dataset__datapath, self) as data_adaptor:

server/common/constants.py

@@ -1,9 +1,6 @@
 from enum import Enum
 
 
-DEFAULT_TOP_N = 10
-
-
 class AugmentedEnum(Enum):
     def __hash__(self):
         return self.value.__hash__()

server/common/default_config.py

@@ -65,6 +65,7 @@ embeddings:
 diffexp:
   enable: true
   lfc_cutoff: 0.01
+  top_n: 10
 
 data_locator:
   s3: