Fix/unit tests (#1159)

* Update `TestCleanup::test_cleanup_all`

Replace hypothesis-based testing with Pytest's parametrize. Instead of
loading randomly generated AnnData objects, versions of the pancreas and
dentate gyrus are used.

* Update `test_datasets.py`

Update Python version for which dataset download is tests.

* Update `TestCleanup`

Increase deadling for `test_cleanup_default_clean_w_random_adata`.

tests/core/test_anndata.py

@@ -2,7 +2,7 @@
 
 import hypothesis.strategies as st
 import pytest
-from hypothesis import given
+from hypothesis import given, settings
 
 import numpy as np
 import pandas as pd
@@ -112,8 +112,23 @@ def test_different_obs_id_length(
 
 
 class TestCleanup(TestBase):
-    @given(adata=get_adata(max_obs=5, max_vars=5), inplace=st.booleans())
-    def test_cleanup_all(self, adata: AnnData, inplace: bool):
+    @pytest.mark.parametrize("dataset", ["pancreas", "dentategyrus"])
+    @pytest.mark.parametrize("n_obs", [50, 100])
+    @pytest.mark.parametrize("layer", [None, "unspliced", "spliced"])
+    @pytest.mark.parametrize("dense", [True, False])
+    @pytest.mark.parametrize("inplace", [True, False])
+    def test_cleanup_all(
+        self, adata, dataset: str, n_obs: int, layer: bool, dense: bool, inplace: bool
+    ):
+        adata = adata(dataset=dataset, n_obs=n_obs, raw=False, preprocessed=True)
+        adata.layers["dummy_layer"] = csr_matrix(np.eye(adata.n_obs, adata.n_vars))
+        adata.uns["dummy_entry"] = {"key": csr_matrix(np.eye(5, 7))}
+
+        if dense:
+            if layer is None:
+                adata.X = adata.X.A
+            else:
+                adata.layers[layer] = adata.layers[layer].A
         returned_adata = cleanup(adata=adata, clean="all", inplace=inplace)
 
         if not inplace:
@@ -122,12 +137,13 @@ def test_cleanup_all(self, adata: AnnData, inplace: bool):
         else:
             assert returned_adata is None
 
-        assert len(adata.layers) == 0
-        assert len(adata.uns) == 0
+        assert list(adata.layers.keys()) == ["Ms", "Mu", "spliced", "unspliced"]
+        assert list(adata.uns.keys()) == ["neighbors"]
         assert len(adata.obs.columns) == 0
         assert len(adata.var.columns) == 0
 
     @given(adata=get_adata(max_obs=5, max_vars=5), inplace=st.booleans())
+    @settings(max_examples=10, deadline=1000)
     def test_cleanup_default_clean_w_random_adata(self, adata: AnnData, inplace: bool):
         n_obs_cols = len(adata.obs.columns)
         n_var_cols = len(adata.var.columns)

tests/datasets/test_datasets.py

@@ -18,7 +18,7 @@ def dentategyrus_adata(tmpdir_factory):
 
 
 @pytest.mark.skipif(
-    sys.version_info[:2] != (3, 8) or sys.platform != "linux",
+    sys.version_info[:2] != (3, 10) or sys.platform != "linux",
     reason="Limit number of downloads to speed up testing.",
 )
 class TestDataSets: