anndata X indexing & version compatibility improvements (#1157)

* revert MatrixProxy; replace with correct use of adata slicing

* work around 0.6 adata slicing bug

* fix incorrect var slice

* simplify slicing of X

* add warning about performance impact of anndata<=0.7

* lint and remove unused code

* improve comment

* lint

* correctly parse versions

* temp files should preserve file suffix if possible - anndata 0.7 compat

* update anndata dependency to 0.6.20

* resolve PR review comments

server/app/util/data_locator.py

@@ -81,8 +81,11 @@ class DataLocator:
             return LocalFilePath(self.path)
 
         # if not local, create a tmp file system object to contain the data,
-        # and clean it up when done.
-        with self.open() as src, tempfile.NamedTemporaryFile(prefix="cellxgene_", delete=False) as tmp:
+        # and clean it up when done.  If the path has a suffix/extension,
+        # do our best to create a file with the same.
+        ext = os.path.splitext(self.path)
+        suffix = None if ext[1] == '' else ext[1]
+        with self.open() as src, tempfile.NamedTemporaryFile(prefix="cellxgene_", suffix=suffix, delete=False) as tmp:
             tmp.write(src.read())
             tmp.close()
             src.close()