removed strict flag

Knowledge-Graph-Hub · Sep 25, 2024 · 11c6e17 · 11c6e17
1 parent 1e94150
commit 11c6e17
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Showing 16 changed files with 1 addition and 16 deletions.
diff --git a/kg_microbe/transform_utils/bacdive/bacdive.py b/kg_microbe/transform_utils/bacdive/bacdive.py
@@ -190,7 +190,6 @@
 
 
 class BacDiveTransform(Transform):
-
     """Template for how the transform class would be designed."""
 
     def __init__(

diff --git a/kg_microbe/transform_utils/bactotraits/bactotraits.py b/kg_microbe/transform_utils/bactotraits/bactotraits.py
@@ -38,7 +38,6 @@
 
 
 class BactoTraitsTransform(Transform):
-
     """
     BactoTraits transform.
 

diff --git a/kg_microbe/transform_utils/ctd/ctd.py b/kg_microbe/transform_utils/ctd/ctd.py
@@ -36,7 +36,6 @@
 
 
 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):

diff --git a/kg_microbe/transform_utils/disbiome/disbiome.py b/kg_microbe/transform_utils/disbiome/disbiome.py
@@ -32,7 +32,6 @@
 
 
 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):

diff --git a/kg_microbe/transform_utils/example_transform/example_transform.py b/kg_microbe/transform_utils/example_transform/example_transform.py
@@ -25,7 +25,6 @@
 
 
 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):

diff --git a/kg_microbe/transform_utils/madin_etal/madin_etal.py b/kg_microbe/transform_utils/madin_etal/madin_etal.py
@@ -70,7 +70,6 @@
 
 
 class MadinEtAlTransform(Transform):
-
     """
     Ingest Madin et al dataset (NCBI/GTDB).
 

diff --git a/kg_microbe/transform_utils/mediadive/mediadive.py b/kg_microbe/transform_utils/mediadive/mediadive.py
@@ -111,7 +111,6 @@
 
 
 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):

diff --git a/kg_microbe/transform_utils/ontologies/ontologies_transform.py b/kg_microbe/transform_utils/ontologies/ontologies_transform.py
@@ -80,7 +80,6 @@
 
 
 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):

diff --git a/kg_microbe/transform_utils/rhea_mappings/rhea_mappings.py b/kg_microbe/transform_utils/rhea_mappings/rhea_mappings.py
@@ -70,7 +70,6 @@
 
 
 class RheaMappingsTransform(Transform):
-
     """Template for how the transform class would be designed."""
 
     def __init__(

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

diff --git a/kg_microbe/transform_utils/uniprot_functional_microbes/uniprot_functional_microbes.py b/kg_microbe/transform_utils/uniprot_functional_microbes/uniprot_functional_microbes.py
@@ -30,7 +30,6 @@
 
 
 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):

diff --git a/kg_microbe/transform_utils/uniprot_human/uniprot_human.py b/kg_microbe/transform_utils/uniprot_human/uniprot_human.py
@@ -30,7 +30,6 @@
 
 
 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):

diff --git a/kg_microbe/transform_utils/uniprot_trembl/uniprot_trembl.py b/kg_microbe/transform_utils/uniprot_trembl/uniprot_trembl.py
@@ -10,7 +10,6 @@
 
 
 class UniprotTrEMBLTransform(Transform):
-
     """Uniprot TrEMBL transform."""
 
     def __init__(

diff --git a/kg_microbe/transform_utils/wallen_etal/wallen_etal.py b/kg_microbe/transform_utils/wallen_etal/wallen_etal.py
@@ -32,7 +32,6 @@
 
 
 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):

diff --git a/kg_microbe/utils/pandas_utils.py b/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"], strict=False)
+        zip(subject_intermediate_df["object"], subject_intermediate_df["subject"])
     )
 
     # Filter the DataFrame to include only rows where the SUBJECT_COLUMN matches any object in the mapping

diff --git a/tests/demo_test.py b/tests/demo_test.py
@@ -6,7 +6,6 @@
 
 
 class TestVersion(unittest.TestCase):
-
     """Test version."""
 
     def test_version_type(self):
Original file line number	Diff line number	Diff line change
Expand Up		@@ -190,7 +190,6 @@


		class BacDiveTransform(Transform):

		"""Template for how the transform class would be designed."""

		def __init__(
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Original file line number	Diff line number	Diff line change
Expand Up		@@ -38,7 +38,6 @@


		class BactoTraitsTransform(Transform):

		"""
		BactoTraits transform.

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Original file line number	Diff line number	Diff line change
Expand Up		@@ -36,7 +36,6 @@


		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):
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Original file line number	Diff line number	Diff line change
Expand Up		@@ -32,7 +32,6 @@


		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):
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Expand Up		@@ -25,7 +25,6 @@


		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):
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Original file line number	Diff line number	Diff line change
Expand Up		@@ -70,7 +70,6 @@


		class MadinEtAlTransform(Transform):

		"""
		Ingest Madin et al dataset (NCBI/GTDB).

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Expand Up		@@ -111,7 +111,6 @@


		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):
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Original file line number	Diff line number	Diff line change
Expand Up		@@ -80,7 +80,6 @@


		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):
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Expand Up		@@ -70,7 +70,6 @@


		class RheaMappingsTransform(Transform):

		"""Template for how the transform class would be designed."""

		def __init__(
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Expand Up		@@ -26,7 +26,6 @@


		class Transform:

		"""Parent class for transforms, that sets up a lot of default file info."""

		DATA_DIR = Path(__file__).parent / "data"
Expand Down