obographs 0.0.5__tar.gz → 0.0.6__tar.gz

{obographs-0.0.5 → obographs-0.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: obographs
-Version: 0.0.5
+Version: 0.0.6
 Summary: A python data model for OBO Graphs
 Keywords: snekpack,cookiecutter
 Author: Charles Tapley Hoyt

{obographs-0.0.5 → obographs-0.0.6}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "obographs"
-version = "0.0.5"
+version = "0.0.6"
 description = "A python data model for OBO Graphs"
 readme = "README.md"
 authors = [
@@ -232,7 +232,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.0.5"
+current_version = "0.0.6"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?(?:\\+(?P<build>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?"
 serialize = [
     "{major}.{minor}.{patch}-{release}+{build}",

{obographs-0.0.5 → obographs-0.0.6}/src/obographs/model.py

@@ -21,7 +21,7 @@ from curies.vocabulary import SynonymScopeOIO
 from pydantic import BaseModel, Field
 
 if TYPE_CHECKING:
-    from .standardized import StandardizedGraph
+    from .standardized import StandardizedGraph, StandardizedGraphDocument
 
 __all__ = [
     "Definition",
@@ -197,6 +197,12 @@ class GraphDocument(BaseModel):
     graphs: list[Graph]
     meta: Meta | None = None
 
+    def standardize(self, converter: curies.Converter) -> StandardizedGraphDocument:
+        """Standardize the graph."""
+        from .standardized import StandardizedGraphDocument
+
+        return StandardizedGraphDocument.from_obograph_raw(self, converter)
+
 
 def get_id_to_node(graph: Graph) -> dict[str, Node]:
     """Get a dictionary from node ID to nodes."""
@@ -214,17 +220,19 @@ def get_id_to_edges(graph: Graph) -> dict[str, list[tuple[str, str]]]:
 # docstr-coverage:excused `overload`
 @overload
 def read(
-    source: str, *, timeout: TimeoutHint = ..., squeeze: Literal[False] = ...
+    source: str | Path, *, timeout: TimeoutHint = ..., squeeze: Literal[False] = ...
 ) -> GraphDocument: ...
 
 
 # docstr-coverage:excused `overload`
 @overload
-def read(source: str, *, timeout: TimeoutHint = ..., squeeze: Literal[True] = ...) -> Graph: ...
+def read(
+    source: str | Path, *, timeout: TimeoutHint = ..., squeeze: Literal[True] = ...
+) -> Graph: ...
 
 
 def read(
-    source: str, *, timeout: TimeoutHint = None, squeeze: bool = True
+    source: str | Path, *, timeout: TimeoutHint = None, squeeze: bool = True
 ) -> Graph | GraphDocument:
     """Read an OBO Graph document.
 
@@ -239,7 +247,7 @@ def read(
 
     :raises ValueError: If squeeze is set to true and multiple graphs are received
     """
-    if (isinstance(source, str) and source.startswith("https://")) or source.startswith("http://"):
+    if isinstance(source, str) and (source.startswith("https://") or source.startswith("http://")):
         import requests
 
         if source.endswith(".gz"):

{obographs-0.0.5 → obographs-0.0.6}/src/obographs/version.py

@@ -12,7 +12,7 @@ __all__ = [
     "get_version",
 ]
 
-VERSION = "0.0.5"
+VERSION = "0.0.6"
 
 
 def get_git_hash() -> str: