RTD build issue; Github CI buid issue;

Author: Mr-Milk

requirements.txt

@@ -31,5 +31,4 @@ pytest-datadir
 # doc
 sphinx
 sphinx-rtd-theme
-
-ujson
+sphinx-autodoc-typehints

tests/test_config_utils.py

@@ -110,15 +110,19 @@ def test_data2adata(shared_datadir):
         'a': [1, 2, 3, 4, 5, 5, 6],
         'b': [4, 5, 6, 7, 8, 9, 2],
     })
-    adata = read_h5ad(shared_datadir / 'small.h5ad')
-    pytest.data = adata
-    col = [0 for _ in range(len(adata.obs))]
+
+    data = read_h5ad(shared_datadir / 'small.h5ad')
+    centroid = data.obs['centroid']
+    if isinstance(centroid[0], bytes):
+        data.obs['centroid'] = [i.decode('utf-8') for i in centroid]
+    pytest.data = data
+    col = [0 for _ in range(len(data.obs))]
     CONFIG.VERBOSE = True
-    df2adata_uns(df, adata, 'test_df')
-    col2adata_obs(col, adata, 'test_col')
+    df2adata_uns(df, data, 'test_df')
+    col2adata_obs(col, data, 'test_col')
     CONFIG.WORKING_ENV = "jupyter_notebook"
-    df2adata_uns(df, adata, 'test_df')
-    col2adata_obs(col, adata, 'test_col')
+    df2adata_uns(df, data, 'test_df')
+    col2adata_obs(col, data, 'test_col')
 
 
 def test_svca(tmpdir):

tests/test_plotting.py

@@ -27,6 +27,9 @@ def test_get_linear_colors():
 
 def test_read_data(shared_datadir):
     data = read_h5ad(shared_datadir / 'small.h5ad')
+    centroid = data.obs['centroid']
+    if isinstance(centroid[0], bytes):
+        data.obs['centroid'] = [i.decode('utf-8') for i in centroid]
     pytest.data = data
 
 

tests/test_spatial_noNeigh.py

@@ -13,6 +13,9 @@
 
 def test_read_data(shared_datadir):
     data = read_h5ad(shared_datadir / 'small.h5ad')
+    centroid = data.obs['centroid']
+    if isinstance(centroid[0], bytes):
+        data.obs['centroid'] = [i.decode('utf-8') for i in centroid]
     pytest.data = data
 
 

tests/test_spatial_useNeigh.py

@@ -13,6 +13,9 @@
 
 def test_read_data(shared_datadir):
     data = read_h5ad(shared_datadir / 'small.h5ad')
+    centroid = data.obs['centroid']
+    if isinstance(centroid[0], bytes):
+        data.obs['centroid'] = [i.decode('utf-8') for i in centroid]
     pytest.data = data
 
 

tests/test_sta.py

@@ -14,6 +14,9 @@
 
 def test_read_data(shared_datadir):
     data = read_h5ad(shared_datadir / 'small.h5ad')
+    centroid = data.obs['centroid']
+    if isinstance(centroid[0], bytes):
+        data.obs['centroid'] = [i.decode('utf-8') for i in centroid]
     pytest.data = data