obographs 0.0.8__tar.gz → 0.0.9__tar.gz

{obographs-0.0.8 → obographs-0.0.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: obographs
-Version: 0.0.8
+Version: 0.0.9
 Summary: A python data model for OBO Graphs
 Keywords: snekpack,cookiecutter
 Author: Charles Tapley Hoyt

{obographs-0.0.8 → obographs-0.0.9}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "obographs"
-version = "0.0.8"
+version = "0.0.9"
 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 = "0.0.8"
+current_version = "0.0.9"
 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-0.0.8 → obographs-0.0.9}/src/obographs/model.py

@@ -239,19 +239,31 @@ def get_id_to_edges(graph: Graph) -> dict[str, list[tuple[str, str]]]:
 # docstr-coverage:excused `overload`
 @overload
 def read(
-    source: str | Path, *, timeout: TimeoutHint = ..., squeeze: Literal[False] = ...
+    source: str | Path,
+    *,
+    timeout: TimeoutHint = ...,
+    squeeze: Literal[False] = ...,
+    encoding: str = ...,
 ) -> GraphDocument: ...
 
 
 # docstr-coverage:excused `overload`
 @overload
 def read(
-    source: str | Path, *, timeout: TimeoutHint = ..., squeeze: Literal[True] = ...
+    source: str | Path,
+    *,
+    timeout: TimeoutHint = ...,
+    squeeze: Literal[True] = ...,
+    encoding: str = ...,
 ) -> Graph: ...
 
 
 def read(
-    source: str | Path, *, timeout: TimeoutHint = None, squeeze: bool = True
+    source: str | Path,
+    *,
+    timeout: TimeoutHint = None,
+    squeeze: bool = True,
+    encoding: str = "utf-8",
 ) -> Graph | GraphDocument:
     """Read an OBO Graph document.
 
@@ -261,6 +273,7 @@ def read(
         only has a single graph and return a :class:`Graph` object. If `true` and
         multiple graphs are received, will raise an error. Set this to `false` to return
         a GraphDocument containing all graphs.
+    :param encoding: The encoding to use for reading the graph
 
     :returns: A graph or graph document
 
@@ -281,10 +294,10 @@ def read(
         if not path.is_file():
             raise FileNotFoundError
         if path.suffix.endswith(".gz"):
-            with gzip.open(path, mode="rt") as file:
+            with gzip.open(path, mode="rt", encoding=encoding) as file:
                 graph_document = GraphDocument.model_validate(json.load(file))
         else:
-            with path.open() as file:
+            with path.open(mode="rt", encoding=encoding) as file:
                 graph_document = GraphDocument.model_validate(json.load(file))
     else:
         raise TypeError(f"Unhandled source: {source}")

{obographs-0.0.8 → obographs-0.0.9}/src/obographs/standardized.py

@@ -4,6 +4,7 @@ from __future__ import annotations
 
 import logging
 from abc import ABC, abstractmethod
+from collections.abc import Iterable
 from typing import Generic, TypeVar, cast
 
 import curies.preprocessing
@@ -411,8 +412,11 @@ class StandardizedDomainRangeAxiom(StandardizedBaseModel[DomainRangeAxiom]):
         cls, obj: DomainRangeAxiom, converter: Converter, *, strict: bool = False
     ) -> Self | None:
         """Parse a raw object."""
+        predicate = _curie_or_uri_to_ref(obj.predicateId, converter, strict=strict)
+        if predicate is None:
+            return None
         return cls(
-            predicate=_curie_or_uri_to_ref(obj.predicateId, converter, strict=strict),
+            predicate=predicate,
             domains=_parse_list(obj.domainClassIds, converter, strict=strict) or [],
             ranges=_parse_list(obj.rangeClassIds, converter, strict=strict) or [],
             all_values_from_edges=[
@@ -528,11 +532,11 @@ class StandardizedLogicalDefinition(StandardizedBaseModel[LogicalDefinition]):
         """Parse a raw object."""
         return cls(
             node=_curie_or_uri_to_ref(obj.definedClassId, converter, strict=strict),
-            geni=_parse_list(obj.genusIds, converter, strict=strict),
-            restrictions=[
+            geni=_parse_list(obj.genusIds, converter, strict=strict) or [],
+            restrictions=_schwoop(
                 StandardizedExistentialRestriction.from_obograph_raw(r, converter, strict=strict)
                 for r in obj.restrictions or []
-            ],
+            ),
             meta=StandardizedMeta.from_obograph_raw(obj.meta, converter, strict=strict),
         )
 
@@ -577,22 +581,22 @@ class StandardizedGraph(StandardizedBaseModel[Graph]):
                 for edge in graph.edges
                 if (s_edge := StandardizedEdge.from_obograph_raw(edge, converter, strict=strict))
             ],
-            equivalent_node_sets=[
+            equivalent_node_sets=_schwoop(
                 StandardizedEquivalentNodeSet.from_obograph_raw(e, converter, strict=strict)
                 for e in graph.equivalentNodesSets or []
-            ],
-            logical_definition_axioms=[
+            ),
+            logical_definition_axioms=_schwoop(
                 StandardizedLogicalDefinition.from_obograph_raw(e, converter, strict=strict)
                 for e in graph.logicalDefinitionAxioms or []
-            ],
-            property_chain_axioms=[
+            ),
+            property_chain_axioms=_schwoop(
                 StandardizedPropertyChainAxiom.from_obograph_raw(e, converter, strict=strict)
                 for e in graph.propertyChainAxioms or []
-            ],
-            domain_range_axioms=[
+            ),
+            domain_range_axioms=_schwoop(
                 StandardizedDomainRangeAxiom.from_obograph_raw(e, converter, strict=strict)
                 for e in graph.domainRangeAxioms or []
-            ],
+            ),
         )
 
     def to_raw(self, converter: Converter) -> Graph:
@@ -637,6 +641,10 @@ class StandardizedGraph(StandardizedBaseModel[Graph]):
         return r
 
 
+def _schwoop(x: Iterable[X | None]) -> list[X]:
+    return [y for y in x if y is not None]
+
+
 class StandardizedGraphDocument(StandardizedBaseModel[GraphDocument]):
     """A standardized graph document."""
 

{obographs-0.0.8 → obographs-0.0.9}/src/obographs/version.py

@@ -12,7 +12,7 @@ __all__ = [
     "get_version",
 ]
 
-VERSION = "0.0.8"
+VERSION = "0.0.9"
 
 
 def get_git_hash() -> str: