h5py 3.0 read str as bytes, force to downgrade;

Author: Mr-Milk

requirements.txt

@@ -1,4 +1,5 @@
 alphashape
+h5py<=2.10.0
 anndata
 bokeh
 colour

tests/test_config_utils.py

@@ -112,9 +112,6 @@ def test_data2adata(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
     col = [0 for _ in range(len(data.obs))]
     CONFIG.VERBOSE = True

tests/test_plotting.py

@@ -27,9 +27,6 @@ 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

@@ -13,9 +13,6 @@
 
 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

@@ -13,9 +13,6 @@
 
 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

@@ -14,9 +14,6 @@
 
 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