Replace anndataread with anndataread h5ad due to 2024 deprecation (#84)

* Replace anndata.read with anndata.read_h5ad

* Update version to 0.1.24

* Fixed assert statements

pandasaurus_cxg/utils/anndata_loader.py

@@ -22,7 +22,7 @@ def load_from_file(file_path: str) -> Optional[anndata.AnnData]:
         with warnings.catch_warnings():
             warnings.simplefilter("ignore", category=anndata.ImplicitModificationWarning)
             try:
-                anndata_obj = anndata.read(file_path, backed="r")
+                anndata_obj = anndata.read_h5ad(file_path, backed="r")
                 return anndata_obj
             except Exception as e:
                 print(f"An error occurred while loading the file: {e}")

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pandasaurus-cxg"
-version = "0.1.23"
+version = "0.1.24"
 description = "Ontology enrichment tool for CxG standard AnnData files."
 authors = ["Ugur Bayindir <[email protected]>"]
 license = "http://www.apache.org/licenses/LICENSE-2.0"

test/graph_generator/test_graph_generator.py

@@ -156,7 +156,7 @@ def test_enrich_rdf_graph(graph_generator_instance_for_kidney):
 
     graph_generator.enrich_rdf_graph()
 
-    assert len(graph_generator.graph) == 1145
+    assert len(graph_generator.graph) == 1147
     assert (
         URIRef(CONSIST_OF.get("iri")),
         RDFS.label,
@@ -173,7 +173,7 @@ def test_enrich_rdf_graph(graph_generator_instance_for_kidney):
                 if str(s).startswith("http://purl.obolibrary.org/obo/CL_")
             ]
         )
-        == 529
+        == 531
     )
 
 

test/test_anndata_analyzer.py

@@ -12,21 +12,21 @@
 def sample_immune_data():
     current_dir = os.path.dirname(os.path.abspath(__file__))
     file_path = os.path.join(current_dir, "data/immune_example.h5ad")
-    return anndata.read(file_path, backed="r")
+    return anndata.read_h5ad(file_path, backed="r")
 
 
 @pytest.fixture
 def sample_anndata_with_uns():
     current_dir = os.path.dirname(os.path.abspath(__file__))
     file_path = os.path.join(current_dir, "data/modified_human_kidney.h5ad")
-    return anndata.read(file_path, backed="r")
+    return anndata.read_h5ad(file_path, backed="r")
 
 
 @pytest.fixture
 def sample_anndata_without_uns():
     current_dir = os.path.dirname(os.path.abspath(__file__))
     file_path = os.path.join(current_dir, "data/human_kidney.h5ad")
-    return anndata.read(file_path, backed="r")
+    return anndata.read_h5ad(file_path, backed="r")
 
 
 @pytest.fixture()

test/test_anndata_enricher.py

@@ -18,7 +18,7 @@
 def sample_immune_data():
     current_dir = os.path.dirname(os.path.abspath(__file__))
     file_path = os.path.join(current_dir, "data/immune_example.h5ad")
-    return anndata.read(file_path, backed="r")
+    return anndata.read_h5ad(file_path, backed="r")
 
 
 @pytest.fixture