Merge pull request #274 from RDFLib/owl_named_graph

Merge named-graph-expansion feature

.github/workflows/ci.yml

@@ -29,7 +29,6 @@ jobs:
     strategy:
       matrix:
         python-version:
-          - '3.8'
           - '3.9'
           - '3.10'
           - '3.11'

.gitignore

@@ -416,7 +416,8 @@ celerybeat-schedule
 # Environments
 .env
 .venv/
-.venv38/
+.venv39/
+.venv311/
 env/
 venv/
 ENV/

CHANGELOG.md

@@ -7,6 +7,24 @@ and this project adheres to [Python PEP 440 Versioning](https://www.python.org/d
 ## [Unreleased]
 - Nothing yet
 
+## [0.29.0] - 2024-11-01
+
+### Added
+- When validating a Dataset instead of a bare Graph, PySHACL will now expand RDFS and OWL-RL inferences into
+  a separate named graph, to avoid polluting the datagraph.
+- When using SHACL Triple Rules from SHACL-AF spec, PySHACL will now add the expressed triples into
+  a separate named graph. This allows you to more easily get the expanded triples back out again afterward.
+
+### Changed
+- PySHACL no longer supports older RDFLib versions
+  - PySHACL relies on the latest OWL-RL version, that in-turn relies on the latest RDFLib version
+  - Therefore PySHACL now requires RDFLib v7.1.1 or newer
+- Dropped Python 3.8 support.
+  - Python developers discontinued Python 3.8 last month
+  - The next version of RDFLib and OWL-RL will not support Python 3.8
+  - Removed Python 3.8 from the RDFLib test suite
+  - Python 3.9-specific typing changes will be incrementally introduced
+
 ## [0.28.1] - 2024-10-25
 
 ### Fixed
@@ -1182,7 +1200,8 @@ just leaves the files open. Now it is up to the command-line client to close the
 
 - Initial version, limited functionality
 
-[Unreleased]: https://github.com/RDFLib/pySHACL/compare/v0.28.1...HEAD
+[Unreleased]: https://github.com/RDFLib/pySHACL/compare/v0.29.0...HEAD
+[0.29.0]: https://github.com/RDFLib/pySHACL/compare/v0.28.1...v0.29.0
 [0.28.1]: https://github.com/RDFLib/pySHACL/compare/v0.28.0...v0.28.1
 [0.28.0]: https://github.com/RDFLib/pySHACL/compare/v0.27.0...v0.28.0
 [0.27.0]: https://github.com/RDFLib/pySHACL/compare/v0.26.0...v0.27.0

Makefile

@@ -56,9 +56,9 @@ endif
 .PHONY: type-check
 type-check: venvcheck	## Validate with MyPy in check-only mode
 ifeq ("$(FilePath)", "")
-	poetry run python3 -m mypy --ignore-missing-imports pyshacl
+	poetry run python3 -m mypy --python-version 3.9 --ignore-missing-imports pyshacl
 else
-	poetry run python3 -m mypy --ignore-missing-imports "$(FilePath)"
+	poetry run python3 -m mypy --python-version 3.9 --ignore-missing-imports "$(FilePath)"
 endif
 
 .PHONY: upgrade

pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "poetry.core.masonry.api"
 [project]
 name = "pyshacl"
 # Black and Ruff both now read target-version from [project.requires-python]
-requires-python = ">=3.8.1"
+requires-python = ">=3.9"
 
 [tool.poetry]
 name = "pyshacl"
@@ -60,11 +60,10 @@ include = [
 ]
 
 [tool.poetry.dependencies]
-python = "^3.8.1"  # Poetry doesn't read from [project.requires-python]
-# Note, 3.8.0 is not supported, only 3.8.1 or above. See:
-# https://github.com/RDFLib/rdflib/blob/3bee979cd0e5b6efc57296b4fc43dd8ede8cf375/CHANGELOG.md?plain=1#L53
-rdflib = {version=">=6.3.2,<8.0", python = ">=3.8.1", extras=["html"]}
-owlrl = ">=6.0.2,<7"
+# The <4 is reauired for compatiblity with OWL-RL that requdires Python <4
+python = ">=3.9,<4"  # Poetry doesn't read from [project.requires-python]
+rdflib = {version=">=7.1.1,<8.0", extras=["html"]}
+owlrl = ">=7.1.2,<8"
 prettytable = [
     {version=">=3.5.0", python = ">=3.8,<3.12"},
     {version=">=3.7.0", python = ">=3.12"}
@@ -77,10 +76,7 @@ sanic-ext = {version=">=23.3, <23.6", optional=true} #For the HTTP service
 sanic-cors = {version="2.2.0", optional=true} #For the HTTP service
 ruff = {version="^0.1.5", optional=true}
 black = {version="24.3.0", optional=true}
-mypy = [
-    {version=">=0.812,<0.900", optional=true, python = "<3.10"},
-    {version=">=0.900,<0.1000", optional=true, python = ">=3.10"}
-    ]
+mypy = {version=">=1.13.0", optional=true}
 types-setuptools = {version="*", optional=true}
 platformdirs = {version="*", optional=true}
 coverage = {version=">6,<7,!=6.0.*,!=6.1,!=6.1.1", optional=true}
@@ -92,10 +88,7 @@ coverage = {version=">6,<7,!=6.0.*,!=6.1,!=6.1.1", optional=true}
 pytest-cov = {version="^2.8.1", optional=true}
 ruff = {version="^0.1.5", optional=true}
 black = {version="24.3.0", optional=true}
-mypy = [
-    {version=">=0.812,<0.900", optional=true, python = "<3.10"},
-    {version=">=0.900,<0.1000", optional=true, python = ">=3.10"}
-    ]
+mypy = {version=">=1.13.0", optional=true}
 types-setuptools = {version="*", optional=true}
 platformdirs = {version="*", optional=true}
 
@@ -206,7 +199,7 @@ testpaths = [
 legacy_tox_ini = """
 [tox]
 skipsdist = true
-envlist = py38, py39, py310, py311, py312, lint, type-checking
+envlist = py39, py310, py311, py312, lint, type-checking
 toxworkdir={env:TOX_WORK_DIR:.tox}
 
 [testenv]
@@ -250,7 +243,7 @@ commands_pre =
     poetry run pip3 install "mypy>=0.812" "types-setuptools"
 commands =
     - poetry show
-    poetry run python3 -m mypy --ignore-missing-imports pyshacl
+    poetry run python3 -m mypy --python-version 3.9 --ignore-missing-imports pyshacl
 
 [gh]
 # Don't include lint or type-checking in gh-actions matrix
@@ -259,6 +252,5 @@ python =
     3.11 = py311
     3.10 = py310
     3.9 = py39
-    3.8 = py38
 
 """

pyshacl/extras/js/rules.py

@@ -1,7 +1,6 @@
 #
 #
-import typing
-from typing import List, Sequence, Union
+from typing import TYPE_CHECKING, List, Optional, Sequence, Union
 
 import rdflib
 
@@ -11,14 +10,18 @@
 
 from .js_executable import JSExecutable
 
-if typing.TYPE_CHECKING:
+if TYPE_CHECKING:
+
+    from rdflib.term import URIRef
 
     from pyshacl.pytypes import GraphLike, RDFNode, SHACLExecutor
     from pyshacl.shape import Shape
     from pyshacl.shapes_graph import ShapesGraph
 
 SH_JSRule = SH.JSRule
 
+JS_RULE_ITERATE_LIMIT = 100
+
 
 class JSRule(SHACLRule):
     __slots__ = ('js_exe',)
@@ -32,6 +35,7 @@ def apply(
         self,
         data_graph: 'GraphLike',
         focus_nodes: Union[Sequence['RDFNode'], None] = None,
+        target_graph_identifier: Optional['URIRef'] = None,
     ) -> int:
         focus_list: Sequence['RDFNode']
         if focus_nodes is not None:
@@ -48,10 +52,10 @@ def apply(
                 return 0
             focus_list = filtered_focus_nodes
         all_added = 0
-        iterate_limit = 100
+        iterate_limit = int(JS_RULE_ITERATE_LIMIT)
         while True:
             if iterate_limit < 1:
-                raise ReportableRuntimeError("Local rule iteration exceeded iteration limit of 100.")
+                raise ReportableRuntimeError(f"JS rule iteration exceeded iteration limit of {JS_RULE_ITERATE_LIMIT}.")
             iterate_limit -= 1
             added = 0
             applicable_nodes = self.filter_conditions(focus_list, data_graph)
@@ -72,10 +76,17 @@ def apply(
                 if this_added:
                     added += 1
             if added > 0:
-                all_added += added
+                if isinstance(data_graph, (rdflib.Dataset, rdflib.ConjunctiveGraph)):
+                    if target_graph_identifier is not None:
+                        target_graph = data_graph.get_context(target_graph_identifier)
+                    else:
+                        target_graph = data_graph.default_context
+                else:
+                    target_graph = data_graph
                 for s in sets_to_add:
                     for t in s:
-                        data_graph.add(t)
+                        target_graph.add(t)
+                all_added += added
                 if self.iterate:
                     continue  # Jump up to iterate
                 else:

pyshacl/inference/custom_rdfs_closure.py

@@ -1,4 +1,6 @@
 # -*- coding: utf-8 -*-
+from typing import TYPE_CHECKING, Optional
+
 try:
     from owlrl import OWL
 
@@ -25,6 +27,9 @@
 from owlrl.OWLRL import OWLRL_Semantics
 from owlrl.RDFSClosure import RDFS_Semantics as OrigRDFSSemantics
 
+if TYPE_CHECKING:
+    from rdflib.graph import Graph
+
 
 class CustomRDFSSemantics(OrigRDFSSemantics):
     def one_time_rules(self):
@@ -49,9 +54,10 @@ class CustomRDFSOWLRLSemantics(CustomRDFSSemantics, OWLRL_Semantics):
         (OWL.DataRange, OWL.equivalentClass, RDFS.Datatype),
     ]
 
-    def __init__(self, graph, axioms, daxioms, rdfs=True):
-        OWLRL_Semantics.__init__(self, graph, axioms, daxioms, rdfs)
-        CustomRDFSSemantics.__init__(self, graph, axioms, daxioms, rdfs)
+    def __init__(self, graph, axioms, daxioms, rdfs: bool = True, destination: Optional['Graph'] = None):
+        # MyPy thinks this is object.__init__ and says the kwargs are incorrect for __init__
+        OWLRL_Semantics.__init__(self, graph, axioms, daxioms, rdfs=rdfs, destination=destination)  # type: ignore[arg-type, call-arg]
+        CustomRDFSSemantics.__init__(self, graph, axioms, daxioms, rdfs=rdfs, destination=destination)  # type: ignore[arg-type, call-arg]
         self.rdfs = True
 
     # noinspection PyMethodMayBeStatic