obographs 0.0.2__tar.gz → 0.0.4__tar.gz

{obographs-0.0.2 → obographs-0.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: obographs
-Version: 0.0.2
+Version: 0.0.4
 Summary: A python data model for OBO Graphs
 Keywords: snekpack,cookiecutter
 Author: Charles Tapley Hoyt
@@ -23,15 +23,8 @@ Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3 :: Only
 Classifier: Typing :: Typed
 Requires-Dist: pydantic
-Requires-Dist: curies
+Requires-Dist: curies>=0.10.19
 Requires-Dist: typing-extensions
-Requires-Dist: sphinx>=8 ; extra == 'docs'
-Requires-Dist: sphinx-rtd-theme>=3.0 ; extra == 'docs'
-Requires-Dist: sphinx-automodapi ; extra == 'docs'
-Requires-Dist: autodoc-pydantic ; extra == 'docs'
-Requires-Dist: requests ; extra == 'network'
-Requires-Dist: pytest ; extra == 'tests'
-Requires-Dist: coverage[toml] ; extra == 'tests'
 Maintainer: Charles Tapley Hoyt
 Maintainer-email: Charles Tapley Hoyt <cthoyt@gmail.com>
 Requires-Python: >=3.10
@@ -40,9 +33,6 @@ Project-URL: Documentation, https://obographs.readthedocs.io
 Project-URL: Funding, https://github.com/sponsors/cthoyt
 Project-URL: Homepage, https://github.com/cthoyt/obographs
 Project-URL: Repository, https://github.com/cthoyt/obographs.git
-Provides-Extra: docs
-Provides-Extra: network
-Provides-Extra: tests
 Description-Content-Type: text/markdown
 
 <!--
@@ -97,7 +87,7 @@ graph_raw = obographs.read(url)
 The OBO Graph JSON schema uses non-Pythonic names, and it's inherently not aware
 of semantics - it uses a combination of URIs and ad-hoc symbols as identifiers.
 `obographs` implements a standardization workflow that creates new data
-structures with parsed/normalized URIs and symbols that has Pythonic nams. Use
+structures with parsed/normalized URIs and symbols that has Pythonic names. Use
 it like:
 
 ```python
@@ -129,18 +119,15 @@ $ python3 -m pip install obographs
 The most recent code and data can be installed directly from GitHub with uv:
 
 ```console
-$ uv --preview pip install git+https://github.com/cthoyt/obographs.git
+$ uv pip install git+https://github.com/cthoyt/obographs.git
 ```
 
 or with pip:
 
 ```console
-$ UV_PREVIEW=1 python3 -m pip install git+https://github.com/cthoyt/obographs.git
+$ python3 -m pip install git+https://github.com/cthoyt/obographs.git
 ```
 
-Note that this requires setting `UV_PREVIEW` mode enabled until the uv build
-backend becomes a stable feature.
-
 ## 👐 Contributing
 
 Contributions, whether filing an issue, making a pull request, or forking, are
@@ -203,18 +190,15 @@ To install in development mode, use the following:
 ```console
 $ git clone git+https://github.com/cthoyt/obographs.git
 $ cd obographs
-$ uv --preview pip install -e .
+$ uv pip install -e .
 ```
 
 Alternatively, install using pip:
 
 ```console
-$ UV_PREVIEW=1 python3 -m pip install -e .
+$ python3 -m pip install -e .
 ```
 
-Note that this requires setting `UV_PREVIEW` mode enabled until the uv build
-backend becomes a stable feature.
-
 ### Updating Package Boilerplate
 
 This project uses `cruft` to keep boilerplate (i.e., configuration, contribution

{obographs-0.0.2 → obographs-0.0.4}/README.md

@@ -50,7 +50,7 @@ graph_raw = obographs.read(url)
 The OBO Graph JSON schema uses non-Pythonic names, and it's inherently not aware
 of semantics - it uses a combination of URIs and ad-hoc symbols as identifiers.
 `obographs` implements a standardization workflow that creates new data
-structures with parsed/normalized URIs and symbols that has Pythonic nams. Use
+structures with parsed/normalized URIs and symbols that has Pythonic names. Use
 it like:
 
 ```python
@@ -82,18 +82,15 @@ $ python3 -m pip install obographs
 The most recent code and data can be installed directly from GitHub with uv:
 
 ```console
-$ uv --preview pip install git+https://github.com/cthoyt/obographs.git
+$ uv pip install git+https://github.com/cthoyt/obographs.git
 ```
 
 or with pip:
 
 ```console
-$ UV_PREVIEW=1 python3 -m pip install git+https://github.com/cthoyt/obographs.git
+$ python3 -m pip install git+https://github.com/cthoyt/obographs.git
 ```
 
-Note that this requires setting `UV_PREVIEW` mode enabled until the uv build
-backend becomes a stable feature.
-
 ## 👐 Contributing
 
 Contributions, whether filing an issue, making a pull request, or forking, are
@@ -156,18 +153,15 @@ To install in development mode, use the following:
 ```console
 $ git clone git+https://github.com/cthoyt/obographs.git
 $ cd obographs
-$ uv --preview pip install -e .
+$ uv pip install -e .
 ```
 
 Alternatively, install using pip:
 
 ```console
-$ UV_PREVIEW=1 python3 -m pip install -e .
+$ python3 -m pip install -e .
 ```
 
-Note that this requires setting `UV_PREVIEW` mode enabled until the uv build
-backend becomes a stable feature.
-
 ### Updating Package Boilerplate
 
 This project uses `cruft` to keep boilerplate (i.e., configuration, contribution

{obographs-0.0.2 → obographs-0.0.4}/pyproject.toml

@@ -1,12 +1,10 @@
 [build-system]
-requires = ["uv>=0.5.13,<0.6.0"]
-# The uv backend entered preview mode in https://github.com/astral-sh/uv/pull/8886/files
-# with the 0.5.0 release. See also https://github.com/astral-sh/uv/issues/3957 for tracking.
-build-backend = "uv"
+requires = ["uv_build>=0.6.6,<0.7"]
+build-backend = "uv_build"
 
 [project]
 name = "obographs"
-version = "0.0.2"
+version = "0.0.4"
 description = "A python data model for OBO Graphs"
 readme = "README.md"
 authors = [
@@ -52,11 +50,12 @@ license-files = [
 requires-python = ">=3.10"
 dependencies = [
     "pydantic",
-    "curies",
+    "curies>=0.10.19",
     "typing-extensions",
 ]
 
-[project.optional-dependencies]
+# see https://peps.python.org/pep-0735/ and https://docs.astral.sh/uv/concepts/dependencies/#dependency-groups
+[dependency-groups]
 tests = [
     "pytest",
     "coverage[toml]",
@@ -67,10 +66,51 @@ docs = [
     "sphinx_automodapi",
     "autodoc_pydantic",
 ]
+lint = [
+    "ruff",
+]
+typing = [
+    { include-group = "tests" },
+    "mypy",
+    "pydantic",
+    "types-requests",
+]
+docs-lint = [
+    { include-group = "docs" },
+    "doc8",
+]
+format-docs = [
+    { include-group = "docs" },
+    "docstrfmt",
+]
+doctests = [
+    "xdoctest",
+    "pygments",
+]
+pyroma = [
+    "pyroma",
+    "pygments",
+]
+# follow https://github.com/astral-sh/uv/issues/6298 for switching to a uv-based version bump workflow
+bump = [
+    "bump-my-version",
+]
+build = [
+    "uv",
+    "uv-build",
+]
+release = [
+    { include-group = "build" },
+    "uv",
+    "keyring",
+]
 network = [
     "requests",
 ]
 
+# see https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#dependencies-optional-dependencies
+# [project.optional-dependencies]
+
 # See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#urls
 # and also https://packaging.python.org/en/latest/specifications/well-known-project-urls/
 [project.urls]
@@ -114,6 +154,9 @@ source = [
 omit = [
     "tests/*",
     "docs/*",
+    "src/obographs/version.py",
+    "src/obographs/__main__.py",
+    "src/obographs/cli.py",
 ]
 
 [tool.coverage.paths]
@@ -189,7 +232,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.0.2"
+current_version = "0.0.4"
 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-0.0.4/src/obographs/__init__.py

@@ -0,0 +1,73 @@
+"""A python data model for OBO Graphs."""
+
+from .model import (
+    Definition,
+    DomainRangeAxiom,
+    Edge,
+    EquivalentNodeSet,
+    ExistentialRestrictionExpression,
+    Graph,
+    GraphDocument,
+    LogicalDefinition,
+    Meta,
+    Node,
+    NodeType,
+    Property,
+    PropertyChainAxiom,
+    PropertyType,
+    Synonym,
+    Xref,
+    read,
+)
+from .standardized import (
+    StandardizedBaseModel,
+    StandardizedDefinition,
+    StandardizedDomainRangeAxiom,
+    StandardizedEdge,
+    StandardizedEquivalentNodeSet,
+    StandardizedExistentialRestriction,
+    StandardizedGraph,
+    StandardizedGraphDocument,
+    StandardizedLogicalDefinition,
+    StandardizedMeta,
+    StandardizedNode,
+    StandardizedProperty,
+    StandardizedPropertyChainAxiom,
+    StandardizedSynonym,
+    StandardizedXref,
+)
+
+__all__ = [
+    "Definition",
+    "DomainRangeAxiom",
+    "Edge",
+    "EquivalentNodeSet",
+    "ExistentialRestrictionExpression",
+    "Graph",
+    "GraphDocument",
+    "LogicalDefinition",
+    "Meta",
+    "Node",
+    "NodeType",
+    "Property",
+    "PropertyChainAxiom",
+    "PropertyType",
+    "StandardizedBaseModel",
+    "StandardizedDefinition",
+    "StandardizedDomainRangeAxiom",
+    "StandardizedEdge",
+    "StandardizedEquivalentNodeSet",
+    "StandardizedExistentialRestriction",
+    "StandardizedGraph",
+    "StandardizedGraphDocument",
+    "StandardizedLogicalDefinition",
+    "StandardizedMeta",
+    "StandardizedNode",
+    "StandardizedProperty",
+    "StandardizedPropertyChainAxiom",
+    "StandardizedSynonym",
+    "StandardizedXref",
+    "Synonym",
+    "Xref",
+    "read",
+]

{obographs-0.0.2 → obographs-0.0.4}/src/obographs/model.py

@@ -9,27 +9,35 @@
 
 from __future__ import annotations
 
+import gzip
 import json
 import logging
 from collections import defaultdict
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Literal, TypeAlias, overload
+from typing import TYPE_CHECKING, Literal, TypeAlias, overload
 
+import curies
+from curies.vocabulary import SynonymScopeOIO
 from pydantic import BaseModel, Field
 
 if TYPE_CHECKING:
-    import curies
-
     from .standardized import StandardizedGraph
 
 __all__ = [
     "Definition",
+    "DomainRangeAxiom",
     "Edge",
+    "EquivalentNodeSet",
+    "ExistentialRestrictionExpression",
     "Graph",
     "GraphDocument",
+    "LogicalDefinition",
     "Meta",
     "Node",
+    "NodeType",
     "Property",
+    "PropertyChainAxiom",
+    "PropertyType",
     "Synonym",
     "Xref",
     "read",
@@ -40,31 +48,24 @@ logger = logging.getLogger(__name__)
 OBO_URI_PREFIX = "http://purl.obolibrary.org/obo/"
 OBO_URI_PREFIX_LEN = len(OBO_URI_PREFIX)
 
-SynonymPredicate: TypeAlias = Literal[
-    "hasExactSynonym",
-    "hasBroadSynonym",
-    "hasNarrowSynonym",
-    "hasRelatedSynonym",
-]
 NodeType: TypeAlias = Literal["CLASS", "PROPERTY", "INDIVIDUAL"]
 
-TimeoutHint = int | float | None
+#: When node type is ``PROPERTY``, this is extra information
+PropertyType: TypeAlias = Literal["ANNOTATION", "OBJECT", "DATA"]
 
-#: A mapping from OBO flat file format internal synonym types to OBO in OWL vocabulary
-#: identifiers. See https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html
-OBO_SYNONYM_TO_OIO: dict[str, SynonymPredicate] = {
-    "EXACT": "hasExactSynonym",
-    "BROAD": "hasBroadSynonym",
-    "NARROW": "hasNarrowSynonym",
-    "RELATED": "hasRelatedSynonym",
-}
+TimeoutHint = int | float | None
 
 
 class Property(BaseModel):
     """Represent a property inside a metadata element."""
 
     pred: str
-    val: str
+    val: str | None = Field(
+        None,
+        description="Stores the value of the property. This can be a string representing a "
+        "literal or IRI. This isn't supposed to be nullable, but it happens a lot - might be a "
+        "bug in OWLAPI or ROBOT",
+    )
     xrefs: list[str] | None = None
     meta: Meta | None = None
 
@@ -86,8 +87,8 @@ class Synonym(BaseModel):
     """Represents a synonym inside an object meta."""
 
     val: str | None = Field(default=None)
-    pred: str = Field(default="hasExactSynonym")
-    synonymType: str | None = Field(examples=["OMO:0003000"])  # noqa:N815
+    pred: SynonymScopeOIO = Field(default="hasExactSynonym")
+    synonymType: str | None = Field(None, examples=["OMO:0003000"])  # noqa:N815
     xrefs: list[str] = Field(
         default_factory=list,
         description="A list of CURIEs/IRIs for provenance for the synonym",
@@ -123,7 +124,52 @@ class Node(BaseModel):
     id: str = Field(..., description="The IRI for the node")
     lbl: str | None = Field(None, description="The name of the node")
     meta: Meta | None = None
-    type: NodeType = Field(..., description="Type of node")
+    type: NodeType | None = Field(None, description="Type of node")
+    propertyType: PropertyType | None = Field(  # noqa:N815
+        None, description="Type of property, if the node type is a property"
+    )
+
+
+class DomainRangeAxiom(BaseModel):
+    """Represents a domain/range axiom."""
+
+    predicateId: str  # noqa:N815
+    domainClassIds: list[str] | None = None  # noqa:N815
+    rangeClassIds: list[str] | None = None  # noqa:N815
+    allValuesFromEdges: list[Edge] | None = None  # noqa:N815
+    meta: Meta | None = None
+
+
+class PropertyChainAxiom(BaseModel):
+    """Represents a property chain axiom."""
+
+    predicateId: str  # noqa:N815
+    chainPredicateIds: list[str]  # noqa:N815
+    meta: Meta | None = None
+
+
+class ExistentialRestrictionExpression(BaseModel):
+    """Represents an existential restriction."""
+
+    propertyId: str  # noqa:N815
+    fillerId: str  # noqa:N815
+
+
+class LogicalDefinition(BaseModel):
+    """Represents a logical definition chain axiom."""
+
+    definedClassId: str  # noqa:N815
+    genusIds: list[str] | None = None  # noqa:N815
+    restrictions: list[ExistentialRestrictionExpression] | None = None
+    meta: Meta | None = None
+
+
+class EquivalentNodeSet(BaseModel):
+    """Represents a set of equivalent nodes."""
+
+    representativeNodeId: str  # noqa:N815
+    nodeIds: list[str]  # noqa:N815
+    meta: Meta | None = None
 
 
 class Graph(BaseModel):
@@ -133,10 +179,10 @@ class Graph(BaseModel):
     meta: Meta | None = None
     nodes: list[Node] = Field(default_factory=list)
     edges: list[Edge] = Field(default_factory=list)
-    equivalentNodesSets: list[Any] = Field(default_factory=list)  # noqa:N815
-    logicalDefinitionAxioms: list[Any] = Field(default_factory=list)  # noqa:N815
-    domainRangeAxioms: list[Any] = Field(default_factory=list)  # noqa:N815
-    propertyChainAxioms: list[Any] = Field(default_factory=list)  # noqa:N815
+    equivalentNodesSets: list[EquivalentNodeSet] = Field(default_factory=list)  # noqa:N815
+    logicalDefinitionAxioms: list[LogicalDefinition] = Field(default_factory=list)  # noqa:N815
+    domainRangeAxioms: list[DomainRangeAxiom] = Field(default_factory=list)  # noqa:N815
+    propertyChainAxioms: list[PropertyChainAxiom] = Field(default_factory=list)  # noqa:N815
 
     def standardize(self, converter: curies.Converter) -> StandardizedGraph:
         """Standardize the graph."""
@@ -205,12 +251,14 @@ def read(
 
     elif isinstance(source, str | Path):
         path = Path(source).expanduser().resolve()
-        if path.is_file():
-            if path.suffix.endswith(".gz"):
-                raise NotImplementedError
-            else:
-                with path.open() as file:
-                    graph_document = GraphDocument.model_validate(json.load(file))
+        if not path.is_file():
+            raise FileNotFoundError
+        if path.suffix.endswith(".gz"):
+            with gzip.open(path, mode="rt") as file:
+                graph_document = GraphDocument.model_validate(json.load(file))
+        else:
+            with path.open() as file:
+                graph_document = GraphDocument.model_validate(json.load(file))
     else:
         raise TypeError(f"Unhandled source: {source}")