Add support for Python 3.13

.github/workflows/ci_tests.yml

@@ -68,7 +68,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - name: Checkout tripper
@@ -107,7 +107,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - name: Checkout tripper

docs/tutorial.md

@@ -223,7 +223,7 @@ Note:
 ...   ?unit rdfs:subClassOf <{EMMO.LengthUnit}> .
 ...   ?unit rdfs:subClassOf ?r .
 ...   ?r rdf:type owl:Restriction .
-...   ?r owl:onProperty <{EMMO.hasSymbolValue}> .
+...   ?r owl:onProperty <{EMMO.unitSymbolValue}> .
 ...   ?r owl:hasValue ?symbol .
 ... }}
 ... """

pyproject.toml

@@ -20,6 +20,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Environment :: Plugins",
     "Natural Language :: English",
     "Operating System :: OS Independent",
@@ -29,11 +30,19 @@ requires-python = ">=3.7"
 dynamic = ["version"]
 
 dependencies = [
-    "typing-extensions>=4.7.0,<4.7.1; python_version<'3.8'",
-    "pint>=0.16.1,<0.25",
+    "typing-extensions>=4.7.0,<4.7.1; python_version<'3.9'",
 ]
 
 [project.optional-dependencies]
+mappings = [
+    "pint>=0.16.1,<0.25",
+    "rdflib>=6.3.0,<7.0.0",
+]
+dataset = [
+    "tripper[mappings]",
+    "PyYaml>=3.0.0,<6.0.3",  # todo: check lower version
+    "requests>=2.0.0,<3.4.1",  # todo: check lower version
+]
 pre-commit = [
     "pre-commit==4.0.1",
     "pylint==2.15.5",
@@ -43,25 +52,17 @@ testing-core = [
     "pytest-cov==4.1.0",
 ]
 testing = [
-    # Consistent with: dependencies (is this needed?)
-    "pint>=0.16.1,<0.24",
-    # Consistent with: testing-core
-    "pytest==7.4.4",
-    "pytest-cov==4.1.0",
-    # testing
-    "EMMOntoPy>=0.5.0,<0.7.1",
-    "rdflib>=6.3.0,<7.0.0",
-    "SPARQLWrapper>=2.0.0,<2.0.1",
-    "DLite-Python>=0.5.1,<0.5.17",
+    "tripper[testing-core,mappings,dataset]",
+    "dlite-python>=0.5.23,<0.5.27; python_version>='3.8' and python_version<'3.13'",
+    "dlite-python>=0.5.25,<0.5.27; python_version>='3.13'",
+    "emmontopy>=0.5.0,<0.7.1; python_version<'3.13'",
     "graphviz>=0.20.1,<0.20.2",
+    "numpy<2.1.0; python_version>='3.13'",
+    "rdflib>=6.3.0,<7.0.0",
+    "sparqlwrapper>=2.0.0,<2.0.1",
 ]
 docs = [
-    # Consistent with: testing
-    "EMMOntoPy>=0.5.0,<0.7.1",
-    "rdflib>=6.3.0,<7.0.0",
-    "SPARQLWrapper>=2.0.0,<2.0.1",
-    "DLite-Python>=0.5.1,<0.5.17",
-    # docs
+    "tripper[testing]",
     "mike==2.1.2",
     "mkdocs==1.5.3",
     "mkdocs-autorefs==0.4.1",
@@ -71,26 +72,7 @@ docs = [
     "mkdocstrings-python-legacy==0.2.3",
 ]
 dev = [
-    # Consistent with: pre-commit
-    "pre-commit==2.21.0",
-    "pylint==2.15.5",
-    # Consistent with: testing-core
-    "pytest==7.4.4",
-    "pytest-cov==4.1.0",
-    # Consistent with testing
-    "EMMOntoPy>=0.5.0,<0.7.1",
-    "rdflib>=6.3.0,<7.0.0",
-    "SPARQLWrapper>=2.0.0,<2.0.1",
-    "DLite-Python>=0.5.1,<0.5.17",
-    "graphviz>=0.20.1,<0.20.2",
-    # Consistent with: docs
-    "mike==2.1.2",
-    "mkdocs==1.5.3",
-    "mkdocs-autorefs==0.4.1",
-    "mkdocs-awesome-pages-plugin==2.9.2",
-    "mkdocs-material==9.5.17",
-    "mkdocstrings==0.22.0",
-    "mkdocstrings-python-legacy==0.2.3",
+    "tripper[pre-commit,docs]",
 ]
 
 [project.urls]
@@ -122,6 +104,7 @@ max-public-methods = 25
 max-locals = 20
 disable = [
     "fixme",
+    "too-many-positional-arguments",
 ]
 good-names = [
     # Default
@@ -132,11 +115,13 @@ good-names = [
     "s", "p", "o",
     # Namespaces
     "EX",
+    # dict, value, file, ...
+    "d", "v", "f",
 ]
 
 [tool.pytest.ini_options]
 minversion = "7.0"
-addopts = "-rs --cov=tripper --cov-report=term --doctest-modules"
+addopts = "-rs --cov=tripper --cov-report=term --doctest-modules --doctest-ignore-import-errors"
 filterwarnings = [
     "ignore:.*imp module.*:DeprecationWarning",
     "ignore:::tripper.literal:243",  # Ignore warning in doctest

tests/backends/test_sparqlwrapper.py

@@ -8,6 +8,7 @@ def test_sparqlwrapper_backend():
     import pytest
 
     pytest.importorskip("SPARQLWrapper")
+    requests = pytest.importorskip("requests")
 
     from tripper import Triplestore
 
@@ -25,5 +26,12 @@ def test_sparqlwrapper_backend():
 
     endpoint_url = "https://query.wikidata.org/sparql"
     ts = Triplestore(backend="sparqlwrapper", base_iri=endpoint_url)
-    res = ts.query(sparql_query)
+
+    # Ignore failures due to too many requests
+    try:
+        res = ts.query(sparql_query)
+    except requests.HTTPError as exc:
+        if "Too Many Requests" not in str(exc):
+            raise
+
     assert res == [("http://www.wikidata.org/entity/Q20", "Norway")]

tests/conftest.py

@@ -80,6 +80,8 @@ def expected_function_triplestore(
         A Turtle-serialized output that would be expected from the Triplestore.
 
     """
+    # pylint: disable=line-too-long
+
     from tripper.utils import function_id
 
     fid = function_id(example_function)

tests/mappings/test_cost.py

@@ -1,30 +1,33 @@
 """Test cost."""
 
-import pytest
 
-pytest.importorskip("rdflib")
+def test_cost():
+    """Test cost"""
+    # pylint: disable=invalid-name
 
-# pylint: disable=wrong-import-position
-from tripper import Triplestore
+    import pytest
 
-ts = Triplestore(backend="rdflib")
+    pytest.importorskip("rdflib")
 
-# Define some prefixed namespaces
-CHEM = ts.bind("chem", "http://onto-ns.com/onto/chemistry#")
-MOL = ts.bind("mol", "http://onto-ns.com/meta/0.1/Molecule#")
-SUB = ts.bind("sub", "http://onto-ns.com/meta/0.1/Substance#")
+    # pylint: disable=wrong-import-position
+    from tripper import Triplestore
 
+    ts = Triplestore(backend="rdflib")
 
-def formula_cost(ts, input_iris, output_iri):
-    """Returns a cost."""
-    # pylint: disable=unused-argument
-    return 2.72
+    # Define some prefixed namespaces
+    CHEM = ts.bind("chem", "http://onto-ns.com/onto/chemistry#")
+    MOL = ts.bind("mol", "http://onto-ns.com/meta/0.1/Molecule#")
+    SUB = ts.bind("sub", "http://onto-ns.com/meta/0.1/Substance#")
 
+    def formula_cost(ts, input_iris, output_iri):
+        """Returns a cost."""
+        # pylint: disable=unused-argument
+        return 2.72
 
-# Add mappings from data models to ontology
-ts.map(MOL.name, CHEM.Identifier, cost=3.14)
-ts.map(SUB.formula, CHEM.Formula, cost=formula_cost)
+    # Add mappings from data models to ontology
+    ts.map(MOL.name, CHEM.Identifier, cost=3.14)
+    ts.map(SUB.formula, CHEM.Formula, cost=formula_cost)
 
-# pylint: disable=protected-access
-assert ts._get_cost(CHEM.Identifier) == 3.14
-assert ts._get_cost(CHEM.Formula) == 2.72
+    # pylint: disable=protected-access
+    assert ts._get_cost(CHEM.Identifier) == 3.14
+    assert ts._get_cost(CHEM.Formula) == 2.72

tests/output/.gitignore

@@ -1 +1,3 @@
 *.ttl
+*.png
+*.tiff

tripper/testutils.py → tests/paths.py

@@ -1,8 +1,4 @@
-"""Motule primarly intended to be imported by tests.
-
-It defines some directories and some utility functions that can be used
-with or without conftest.
-"""
+"""Test paths"""
 
 from pathlib import Path
 

tests/test_add_function.py

@@ -1,6 +1,6 @@
 """Test Triplestore.add_function()"""
 
-# pylint: disable=invalid-name
+# pylint: disable=invalid-name,import-outside-toplevel
 
 
 def test_add_function():

tests/test_custom_backend.py

@@ -1,11 +1,16 @@
-"""Test custom plugin."""
+"""Test custom backend."""
 
-from tripper import Triplestore
+# pylint: disable=import-outside-toplevel
 
-# Test relative import
-ts = Triplestore(backend="backends.dummy", package="backends")
-assert list(ts.triples()) == [
-    ("a", "b", "c"),
-    ("d", "e", "f"),
-    ("g", "h", "i"),
-]
+
+def test_custom_backend():
+    """Test custom backend."""
+    from tripper import Triplestore
+
+    # Test relative import
+    ts = Triplestore(backend="backends.dummy", package="backends")
+    assert list(ts.triples()) == [
+        ("a", "b", "c"),
+        ("d", "e", "f"),
+        ("g", "h", "i"),
+    ]

tests/test_eval_function.py

@@ -1,54 +1,56 @@
 """Test Triplestore.eval_function()"""
 
+# pylint: disable=import-outside-toplevel
+
 import pytest
 
-from tripper import Triplestore
-
-pytest.importorskip("rdflib")
-
-
-def func(a, b):
-    """Returns the sum of `a` and `b`."""
-    # pylint: disable=invalid-name
-    return a + b
-
-
-ts = Triplestore(backend="rdflib")
-EX = ts.bind("ex", "http://example.com/ex#")
-
-# Test to add function in current scope
-iri = ts.add_function(
-    func,
-    expects=[EX.arg1, EX.arg2],
-    returns=EX.sum,
-    standard="emmo",
-)
-assert ts.eval_function(func_iri=iri, args=(2, 3)) == 5
-
-
-# Test to add a function from the standard library. The hashlib module
-# is not expected to be imported in the current scope
-iri2 = ts.add_function(
-    EX.shake256,
-    expects=[EX.Bytes],
-    returns=EX.ShakeVar,
-    func_name="shake_256",
-    module_name="hashlib",
-)
-shakevar = ts.eval_function(iri2, (b"a",))
-assert shakevar.hexdigest(4) == "867e2cb0"
-
-
-# Test to add a function from a pypi package.
-iri3 = ts.add_function(
-    EX.UFloat,
-    expects=[EX.Uncertainty],
-    returns=EX.UUID,
-    func_name="ufloat",
-    module_name="uncertainties",
-    # package_name="uncertainties",
-    pypi_package_name="uncertainties==3.1.7",
-)
-val = ts.eval_function(iri3, args=(1, 0.1))
-assert val.n == 1
-assert val.s == 0.1
+
+def eval_function():
+    """Test Triplestore.eval_function()"""
+
+    from tripper import Triplestore
+
+    pytest.importorskip("rdflib")
+
+    def func(a, b):
+        """Returns the sum of `a` and `b`."""
+        # pylint: disable=invalid-name
+        return a + b
+
+    ts = Triplestore(backend="rdflib")
+    EX = ts.bind("ex", "http://example.com/ex#")
+
+    # Test to add function in current scope
+    iri = ts.add_function(
+        func,
+        expects=[EX.arg1, EX.arg2],
+        returns=EX.sum,
+        standard="emmo",
+    )
+    assert ts.eval_function(func_iri=iri, args=(2, 3)) == 5
+
+    # Test to add a function from the standard library. The hashlib module
+    # is not expected to be imported in the current scope
+    iri2 = ts.add_function(
+        EX.shake256,
+        expects=[EX.Bytes],
+        returns=EX.ShakeVar,
+        func_name="shake_256",
+        module_name="hashlib",
+    )
+    shakevar = ts.eval_function(iri2, (b"a",))
+    assert shakevar.hexdigest(4) == "867e2cb0"
+
+    # Test to add a function from a pypi package.
+    iri3 = ts.add_function(
+        EX.UFloat,
+        expects=[EX.Uncertainty],
+        returns=EX.UUID,
+        func_name="ufloat",
+        module_name="uncertainties",
+        # package_name="uncertainties",
+        pypi_package_name="uncertainties==3.1.7",
+    )
+    val = ts.eval_function(iri3, args=(1, 0.1))
+    assert val.n == 1
+    assert val.s == 0.1

tests/test_get_data.py

@@ -1,6 +1,6 @@
 """Test Triplestore.get_data() and related methods."""
 
-# pylint: disable=unused-argument,invalid-name
+# pylint: disable=unused-argument,invalid-name,import-outside-toplevel
 
 
 def test_get_data():