biocypher 0.6.2__py3-none-any.whl → 0.8.0__py3-none-any.whl

biocypher/output/write/relational/_postgresql.py

@@ -1,5 +1,5 @@
-import os
 import glob
+import os
 
 from biocypher._logger import logger
 from biocypher.output.write._batch_writer import _BatchWriter
@@ -52,9 +52,7 @@ class _PostgreSQLBatchWriter(_BatchWriter):
         try:
             return self.DATA_TYPE_LOOKUP[string]
         except KeyError:
-            logger.info(
-                'Could not determine data type {string}. Using default "VARCHAR"'
-            )
+            logger.info('Could not determine data type {string}. Using default "VARCHAR"')
             return "VARCHAR"
 
     def _quote_string(self, value: str) -> str:
@@ -147,9 +145,7 @@ class _PostgreSQLBatchWriter(_BatchWriter):
                     command += f"DROP TABLE IF EXISTS {pascal_label};\n"
 
                 # table creation requires comma separation
-                command += (
-                    f'CREATE TABLE {pascal_label}({",".join(columns)});\n'
-                )
+                command += f"CREATE TABLE {pascal_label}({','.join(columns)});\n"
                 f.write(command)
 
                 for parts_path in parts_paths:
@@ -246,9 +242,7 @@ class _PostgreSQLBatchWriter(_BatchWriter):
                     command += f"DROP TABLE IF EXISTS {pascal_label};\n"
 
                 # table creation requires comma separation
-                command += (
-                    f'CREATE TABLE {pascal_label}({",".join(out_list)});\n'
-                )
+                command += f"CREATE TABLE {pascal_label}({','.join(out_list)});\n"
                 f.write(command)
 
                 for parts_path in parts_paths:
@@ -299,9 +293,7 @@ class _PostgreSQLBatchWriter(_BatchWriter):
             if {self.db_password}:
                 # set password variable inline
                 import_call += f"PGPASSWORD={self.db_password} "
-            import_call += (
-                f"{self.import_call_bin_prefix}psql -f {import_file_path}"
-            )
+            import_call += f"{self.import_call_bin_prefix}psql -f {import_file_path}"
             import_call += f" --dbname {self.db_name}"
             import_call += f" --host {self.db_host}"
             import_call += f" --port {self.db_port}"

biocypher/output/write/relational/_sqlite.py

@@ -44,7 +44,9 @@ class _SQLiteBatchWriter(_PostgreSQLBatchWriter):
             import_call += f'echo "Importing {table_part}..."\n'
             separator = self.delim
             import_part = f".import {table_part} {table_name}"
-            import_call += f"{self.import_call_bin_prefix}sqlite3 -separator $'{separator}' {self.db_name} \"{import_part}\""
+            import_call += (
+                f"{self.import_call_bin_prefix}sqlite3 -separator $'{separator}' {self.db_name} \"{import_part}\""
+            )
             import_call += '\necho "Done!"\n'
             import_call += "\n"
 

{biocypher-0.6.2.dist-info → biocypher-0.8.0.dist-info}/LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022 Saez Lab
+Copyright (c) 2022-2025 BioCypher developers
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

{biocypher-0.6.2.dist-info → biocypher-0.8.0.dist-info}/METADATA

@@ -1,12 +1,12 @@
 Metadata-Version: 2.1
 Name: biocypher
-Version: 0.6.2
+Version: 0.8.0
 Summary: A unifying framework for biomedical research knowledge graphs
 Home-page: https://github.com/biocypher/biocypher
 License: MIT
 Author: Sebastian Lobentanzer
 Author-email: sebastian.lobentanzer@gmail.com
-Requires-Python: >=3.9,<4.0
+Requires-Python: >=3.10,<4.0
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
@@ -15,9 +15,9 @@ Classifier: Natural Language :: English
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Requires-Dist: PyYAML (>=5.0)
 Requires-Dist: appdirs

biocypher-0.8.0.dist-info/RECORD

@@ -0,0 +1,43 @@
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+biocypher/_config/test_schema_config_disconnected.yaml,sha256=Qm8FLxEn2spHcyj_5F859KjcDvKSxNhxDvi4b4LLkvQ,68
+biocypher/_config/test_schema_config_extended.yaml,sha256=wn3A76142hhjnImhMF6RODbCFESTJ2TtPvcFdIFsAT0,3309
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+biocypher/_create.py,sha256=QsvXrwEQ8k0uNXvCG06UKejvw-QsJwzSaumrBjx9n1k,9884
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+biocypher/_get.py,sha256=2kjiBFu_onGUhgOpV7IMfGX67jyY1rpHg_GWncEUdrc,13278
+biocypher/_logger.py,sha256=y9dh3SPJOCWXnkFSYSK7aj_-pB7zlAkNCf43Dp1lt74,2941
+biocypher/_mapping.py,sha256=ntspG2C_NaQODhWTBFk0CDvolkOCjtqlQ9E-NkJAuTg,9030
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+biocypher/_translate.py,sha256=sXyXIg6hpR6Y-dp8NtoAN-H4mzrGI4t1ivlBGxaeqWM,16379
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+biocypher/output/connect/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+biocypher/output/in_memory/_get_in_memory_kg.py,sha256=JuNwVx-qABeLikkI9VXQJNQH8xQWvYLEK_KKz3BrXPI,937
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+biocypher/output/write/graph/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+biocypher/output/write/graph/_arangodb.py,sha256=NBnVJa4WuK7WNTIAXOg62YjAMAQfEZtcJX97erNLgSw,7794
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+biocypher/output/write/relational/_csv.py,sha256=m0BSQXts88Qu5AEvoIgnwRz54ia38g4VN3PaA3LCYM8,2807
+biocypher/output/write/relational/_postgresql.py,sha256=RckQJBiuwvDmHAyXxS8zCavYqDecHHWW_piofurokfQ,11965
+biocypher/output/write/relational/_sqlite.py,sha256=BuGWOeeNA83lbUvjpkzqcR9_baWLsbfmLXBKe4O1EPE,2105
+biocypher-0.8.0.dist-info/LICENSE,sha256=oejgxuxyjSnyPw3YPloz6-dCBB_nYizJ4jDQnr-xZUU,1082
+biocypher-0.8.0.dist-info/METADATA,sha256=VByGBm1JcK0yiXCq2aNWSAbguf5_5Lv8rCDTyG1uOLs,10643
+biocypher-0.8.0.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
+biocypher-0.8.0.dist-info/RECORD,,

{biocypher-0.6.2.dist-info → biocypher-0.8.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.6.1
+Generator: poetry-core 1.8.1
 Root-Is-Purelib: true
 Tag: py3-none-any

biocypher-0.6.2.dist-info/RECORD

@@ -1,39 +0,0 @@
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-biocypher/_config/__init__.py,sha256=fFHRFYxE2MtDAQWL6upe--MJ1vw3Z8CwIPhF2gW8cRU,3698
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-biocypher/_config/test_schema_config_disconnected.yaml,sha256=Qm8FLxEn2spHcyj_5F859KjcDvKSxNhxDvi4b4LLkvQ,68
-biocypher/_config/test_schema_config_extended.yaml,sha256=wn3A76142hhjnImhMF6RODbCFESTJ2TtPvcFdIFsAT0,3309
-biocypher/_core.py,sha256=m4o4Szv2xY2gl3PnNAA9m7Gg5Sgd8iR9THv3RDyZlQ8,22618
-biocypher/_create.py,sha256=vpUchUdEpWupZi1LgFLxAWMtqoBwnWbP7PwEDUCBS4A,10202
-biocypher/_deduplicate.py,sha256=BBvfpXzu6L5YDY5FdtXxnf8YlsbJpbCE8RdUoKsm0n0,4949
-biocypher/_get.py,sha256=1FHs4n2R2k7OVWtVe7euF2J5WpsUXsFAmnpdSYuhLvY,13817
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-biocypher/_ontology.py,sha256=G5k-bnzvPZUqhLPxtoOPFa4OSQ4JpufgozVakLTjwLg,31789
-biocypher/_translate.py,sha256=JafvhtVaFSpruRfYh9BzjVbvDF1Mhg7LLKMDZHWkRjg,16496
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-biocypher/output/write/relational/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biocypher/output/write/relational/_csv.py,sha256=eyAtmwfCNYnuVbkpd0rUoo9KgG2KPgopZVA3X97tRLU,2919
-biocypher/output/write/relational/_postgresql.py,sha256=MRgDicNRW0KWene1nag4FgJ-nEUlpkulatG1S8D33s0,12107
-biocypher/output/write/relational/_sqlite.py,sha256=ozElhca1YCYq8R-VFh-LDsnPBaXVJm2cvEboBK2LVVY,2073
-biocypher-0.6.2.dist-info/LICENSE,sha256=SjUaQkq671iQUZOxEUpC4jvJxXOlfSiHTTueyz9kXJM,1065
-biocypher-0.6.2.dist-info/METADATA,sha256=ZJfAl8_BsK1mRwFFy0HJOlkLKGiAByTeEdlwHX3C8Ec,10641
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