prepare - work around anndata bug (#1260)

* work around anndata bug 344

* fix accidental cut and paste error

* Use modified make_index_unique function

Temporarily copy code from https://github.com/theislab/anndata/pull/345
until the issue is resolved and released.

* Add notes and test for make_index_unique

* Lint fix

* Format python

Co-authored-by: Matt Weiden <538456+mweiden@users.noreply.github.com>

server/test/test_anndata_adaptor.py

@@ -40,7 +40,7 @@ class AdaptorTest(unittest.TestCase):
             "single_dataset__var_names": None,
             "diffexp__lfc_cutoff": 0.01,
             "adaptor__anndata_adaptor__backed": self.backed,
-            "single_dataset__datapath" : self.data_locator
+            "single_dataset__datapath": self.data_locator,
         }
         config = AppConfig()
         config.update(**args)

server/test/test_cli_prepare.py

@@ -0,0 +1,15 @@
+import unittest
+
+import pandas as pd
+
+from server.cli.prepare import make_index_unique
+
+
+class CLIPrepareTests(unittest.TestCase):
+    """ Test cases for CLI prepare logic """
+
+    def test_make_index_unique(self):
+        index = pd.Index(["SNORD113", "SNORD113", "SNORD113-1"])
+        result = make_index_unique(index)
+        expected = pd.Index(["SNORD113", "SNORD113-2", "SNORD113-1"])
+        self.assertTrue(all(left == right for left, right in zip(result.values, expected.values)))