Merge remote-tracking branch 'origin/41-allow-for-specification-of-ge…

…ne-identifier-to-use-in-phenopacket' into 41-allow-for-specification-of-gene-identifier-to-use-in-phenopacket

# Conflicts:
#	src/phenotype2phenopacket/add/add_genes.py
#	src/phenotype2phenopacket/cli_add.py

src/phenotype2phenopacket/utils/phenopacket_utils.py

@@ -11,6 +11,8 @@
 import polars as pl
 from google.protobuf.timestamp_pb2 import Timestamp
 from oaklib.implementations import ProntoImplementation
+from pheval.utils.phenopacket_utils import GeneIdentifierUpdater, create_json_message
+
 from phenopackets import (
     Age,
     Diagnosis,
@@ -26,8 +28,6 @@
     Resource,
     TimeElement,
 )
-from pheval.utils.phenopacket_utils import GeneIdentifierUpdater, create_json_message
-
 from phenotype2phenopacket.utils.utils import is_float
 
 

tests/test_phenopacket_utils.py

@@ -3,6 +3,13 @@
 from unittest.mock import Mock, patch
 
 import polars as pl
+from pheval.utils.phenopacket_utils import (
+    GeneIdentifierUpdater,
+    create_gene_identifier_map,
+    create_hgnc_dict,
+)
+from polars.testing import assert_frame_equal
+
 from phenopackets import (
     Age,
     Diagnosis,
@@ -19,13 +26,6 @@
     Resource,
     TimeElement,
 )
-from pheval.utils.phenopacket_utils import (
-    GeneIdentifierUpdater,
-    create_gene_identifier_map,
-    create_hgnc_dict,
-)
-from polars.testing import assert_frame_equal
-
 from phenotype2phenopacket.utils.phenopacket_utils import (
     OnsetTerm,
     PhenopacketInterpretationExtender,