biocypher 0.9.5__tar.gz → 0.9.7__tar.gz

{biocypher-0.9.5 → biocypher-0.9.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biocypher
-Version: 0.9.5
+Version: 0.9.7
 Summary: A unifying framework for biomedical research knowledge graphs
 Home-page: https://github.com/biocypher/biocypher
 License: MIT
@@ -62,7 +62,7 @@ the docs [here](https://biocypher.org).
            margin-left: auto;
            margin-right: auto;
            width: 70%;"
-    src="docs/graphical_abstract.png"
+    src="docs/assets/img/graphical-abstract-biocypher.png"
     alt="Graphical Abstract">
 </img>
 

{biocypher-0.9.5 → biocypher-0.9.7}/README.md

@@ -27,7 +27,7 @@ the docs [here](https://biocypher.org).
            margin-left: auto;
            margin-right: auto;
            width: 70%;"
-    src="docs/graphical_abstract.png"
+    src="docs/assets/img/graphical-abstract-biocypher.png"
     alt="Graphical Abstract">
 </img>
 

{biocypher-0.9.5 → biocypher-0.9.7}/biocypher/_metadata.py

@@ -10,7 +10,7 @@ import pathlib
 
 import toml
 
-_VERSION = "0.9.5"
+_VERSION = "0.9.7"
 
 
 def get_metadata():

{biocypher-0.9.5 → biocypher-0.9.7}/biocypher/_translate.py

@@ -37,15 +37,12 @@ class Translator:
 
         Args:
         ----
-            leaves:
-                Dictionary detailing the leaves of the hierarchy
-                tree representing the structure of the graph; the leaves are
-                the entities that will be direct components of the graph,
-                while the intermediary nodes are additional labels for
-                filtering purposes.
+            ontology (Ontology): An Ontology object providing schema and mapping details.
             strict_mode:
-                If True, the translator will raise an error if input data do not
-                carry source, licence, and version information.
+                strict_mode (bool, optional): If True, enforces that every node and edge carries
+                the required 'source', 'licence', and 'version' properties. Raises ValueError
+                if these are missing. Defaults to False.
+
 
         """
         self.ontology = ontology

{biocypher-0.9.5 → biocypher-0.9.7}/biocypher/output/write/graph/_neo4j.py

@@ -278,9 +278,7 @@ class _Neo4jBatchWriter(_BatchWriter):
         """
         import_call_neo4j_v4 = self._get_import_call("import", "--database=", "--force=")
         import_call_neo4j_v5 = self._get_import_call("database import full", "", "--overwrite-destination=")
-        neo4j_version_check = (
-            f"version=$({self._get_default_import_call_bin_prefix()}neo4j-admin --version | cut -d '.' -f 1)"
-        )
+        neo4j_version_check = f"version=$({self.import_call_bin_prefix}neo4j-admin --version | cut -d '.' -f 1)"
 
         import_script = (
             f"#!/bin/bash\n{neo4j_version_check}\nif [[ $version -ge 5 ]]; "

{biocypher-0.9.5 → biocypher-0.9.7}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biocypher"
-version = "0.9.5"
+version = "0.9.7"
 description = "A unifying framework for biomedical research knowledge graphs"
 authors = [
     "Sebastian Lobentanzer <sebastian.lobentanzer@gmail.com>",
@@ -59,7 +59,7 @@ hypothesis = "^6.50.1"
 ipython = "^8.7.0"
 ipykernel = "^6.23.1"
 coverage-badge = "^1.1.0"
-nbsphinx = "^0.9.5"
+nbsphinx = "^0.9.7"
 ruff = "^0.2.0"
 mike = "^2.1.3"