biocypher 0.6.2__tar.gz → 0.8.0__tar.gz

{biocypher-0.6.2 → biocypher-0.8.0}/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 → biocypher-0.8.0}/PKG-INFO

@@ -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-0.6.2 → biocypher-0.8.0}/biocypher/__init__.py

@@ -1,13 +1,3 @@
-#!/usr/bin/env python
-
-#
-# Copyright 2021, Heidelberg University Clinic
-#
-# File author(s): Sebastian Lobentanzer
-#                 ...
-#
-# Distributed under MIT licence, see the file `LICENSE`.
-#
 """
 BioCypher: a unifying framework for biomedical knowledge graphs.
 """
@@ -25,10 +15,10 @@ __all__ = [
     "APIRequest",
 ]
 
-from ._get import APIRequest, FileDownload
-from ._core import BioCypher
 from ._config import config, module_data
-from ._logger import log, logger, logfile
+from ._core import BioCypher
+from ._get import APIRequest, FileDownload
+from ._logger import log, logfile, logger
 from ._metadata import __author__, __version__
 
 

{biocypher-0.6.2 → biocypher-0.8.0}/biocypher/_config/__init__.py

@@ -1,13 +1,3 @@
-#!/usr/bin/env python
-
-#
-# Copyright 2021, Heidelberg University Clinic
-#
-# File author(s): Sebastian Lobentanzer
-#                 ...
-#
-# Distributed under MIT licence, see the file `LICENSE`.
-#
 """
 Module data directory, including:
 
@@ -15,12 +5,13 @@ Module data directory, including:
 * The default config files
 """
 
-from typing import Any, Optional
 import os
 import warnings
 
-import yaml
+from typing import Any, Optional
+
 import appdirs
+import yaml
 
 __all__ = ["module_data", "module_data_path", "read_config", "config", "reset"]
 
@@ -88,21 +79,13 @@ def read_config() -> dict:
     defaults = module_data("biocypher_config")
     user = _read_yaml(_USER_CONFIG_FILE) or {}
     # TODO account for .yml?
-    local = (
-        _read_yaml("biocypher_config.yaml")
-        or _read_yaml("config/biocypher_config.yaml")
-        or {}
-    )
+    local = _read_yaml("biocypher_config.yaml") or _read_yaml("config/biocypher_config.yaml") or {}
 
     for key in defaults:
-        value = (
-            local[key] if key in local else user[key] if key in user else None
-        )
+        value = local[key] if key in local else user[key] if key in user else None
 
         if value is not None:
-            if isinstance(
-                defaults[key], str
-            ):  # first level config (like title)
+            if isinstance(defaults[key], str):  # first level config (like title)
                 defaults[key] = value
             else:
                 defaults[key].update(value)

{biocypher-0.6.2 → biocypher-0.8.0}/biocypher/_config/biocypher_config.yaml

@@ -30,12 +30,13 @@ biocypher:
     # switch_label_and_id: true
 
   ### Optional parameters ###
-
   ## Logging
   # Write log to disk
+
   log_to_disk: true
 
   # Activate more granular logging
+
   debug: true
 
   # Change the log directory
@@ -85,6 +86,14 @@ neo4j:
   array_delimiter: "|"
   quote_character: "'"
 
+  # How to write the labels in the export files.
+
+  labels_order: "Ascending" # Default: From more specific to more generic.
+  # Or:
+  # labels_order: "Descending" # From more generic to more specific.
+  # labels_order: "Alphabetical" # Alphabetically. Legacy option.
+  # labels_order: "Leaves" # Only the more specific label.
+
   ## MultiDB functionality
   ## Set to false for using community edition or older versions of Neo4j
 
@@ -102,8 +111,8 @@ neo4j:
 
 postgresql:
   ### PostgreSQL configuration ###
-
   # PostgreSQL connection credentials
+
   database_name: postgres # DB name
   user: postgres # user name
   password: postgres # password
@@ -111,6 +120,7 @@ postgresql:
   port: 5432 # port
 
   # PostgreSQL import batch writer settings
+
   quote_character: '"'
   delimiter: '\t'
   # import_call_bin_prefix: '' # path to "psql"
@@ -122,11 +132,12 @@ rdf:
 
 sqlite:
   ### SQLite configuration ###
-
   # SQLite connection credentials
+
   database_name: sqlite.db # DB name
 
   # SQLite import batch writer settings
+
   quote_character: '"'
   delimiter: '\t'
   # import_call_bin_prefix: '' # path to "sqlite3"