biocypher 0.9.0__tar.gz → 0.9.2__tar.gz

{biocypher-0.9.0 → biocypher-0.9.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biocypher
-Version: 0.9.0
+Version: 0.9.2
 Summary: A unifying framework for biomedical research knowledge graphs
 Home-page: https://github.com/biocypher/biocypher
 License: MIT
@@ -27,7 +27,6 @@ Requires-Dist: networkx (>=3.0,<4.0)
 Requires-Dist: pandas (>=2.0.1,<3.0.0)
 Requires-Dist: pooch (>=1.7.0,<2.0.0)
 Requires-Dist: rdflib (>=6.2.0,<7.0.0)
-Requires-Dist: stringcase (>=1.2.0,<2.0.0)
 Requires-Dist: tqdm (>=4.65.0,<5.0.0)
 Requires-Dist: treelib (==1.6.4)
 Project-URL: Bug Tracker, https://github.com/biocypher/biocypher/issues

{biocypher-0.9.0 → biocypher-0.9.2}/biocypher/_core.py

@@ -118,6 +118,15 @@ class BioCypher:
         else:
             self._offline = offline
 
+        # Check if pandas/tabular is being used in offline mode
+        if self._offline and self._dbms.lower() in ["pandas", "tabular"]:
+            msg = (
+                f"The '{self._dbms}' DBMS is only available in online mode. "
+                f"If you want to write CSV files, use 'csv' as the DBMS. "
+                f"If you want to use pandas, set 'offline: false' in your configuration."
+            )
+            raise ValueError(msg)
+
         if strict_mode is None:
             self._strict_mode = self.base_config["strict_mode"]
         else:
@@ -225,19 +234,31 @@ class BioCypher:
         The knowledge graph is returned based on the `dbms` parameter in
         the biocypher configuration file.
 
+        TODO: These conditionals are a hack, we need to refactor the in-memory
+        KG to be generic, and simplify access and conversion to output formats.
+
         Returns
         -------
              Any: knowledge graph.
 
         """
+        # If we're using an in-memory KG and it already exists, return it directly
+        if self._in_memory_kg and self._is_online_and_in_memory():
+            return self._in_memory_kg.get_kg()
+
+        # Otherwise, initialize and populate the in-memory KG
         if not self._in_memory_kg:
             self._initialize_in_memory_kg()
         if not self._translator:
             self._get_translator()
-        tnodes = self._translator.translate_entities(self._nodes)
-        tedges = self._translator.translate_entities(self._edges)
-        self._in_memory_kg.add_nodes(tnodes)
-        self._in_memory_kg.add_edges(tedges)
+
+        # These attributes might not exist when using in-memory KG directly
+        if hasattr(self, "_nodes") and hasattr(self, "_edges"):
+            tnodes = self._translator.translate_entities(self._nodes)
+            tedges = self._translator.translate_entities(self._edges)
+            self._in_memory_kg.add_nodes(tnodes)
+            self._in_memory_kg.add_edges(tedges)
+
         return self._in_memory_kg.get_kg()
 
     def _get_deduplicator(self) -> Deduplicator:

{biocypher-0.9.0 → biocypher-0.9.2}/biocypher/_metadata.py

@@ -10,7 +10,7 @@ import pathlib
 
 import toml
 
-_VERSION = "0.9.0"
+_VERSION = "0.9.2"
 
 
 def get_metadata():

{biocypher-0.9.0 → biocypher-0.9.2}/biocypher/_misc.py

@@ -1,22 +1,18 @@
-"""
-Handy functions for use in various places.
-"""
+"""Handy functions for use in various places."""
 
 import re
 
-from collections.abc import Iterable
-from typing import (
-    Any,
+from collections.abc import (
     Generator,
     ItemsView,
+    Iterable,
     KeysView,
     Mapping,
-    Union,
     ValuesView,
 )
+from typing import Any
 
 import networkx as nx
-import stringcase
 
 from treelib import Tree
 
@@ -48,10 +44,7 @@ LIST_LIKE = (
 
 
 def to_list(value: Any) -> list:
-    """
-    Ensures that ``value`` is a list.
-    """
-
+    """Ensure that ``value`` is a list."""
     if isinstance(value, LIST_LIKE):
         value = list(value)
 
@@ -62,17 +55,12 @@ def to_list(value: Any) -> list:
 
 
 def ensure_iterable(value: Any) -> Iterable:
-    """
-    Returns iterables, except strings, wraps simple types into tuple.
-    """
-
+    """Return iterables, except strings, wrap simple types into tuple."""
     return value if isinstance(value, LIST_LIKE) else (value,)
 
 
-def create_tree_visualisation(inheritance_graph: Union[dict, nx.Graph]) -> Tree:
-    """
-    Creates a visualisation of the inheritance tree using treelib.
-    """
+def create_tree_visualisation(inheritance_graph: dict | nx.Graph) -> Tree:
+    """Create a visualisation of the inheritance tree using treelib."""
     inheritance_tree = _get_inheritance_tree(inheritance_graph)
     classes, root = _find_root_node(inheritance_tree)
 
@@ -91,38 +79,42 @@ def create_tree_visualisation(inheritance_graph: Union[dict, nx.Graph]) -> Tree:
     return tree
 
 
-def _get_inheritance_tree(inheritance_graph: Union[dict, nx.Graph]) -> dict:
-    """Transforms an inheritance_graph into an inheritance_tree.
+def _get_inheritance_tree(inheritance_graph: dict | nx.Graph) -> dict | None:
+    """Transform an inheritance_graph into an inheritance_tree.
 
     Args:
+    ----
         inheritance_graph: A dict or nx.Graph representing the inheritance graph.
 
     Returns:
+    -------
         A dict representing the inheritance tree.
+
     """
     if isinstance(inheritance_graph, nx.Graph):
         inheritance_tree = nx.to_dict_of_lists(inheritance_graph)
 
         multiple_parents_present = _multiple_inheritance_present(inheritance_tree)
         if multiple_parents_present:
-            logger.warning(
+            msg = (
                 "The ontology contains multiple inheritance (one child node "
                 "has multiple parent nodes). This is not visualized in the "
                 "following hierarchy tree (the child node is only added once). "
                 "If you wish to browse all relationships of the parsed "
                 "ontologies, write a graphml file to disk using "
-                "`to_disk = <directory>` and view this file."
+                "`to_disk = <directory>` and view this file.",
             )
-
+            logger.warning(msg)
         # unlist values
         inheritance_tree = {k: v[0] for k, v in inheritance_tree.items() if v}
         return inheritance_tree
     elif not _multiple_inheritance_present(inheritance_graph):
         return inheritance_graph
+    return None  # Explicit return for the case when neither condition is met
 
 
 def _multiple_inheritance_present(inheritance_tree: dict) -> bool:
-    """Checks if multiple inheritance is present in the inheritance_tree."""
+    """Check if multiple inheritance is present in the inheritance_tree."""
     return any(len(value) > 1 for value in inheritance_tree.values())
 
 
@@ -134,7 +126,9 @@ def _find_root_node(inheritance_tree: dict) -> tuple[set, str]:
         if "entity" in root:
             root = "entity"  # TODO: default: good standard?
         else:
-            raise ValueError("Inheritance tree cannot have more than one root node. " f"Found {len(root)}: {root}.")
+            msg = f"Inheritance tree cannot have more than one root node. Found {len(root)}: {root}."
+            logger.error(msg)
+            raise ValueError(msg)
     else:
         root = root[0]
     if not root:
@@ -158,53 +152,62 @@ def from_pascal(s: str, sep: str = " ") -> str:
 
 
 def pascalcase_to_sentencecase(s: str) -> str:
-    """
-    Convert PascalCase to sentence case.
+    """Convert PascalCase to sentence case.
 
     Args:
+    ----
         s: Input string in PascalCase
 
     Returns:
+    -------
         string in sentence case form
+
     """
     return from_pascal(s, sep=" ")
 
 
 def snakecase_to_sentencecase(s: str) -> str:
-    """
-    Convert snake_case to sentence case.
+    """Convert snake_case to sentence case.
 
     Args:
+    ----
         s: Input string in snake_case
 
     Returns:
+    -------
         string in sentence case form
+
     """
-    return stringcase.sentencecase(s).lower()
+    return " ".join(word.lower() for word in s.split("_"))
 
 
 def sentencecase_to_snakecase(s: str) -> str:
-    """
-    Convert sentence case to snake_case.
+    """Convert sentence case to snake_case.
 
     Args:
+    ----
         s: Input string in sentence case
 
     Returns:
+    -------
         string in snake_case form
+
     """
-    return stringcase.snakecase(s).lower()
+    return "_".join(s.lower().split())
 
 
 def sentencecase_to_pascalcase(s: str, sep: str = r"\s") -> str:
-    """
-    Convert sentence case to PascalCase.
+    """Convert sentence case to PascalCase.
 
     Args:
+    ----
         s: Input string in sentence case
+        sep: Separator for the words in the input string
 
     Returns:
+    -------
         string in PascalCase form
+
     """
     return re.sub(
         r"(?:^|[" + sep + "])([a-zA-Z])",
@@ -214,15 +217,18 @@ def sentencecase_to_pascalcase(s: str, sep: str = r"\s") -> str:
 
 
 def to_lower_sentence_case(s: str) -> str:
-    """
-    Convert any string to lower sentence case. Works with snake_case,
-    PascalCase, and sentence case.
+    """Convert any string to lower sentence case.
+
+    Works with snake_case, PascalCase, and sentence case.
 
     Args:
+    ----
         s: Input string
 
     Returns:
+    -------
         string in lower sentence case form
+
     """
     if "_" in s:
         return snakecase_to_sentencecase(s)
@@ -234,15 +240,17 @@ def to_lower_sentence_case(s: str) -> str:
         return s
 
 
-def is_nested(lst) -> bool:
-    """
-    Check if a list is nested.
+def is_nested(lst: list) -> bool:
+    """Check if a list is nested.
 
     Args:
+    ----
         lst (list): The list to check.
 
     Returns:
+    -------
         bool: True if the list is nested, False otherwise.
+
     """
     for item in lst:
         if isinstance(item, list):

{biocypher-0.9.0 → biocypher-0.9.2}/biocypher/output/write/_get_writer.py

@@ -75,7 +75,7 @@ def get_writer(
         instance: an instance of the selected writer class.
 
     """
-    dbms_config = _config(dbms)
+    dbms_config = _config(dbms) or {}
 
     writer = DBMS_TO_CLASS[dbms]
 

{biocypher-0.9.0 → biocypher-0.9.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biocypher"
-version = "0.9.0"
+version = "0.9.2"
 description = "A unifying framework for biomedical research knowledge graphs"
 authors = [
     "Sebastian Lobentanzer <sebastian.lobentanzer@gmail.com>",
@@ -40,7 +40,6 @@ appdirs = "*"
 treelib = "1.6.4"
 rdflib = "^6.2.0"
 networkx = "^3.0"
-stringcase = "^1.2.0"
 neo4j-utils = "0.0.7"
 pandas = "^2.0.1"
 pooch = "^1.7.0"