formatted

kg_microbe/transform_utils/bacdive/bacdive.py

@@ -190,6 +190,7 @@
 
 
 class BacDiveTransform(Transform):
+
     """Template for how the transform class would be designed."""
 
     def __init__(

kg_microbe/transform_utils/bactotraits/bactotraits.py

@@ -38,6 +38,7 @@
 
 
 class BactoTraitsTransform(Transform):
+
     """
     BactoTraits transform.
 

kg_microbe/transform_utils/ctd/ctd.py

@@ -36,6 +36,7 @@
 
 
 class CTDTransform(Transform):
+
     """A class used to represent a transformation process for UniProt data."""
 
     def __init__(self, input_dir: Optional[Path] = None, output_dir: Optional[Path] = None):

kg_microbe/transform_utils/disbiome/disbiome.py

@@ -32,6 +32,7 @@
 
 
 class DisbiomeTransform(Transform):
+
     """A class used to represent a transformation process for Disbiome data."""
 
     def __init__(self, input_dir: Optional[Path] = None, output_dir: Optional[Path] = None):

kg_microbe/transform_utils/example_transform/example_transform.py

@@ -25,6 +25,7 @@
 
 
 class YourTransform(Transform):
+
     """Template for how the transform class would be designed."""
 
     def __init__(self, input_dir: Optional[Path] = None, output_dir: Optional[Path] = None):

kg_microbe/transform_utils/madin_etal/madin_etal.py

@@ -70,6 +70,7 @@
 
 
 class MadinEtAlTransform(Transform):
+
     """
     Ingest Madin et al dataset (NCBI/GTDB).
 

kg_microbe/transform_utils/mediadive/mediadive.py

@@ -111,6 +111,7 @@
 
 
 class MediaDiveTransform(Transform):
+
     """Template for how the transform class would be designed."""
 
     def __init__(self, input_dir: Optional[Path] = None, output_dir: Optional[Path] = None):

kg_microbe/transform_utils/ontologies/ontologies_transform.py

@@ -80,6 +80,7 @@
 
 
 class OntologiesTransform(Transform):
+
     """OntologyTransform parses an Obograph JSON form of an Ontology into nodes nad edges."""
 
     def __init__(self, input_dir: Optional[Path] = None, output_dir: Optional[Path] = None):

kg_microbe/transform_utils/rhea_mappings/rhea_mappings.py

@@ -70,6 +70,7 @@
 
 
 class RheaMappingsTransform(Transform):
+
     """Template for how the transform class would be designed."""
 
     def __init__(

kg_microbe/transform_utils/transform.py

@@ -26,6 +26,7 @@
 
 
 class Transform:
+
     """Parent class for transforms, that sets up a lot of default file info."""
 
     DATA_DIR = Path(__file__).parent / "data"

kg_microbe/transform_utils/uniprot_functional_microbes/uniprot_functional_microbes.py

@@ -30,6 +30,7 @@
 
 
 class UniprotFunctionalMicrobesTransform(Transform):
+
     """A class used to represent a transformation process for UniProt data."""
 
     def __init__(self, input_dir: Optional[Path] = None, output_dir: Optional[Path] = None):

kg_microbe/transform_utils/uniprot_human/uniprot_human.py

@@ -30,6 +30,7 @@
 
 
 class UniprotHumanTransform(Transform):
+
     """A class used to represent a transformation process for UniProt data."""
 
     def __init__(self, input_dir: Optional[Path] = None, output_dir: Optional[Path] = None):

kg_microbe/transform_utils/uniprot_trembl/uniprot_trembl.py

@@ -10,6 +10,7 @@
 
 
 class UniprotTrEMBLTransform(Transform):
+
     """Uniprot TrEMBL transform."""
 
     def __init__(

kg_microbe/transform_utils/wallen_etal/wallen_etal.py

@@ -32,6 +32,7 @@
 
 
 class WallenEtAlTransform(Transform):
+
     """A class used to represent a transformation process for PdMetagenomics data."""
 
     def __init__(self, input_dir: Optional[Path] = None, output_dir: Optional[Path] = None):

kg_microbe/utils/pandas_utils.py

@@ -101,7 +101,7 @@ def establish_transitive_relationship(
     #     list_of_dfs_to_append.append(transitive_relations_df)
     # Create a dictionary to map objects to subjects
     object_to_subject = dict(
-        zip(subject_intermediate_df["object"], subject_intermediate_df["subject"])
+        zip(subject_intermediate_df["object"], subject_intermediate_df["subject"], strict=False)
     )
 
     # Filter the DataFrame to include only rows where the SUBJECT_COLUMN matches any object in the mapping

tests/demo_test.py

@@ -6,6 +6,7 @@
 
 
 class TestVersion(unittest.TestCase):
+
     """Test version."""
 
     def test_version_type(self):