[patch] Update action version

.github/workflows/daily.yml

@@ -8,5 +8,5 @@ on:
 
 jobs:
   codeql:
-    uses: pyiron/actions/.github/workflows/tests-and-coverage.yml@actions-3.3.3
+    uses: pyiron/actions/.github/workflows/tests-and-coverage.yml@actions-4.0.1
     secrets: inherit

.github/workflows/dependabot-pr.yml

@@ -6,5 +6,5 @@ on:
 
 jobs:
   pyiron:
-    uses: pyiron/actions/.github/workflows/dependabot-pr.yml@actions-3.3.3
+    uses: pyiron/actions/.github/workflows/dependabot-pr.yml@actions-4.0.1
     secrets: inherit

.github/workflows/pr-labeled.yml

@@ -8,5 +8,5 @@ on:
 
 jobs:
   pyiron:
-    uses: pyiron/actions/.github/workflows/pr-labeled.yml@actions-3.3.3
+    uses: pyiron/actions/.github/workflows/pr-labeled.yml@actions-4.0.1
     secrets: inherit

.github/workflows/pr-target-opened.yml

@@ -8,5 +8,5 @@ on:
 
 jobs:
   pyiron:
-    uses: pyiron/actions/.github/workflows/pr-target-opened.yml@actions-3.3.3
+    uses: pyiron/actions/.github/workflows/pr-target-opened.yml@actions-4.0.1
     secrets: inherit

.github/workflows/preview-release.yml

@@ -10,7 +10,7 @@ on:
 
 jobs:
   pyiron:
-    uses: pyiron/actions/.github/workflows/pyproject-release.yml@actions-3.3.3
+    uses: pyiron/actions/.github/workflows/pyproject-release.yml@actions-4.0.1
     secrets: inherit
     with:
       runner: 'ubuntu-22.04' # with ubuntu > 22.04, pip is broken

.github/workflows/push-pull.yml

@@ -9,7 +9,7 @@ on:
 
 jobs:
   pyiron:
-    uses: pyiron/actions/.github/workflows/push-pull.yml@actions-3.3.3
+    uses: pyiron/actions/.github/workflows/push-pull.yml@actions-4.0.1
     with:
       runner: 'ubuntu-22.04' # with ubuntu > 22.04, pip is broken
       python-version-alt3: 'exclude'  # No python 3.9

.github/workflows/weekly.yml

@@ -8,5 +8,5 @@ on:
 
 jobs:
   codeql:
-    uses: pyiron/actions/.github/workflows/codeql.yml@actions-3.3.3
+    uses: pyiron/actions/.github/workflows/codeql.yml@actions-4.0.1
     secrets: inherit

docs/conf.py

@@ -12,10 +12,11 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys
+import importlib.util
 import os
 import shutil
 import subprocess
+
 from sphinx.ext.apidoc import main
 
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -147,12 +148,13 @@
 #    raise ImportError("You need to install bootstrap: pip install sphinx_bootstrap_theme")
 #    html_theme = 'default'
 
-try:
-    import sphinx_rtd_theme
 
+if importlib.util.find_spec("sphinx_rtd_theme") is not None:
+    # sphinx_rtd_theme is available
     html_theme = "sphinx_rtd_theme"
-except ImportError:
-    html_theme = "default"
+else:
+    # fallback theme
+    html_theme = "alabaster"
 
 
 # Theme options are theme-specific and customize the look and feel of a theme

notebooks/example.ipynb

@@ -29,8 +29,8 @@
    "source": [
     "from pint import UnitRegistry\n",
     "\n",
-    "from semantikon.typing import u\n",
-    "from semantikon.converter import units"
+    "from semantikon.converter import units\n",
+    "from semantikon.typing import u"
    ]
   },
   {

semantikon/_version.py

@@ -11,12 +11,12 @@
 """Git implementation of _version.py."""
 
 import errno
+import functools
 import os
 import re
 import subprocess
 import sys
 from typing import Any, Callable, Dict, List, Optional, Tuple
-import functools
 
 
 def get_keywords() -> Dict[str, str]:

semantikon/converter.py

@@ -2,17 +2,18 @@
 # Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
 # Distributed under the terms of "New BSD License", see the LICENSE file.
 
-from pint import Quantity
 import inspect
+import sys
 from functools import wraps
+from typing import get_args, get_origin, get_type_hints
+
+from pint import Quantity
 from pint.registry_helpers import (
     _apply_defaults,
     _parse_wrap_args,
-    _to_units_container,
     _replace_units,
+    _to_units_container,
 )
-from typing import get_origin, get_args, get_type_hints
-import sys
 
 __author__ = "Sam Waseda"
 __copyright__ = (

semantikon/ontology.py

@@ -1,11 +1,12 @@
-from typing import TypeAlias, Any
 import warnings
-
-from rdflib import Graph, Literal, RDF, RDFS, URIRef, OWL, PROV, Namespace, BNode, SH
 from dataclasses import is_dataclass
-from semantikon.converter import meta_to_dict, get_function_dict
-from semantikon.qudt import UnitsDict
+from typing import Any, TypeAlias
+
 from owlrl import DeductiveClosure, OWLRL_Semantics
+from rdflib import OWL, PROV, RDF, RDFS, SH, BNode, Graph, Literal, Namespace, URIRef
+
+from semantikon.converter import get_function_dict, meta_to_dict
+from semantikon.qudt import UnitsDict
 
 
 class SNS:
@@ -267,7 +268,7 @@ def _validate_values_by_python(graph: Graph) -> list:
         if on_property and some_values_from:
             for cls in graph.subjects(OWL.equivalentClass, restrictions):
                 for instance in graph.subjects(RDF.type, cls):
-                    if not (instance, on_property, some_values_from) in graph:
+                    if (instance, on_property, some_values_from) not in graph:
                         missing_triples.append(
                             (instance, on_property, some_values_from)
                         )

semantikon/qudt.py

@@ -1,9 +1,8 @@
 import os
-from rdflib import Graph, RDFS, URIRef
-from pint import UnitRegistry
-from pint.errors import UndefinedUnitError, OffsetUnitCalculusError, DimensionalityError
-from tokenize import TokenError
+
 import requests
+from pint import UnitRegistry
+from rdflib import RDFS, Graph, URIRef
 
 
 def _is_english_label(pred, obj):

semantikon/typing.py

@@ -1,4 +1,5 @@
 from typing import Annotated, get_origin
+
 from semantikon.converter import parse_metadata
 
 __author__ = "Sam Waseda"

semantikon/visualize.py

@@ -1,7 +1,8 @@
-from rdflib import RDF, URIRef, Literal, BNode
-from graphviz import Digraph
 from string import Template
 
+from graphviz import Digraph
+from rdflib import RDF, BNode, Literal, URIRef
+
 from semantikon.ontology import SNS
 
 

semantikon/workflow.py

@@ -1,12 +1,13 @@
 import ast
-import networkx as nx
-from networkx.algorithms.dag import topological_sort
+import copy
 import inspect
+import warnings
 from collections import deque
 from functools import cached_property
-import warnings
 from hashlib import sha256
-import copy
+
+import networkx as nx
+from networkx.algorithms.dag import topological_sort
 
 from semantikon.converter import parse_input_args, parse_output_args
 

setup.py

@@ -1,6 +1,5 @@
-from setuptools import setup
-
 import versioneer
+from setuptools import setup
 
 setup(
     version=versioneer.get_version(),

tests/unit/test_dataclass.py

@@ -1,8 +1,9 @@
 import unittest
-from semantikon.typing import u
-from typing import Annotated
 from dataclasses import dataclass
-from semantikon.converter import semantikon_class, parse_metadata
+from typing import Annotated
+
+from semantikon.converter import parse_metadata, semantikon_class
+from semantikon.typing import u
 
 
 @semantikon_class

tests/unit/test_ontology.py

@@ -1,30 +1,23 @@
 import unittest
+from dataclasses import dataclass
 from textwrap import dedent
-from rdflib import Graph, OWL, Namespace, URIRef, Literal, RDF, RDFS, SH, PROV
-from owlrl import DeductiveClosure, OWLRL_Semantics
-from pyshacl import validate
+
 from graphviz import Digraph
-from semantikon.typing import u
-from semantikon.converter import (
-    parse_input_args,
-    parse_output_args,
-    parse_metadata,
-    get_function_dict,
-)
+from pyshacl import validate
+from rdflib import OWL, PROV, RDF, RDFS, SH, Literal, Namespace, URIRef
+
 from semantikon.ontology import (
-    get_knowledge_graph,
+    NS,
     SNS,
-    _inherit_properties,
-    validate_values,
+    _parse_cancel,
     dataclass_to_knowledge_graph,
+    get_knowledge_graph,
     serialize_data,
-    _parse_cancel,
-    NS,
+    validate_values,
 )
-from semantikon.workflow import workflow, separate_types, separate_functions
+from semantikon.typing import u
 from semantikon.visualize import visualize
-from dataclasses import dataclass
-
+from semantikon.workflow import workflow
 
 EX = Namespace("http://example.org/")
 
@@ -537,7 +530,6 @@ def test_dataclass(self):
             (URIRef(f"{i_txt}.parameters.a.value"), RDF.value, Literal(2)),
             (URIRef(o_txt), SNS.hasValue, URIRef(f"{o_txt}.E.value")),
         )
-        s = graph.serialize(format="turtle")
         for ii, triple in enumerate(triples):
             with self.subTest(i=ii):
                 self.assertEqual(

tests/unit/test_parsers.py

@@ -1,11 +1,18 @@
 import unittest
-from semantikon.typing import u
+from typing import TYPE_CHECKING
+
 from semantikon.converter import (
+    get_function_dict,
     parse_input_args,
-    parse_output_args,
     parse_metadata,
-    get_function_dict,
+    parse_output_args,
 )
+from semantikon.typing import u
+
+if TYPE_CHECKING:
+
+    class Atoms:
+        pass
 
 
 class TestParser(unittest.TestCase):
@@ -114,13 +121,15 @@ def get_speed_multiple_args(
                 return distance / time
             else:
                 return distance / duration
+
         input_args = parse_input_args(get_speed_multiple_args)
         for value, key in zip(input_args.values(), ["meter", "second", "second"]):
             self.assertEqual(value["units"], key)
 
     def test_future(self):
         def test_another_future(x: "Atoms", y: "u(float, units='second')") -> "Atoms":
             return x
+
         input_args = parse_input_args(test_another_future)
         self.assertEqual(input_args["x"]["dtype"], "Atoms")
         self.assertIn("units", input_args["y"])

tests/unit/test_qudt.py

@@ -1,4 +1,5 @@
 import unittest
+
 from semantikon.qudt import UnitsDict
 
 

tests/unit/test_tests.py

@@ -1,4 +1,5 @@
 import unittest
+
 import semantikon
 
 

tests/unit/test_units.py

@@ -1,8 +1,10 @@
 import unittest
-from semantikon.typing import u
-from semantikon.converter import units
+
 from pint import UnitRegistry
 
+from semantikon.converter import units
+from semantikon.typing import u
+
 
 @units
 def get_speed_multiple_outputs(

tests/unit/test_workflow.py

@@ -1,18 +1,17 @@
 import unittest
+
 from semantikon.typing import u
 from semantikon.workflow import (
-    analyze_function,
-    get_return_variables,
     _get_output_counts,
-    get_workflow_dict,
-    workflow,
+    analyze_function,
     find_parallel_execution_levels,
     get_node_dict,
-    separate_types,
+    get_return_variables,
+    get_workflow_dict,
     separate_functions,
+    separate_types,
+    workflow,
 )
-import numpy as np
-import json
 
 
 def operation(x: float, y: float) -> tuple[float, float]: