Boost max testing version to 3.12

.travis.yml

@@ -1,15 +1,21 @@
 language: python
-dist: bionic
+dist: focal
 python:
 - '3.8'
 - '3.9'
 - '3.10'
 - '3.11'
+- '3.12'
 env:
-  - UPGRADES="-U pint pandas"
+  - UPGRADES="-U --only-binary 'pint,pandas' pint pandas"
   - UPGRADES=""
+jobs:
+  exclude:
+    - python: '3.12'
+      env: UPGRADES=""
 install:
   - pip install --only-binary ':all:' -r requirements.txt
+  - test $TRAVIS_PYTHON_VERSION != "3.12" || perl -pi -E 's/^.*(?:pandas|flake8-docstrings).*$//' test_requirements.txt
   - pip install --only-binary ':all:' -r test_requirements.txt
   - pip install $UPGRADES -e .
 script:

gemd/demo/strehlow_and_cook.py

@@ -289,15 +289,15 @@ def real_mapper(prop):
                         template = tmpl[name_map[attr['name']]]
 
                 # Move into GEMD structure
-                if type(template) == PropertyTemplate:
+                if isinstance(template, PropertyTemplate):
                     msr.properties.append(
                         Property(name=template.name,
                                  template=template,
                                  value=content_map[type(template.bounds)](attr),
                                  origin=origin,
                                  notes=method
                                  ))
-                elif type(template) == ConditionTemplate:
+                elif isinstance(template, ConditionTemplate):
                     msr.conditions.append(
                         Condition(name=template.name,
                                   template=template,

gemd/entity/base_entity.py

@@ -100,7 +100,7 @@ def to_link(self,
 
         return LinkByUID(scope=scope, id=uid)
 
-    def all_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:
+    def all_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:  # noqa: F821
         """Return a set of all immediate dependencies (no recursion)."""
         result = set()
         queue = [type(self)]

gemd/entity/bounds/base_bounds.py

@@ -9,7 +9,7 @@ class BaseBounds(DictSerializable):
     """Base class for bounds, including RealBounds and CategoricalBounds."""
 
     @abstractmethod
-    def contains(self, bounds: Union["BaseBounds", "BaseValue"]):
+    def contains(self, bounds: Union["BaseBounds", "BaseValue"]):  # noqa: F821
         """
         Check if another bounds is contained within this bounds.
 
@@ -36,7 +36,7 @@ def contains(self, bounds: Union["BaseBounds", "BaseValue"]):
         raise TypeError('{} is not a Bounds object'.format(bounds))
 
     @abstractmethod
-    def union(self, *others: Union["BaseBounds", "BaseValue"]) -> "BaseBounds":
+    def union(self, *others: Union["BaseBounds", "BaseValue"]) -> "BaseBounds":  # noqa: F821
         """
         Return the union of this bounds and other bounds.
 
@@ -56,7 +56,7 @@ def union(self, *others: Union["BaseBounds", "BaseValue"]) -> "BaseBounds":
         pass  # pragma: no cover
 
     @abstractmethod
-    def update(self, *others: Union["BaseBounds", "BaseValue"]):
+    def update(self, *others: Union["BaseBounds", "BaseValue"]):  # noqa: F821
         """
         Update this bounds to include other bounds.
 

gemd/entity/bounds/categorical_bounds.py

@@ -39,7 +39,7 @@ def categories(self, categories: Optional[Iterable[str]]):
         if not all(isinstance(x, str) for x in self.categories):
             raise ValueError("All the categories must be strings")
 
-    def contains(self, bounds: Union[BaseBounds, "BaseValue"]) -> bool:
+    def contains(self, bounds: Union[BaseBounds, "BaseValue"]) -> bool:  # noqa: F821
         """
         Check if another bounds object or value objects is contained by this bounds.
 
@@ -69,8 +69,8 @@ def contains(self, bounds: Union[BaseBounds, "BaseValue"]) -> bool:
         return bounds.categories.issubset(self.categories)
 
     def union(self,
-              *others: Union["CategoricalBounds", "CategoricalValue"]
-              ) -> "CategoricalBounds":
+              *others: Union["CategoricalBounds", "CategoricalValue"]  # noqa: F821
+              ) -> "CategoricalBounds":  # noqa: F821
         """
         Return the union of this bounds and other bounds.
 
@@ -102,7 +102,7 @@ def union(self,
             result.update(bounds.categories)
         return CategoricalBounds(result)
 
-    def update(self, *others: Union["CategoricalBounds", "CategoricalValue"]):
+    def update(self, *others: Union["CategoricalBounds", "CategoricalValue"]):  # noqa: F821
         """
         Update this bounds to include other bounds.
 

gemd/entity/bounds/composition_bounds.py

@@ -39,7 +39,7 @@ def components(self, value):
         if not all(isinstance(x, str) for x in self.components):
             raise ValueError("All the components must be strings")
 
-    def contains(self, bounds: Union[BaseBounds, "BaseValue"]) -> bool:
+    def contains(self, bounds: Union[BaseBounds, "BaseValue"]) -> bool:  # noqa: F821
         """
         Check if another bounds or value object is contained by this bounds.
 
@@ -69,8 +69,8 @@ def contains(self, bounds: Union[BaseBounds, "BaseValue"]) -> bool:
         return bounds.components.issubset(self.components)
 
     def union(self,
-              *others: Union["CompositionBounds", "CompositionValue"]
-              ) -> "CompositionBounds":
+              *others: Union["CompositionBounds", "CompositionValue"]  # noqa: F821
+              ) -> "CompositionBounds":  # noqa: F821
         """
         Return the union of this bounds and other bounds.
 
@@ -102,7 +102,7 @@ def union(self,
             result.update(bounds.components)
         return CompositionBounds(result)
 
-    def update(self, *others: Union["CompositionBounds", "CompositionValue"]):
+    def update(self, *others: Union["CompositionBounds", "CompositionValue"]):  # noqa: F821
         """
         Update this bounds to include other bounds.
 

gemd/entity/bounds/integer_bounds.py

@@ -30,7 +30,7 @@ def __init__(self, lower_bound=None, upper_bound=None):
         if self.upper_bound < self.lower_bound:
             raise ValueError("Upper bound must be greater than or equal to lower bound")
 
-    def contains(self, bounds: Union[BaseBounds, "BaseValue"]) -> bool:
+    def contains(self, bounds: Union[BaseBounds, "BaseValue"]) -> bool:  # noqa: F821
         """
         Check if another bounds or value object is a subset of this range.
 
@@ -59,7 +59,9 @@ def contains(self, bounds: Union[BaseBounds, "BaseValue"]) -> bool:
 
         return bounds.lower_bound >= self.lower_bound and bounds.upper_bound <= self.upper_bound
 
-    def union(self, *others: Union["IntegerBounds", "IntegerValue"]) -> "IntegerBounds":
+    def union(self,
+              *others: Union["IntegerBounds", "IntegerValue"]  # noqa: F821
+              ) -> "IntegerBounds":  # noqa: F821
         """
         Return the union of this bounds and other bounds.
 
@@ -94,7 +96,7 @@ def union(self, *others: Union["IntegerBounds", "IntegerValue"]) -> "IntegerBoun
                 upper = bounds.upper_bound
         return IntegerBounds(lower_bound=lower, upper_bound=upper)
 
-    def update(self, *others: Union["IntegerBounds", "IntegerValue"]):
+    def update(self, *others: Union["IntegerBounds", "IntegerValue"]):  # noqa: F821
         """
         Update this bounds to include other bounds.
 

gemd/entity/bounds/molecular_structure_bounds.py

@@ -11,7 +11,7 @@
 class MolecularStructureBounds(BaseBounds, typ="molecular_structure_bounds"):
     """Molecular bounds, with no component or substructural restrictions (yet)."""
 
-    def contains(self, bounds: Union[BaseBounds, "BaseValue"]) -> bool:
+    def contains(self, bounds: Union[BaseBounds, "BaseValue"]) -> bool:  # noqa: F821
         """
         Check if another bounds or value object is contained by this bounds.
 
@@ -41,8 +41,8 @@ def contains(self, bounds: Union[BaseBounds, "BaseValue"]) -> bool:
         return True
 
     def union(self,
-              *others: Union["MolecularStructureBounds", "MolecularValue"]
-              ) -> "MolecularStructureBounds":
+              *others: Union["MolecularStructureBounds", "MolecularValue"]  # noqa: F821
+              ) -> "MolecularStructureBounds":  # noqa: F821
         """
         Return the union of this bounds and other bounds.
 
@@ -69,7 +69,7 @@ def union(self,
                             f"expected molecular structure, found {misses}")
         return MolecularStructureBounds()
 
-    def update(self, *others: Union["MolecularStructureBounds", "MolecularValue"]):
+    def update(self, *others: Union["MolecularStructureBounds", "MolecularValue"]):  # noqa: F821
         """
         Update this bounds to include other bounds.
 

gemd/entity/bounds/real_bounds.py

@@ -49,7 +49,7 @@ def default_units(self, default_units):
                              "Use an empty string for a dimensionless quantity.")
         self._default_units = units.parse_units(default_units)
 
-    def contains(self, bounds: Union[BaseBounds, "BaseValue"]) -> bool:
+    def contains(self, bounds: Union[BaseBounds, "BaseValue"]) -> bool:  # noqa: F821
         """
         Check if another bounds or value object is a subset of this range.
 
@@ -84,7 +84,7 @@ def contains(self, bounds: Union[BaseBounds, "BaseValue"]) -> bool:
 
         return bounds.lower_bound >= lower and bounds.upper_bound <= upper
 
-    def union(self, *others: Union["RealBounds", "ContinuousValue"]) -> "RealBounds":
+    def union(self, *others: Union["RealBounds", "ContinuousValue"]) -> "RealBounds":  # noqa: F821
         """
         Return the union of this bounds and other bounds.
 
@@ -123,7 +123,7 @@ def union(self, *others: Union["RealBounds", "ContinuousValue"]) -> "RealBounds"
                 upper = bnd_hi
         return RealBounds(lower_bound=lower, upper_bound=upper, default_units=unit_)
 
-    def update(self, *others: Union["RealBounds", "ContinuousValue"]):
+    def update(self, *others: Union["RealBounds", "ContinuousValue"]):  # noqa: F821
         """
         Update this bounds to include other bounds.
 

gemd/entity/dict_serializable.py

@@ -18,9 +18,9 @@ class DictSerializableMeta(ABCMeta):
 
     _class: Dict[str, type] = {}
 
-    def __new__(mcs, name, bases, *args,
+    def __new__(mcs, name, bases, *args,  # noqa: D102
                 typ: str = None, skip: Set[str] = frozenset(),
-                **kwargs):  # noqa: D102
+                **kwargs):
         return super().__new__(mcs, name, bases, *args, **kwargs)
 
     def __init__(cls, name, bases, *args, typ: str = None, skip: Set[str] = frozenset(), **kwargs):

gemd/entity/has_dependencies.py

@@ -7,5 +7,5 @@ class HasDependencies(ABC):
     """Mix-in trait for objects that reference other objects."""
 
     @abstractmethod
-    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:
+    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:  # noqa: F821
         """All dependencies (objects) that this class introduces."""

gemd/entity/object/has_conditions.py

@@ -34,6 +34,6 @@ def conditions(self, conditions: Union[Condition, Iterable[Condition]]):
         checker = self._generate_template_check(HasConditionTemplates.validate_condition)
         self._conditions = validate_list(conditions, Condition, trigger=checker)
 
-    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:
+    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:  # noqa: F821
         """Return a set of all immediate dependencies (no recursion)."""
         return {cond.template for cond in self.conditions if cond.template is not None}

gemd/entity/object/has_material.py

@@ -20,6 +20,6 @@ def material(self) -> Union[BaseObject, LinkByUID]:
     def material(self, spec: Union[BaseObject, LinkByUID]):
         """Set the material."""
 
-    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:
+    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:  # noqa: F821
         """Return a set of all immediate dependencies (no recursion)."""
         return {self.material} if self.material is not None else set()

gemd/entity/object/has_parameters.py

@@ -34,6 +34,6 @@ def parameters(self, parameters: Union[Parameter, Iterable[Parameter]]):
         checker = self._generate_template_check(HasParameterTemplates.validate_parameter)
         self._parameters = validate_list(parameters, Parameter, trigger=checker)
 
-    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:
+    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:  # noqa: F821
         """Return a set of all immediate dependencies (no recursion)."""
         return {param.template for param in self.parameters if param.template is not None}

gemd/entity/object/has_process.py

@@ -20,6 +20,6 @@ def process(self) -> Union[BaseObject, LinkByUID]:
     def process(self, process: Union[BaseObject, LinkByUID]):
         """Set the process."""
 
-    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:
+    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:  # noqa: F821
         """Return a set of all immediate dependencies (no recursion)."""
         return {self.process} if self.process is not None else set()

gemd/entity/object/has_properties.py

@@ -34,6 +34,6 @@ def properties(self, properties: Union[Property, Iterable[Property]]):
         checker = self._generate_template_check(HasPropertyTemplates.validate_property)
         self._properties = validate_list(properties, Property, trigger=checker)
 
-    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:
+    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:  # noqa: F821
         """Return a set of all immediate dependencies (no recursion)."""
         return {prop.template for prop in self.properties if prop.template is not None}

gemd/entity/object/has_spec.py

@@ -51,6 +51,6 @@ def template(self) -> Optional[Union[BaseTemplate, LinkByUID]]:
         else:
             return None
 
-    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:
+    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:  # noqa: F821
         """Return a set of all immediate dependencies (no recursion)."""
         return {self.spec} if self.spec is not None else set()

gemd/entity/object/has_template.py

@@ -42,6 +42,6 @@ def template(self, template: Optional[Union[BaseTemplate, LinkByUID]]):
             raise TypeError(f"Template must be a {self._template_type()} or LinkByUID, "
                             f"not {type(template)}")
 
-    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:
+    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:  # noqa: F821
         """Return a set of all immediate dependencies (no recursion)."""
         return {self.template} if self.template is not None else set()

gemd/entity/object/material_run.py

@@ -91,7 +91,7 @@ def process(self, process: Union[ProcessRun, LinkByUID]):
             raise TypeError("process must be a ProcessRun or LinkByUID: {}".format(process))
 
     @property
-    def measurements(self) -> List["MeasurementRun"]:
+    def measurements(self) -> List["MeasurementRun"]:  # noqa: F821
         """Get a read-only list of the measurement runs."""
         return self._measurements
 

gemd/entity/object/process_run.py

@@ -86,12 +86,12 @@ def __init__(self,
         self._output_material = None
 
     @property
-    def output_material(self) -> Optional["MaterialRun"]:
+    def output_material(self) -> Optional["MaterialRun"]:  # noqa: F821
         """Get the output material run."""
         return self._output_material
 
     @property
-    def ingredients(self) -> List["IngredientRun"]:
+    def ingredients(self) -> List["IngredientRun"]:  # noqa: F821
         """Get the input ingredient runs."""
         return self._ingredients
 

gemd/entity/object/process_spec.py

@@ -90,7 +90,7 @@ def _template_type() -> Type:
         return ProcessTemplate
 
     @property
-    def ingredients(self) -> List["IngredientSpec"]:
+    def ingredients(self) -> List["IngredientSpec"]:  # noqa: F821
         """Get the list of input ingredient specs."""
         return self._ingredients
 

gemd/entity/template/has_condition_templates.py

@@ -83,6 +83,6 @@ def validate_condition(self, condition: "Condition") -> bool:  # noqa: F821
         else:
             return True  # Nothing to check against
 
-    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:
+    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:  # noqa: F821
         """Return a set of all immediate dependencies (no recursion)."""
         return {attr[0] for attr in self.conditions}

gemd/entity/template/has_parameter_templates.py

@@ -83,6 +83,6 @@ def validate_parameter(self, parameter: "Parameter") -> bool:  # noqa: F821
         else:
             return True  # Nothing to check against
 
-    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:
+    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:  # noqa: F821
         """Return a set of all immediate dependencies (no recursion)."""
         return {attr[0] for attr in self.parameters}

gemd/entity/template/has_property_templates.py

@@ -63,7 +63,9 @@ def properties(self, properties: Iterable[Union[Union[PropertyTemplate, LinkByUI
                                          trigger=BaseTemplate._homogenize_ranges
                                          )
 
-    def validate_property(self, prop: Union["Property", "PropertyAndConditions"]) -> bool:
+    def validate_property(self,
+                          prop: Union["Property", "PropertyAndConditions"]  # noqa: F821
+                          ) -> bool:  # noqa: F821
         """Check if the property is consistent w/ this template."""
         from gemd.entity.attribute import PropertyAndConditions
         if isinstance(prop, PropertyAndConditions):
@@ -83,6 +85,6 @@ def validate_property(self, prop: Union["Property", "PropertyAndConditions"]) ->
         else:
             return True  # Nothing to check against
 
-    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:
+    def _local_dependencies(self) -> Set[Union["BaseEntity", "LinkByUID"]]:  # noqa: F821
         """Return a set of all immediate dependencies (no recursion)."""
         return {attr[0] for attr in self.properties}

gemd/util/impl.py

@@ -338,7 +338,7 @@ def substitute_objects(obj,
         method = _substitute
 
     return method(obj,
-                  sub=lambda l: index.get(l, l),
+                  sub=lambda link: index.get(link, link),
                   applies=lambda o: cached_isinstance(o, LinkByUID))
 
 

setup.py

@@ -4,7 +4,7 @@
 packages.append("")
 
 setup(name='gemd',
-      version='1.16.8',
+      version='1.16.9',
       python_requires='>=3.8',
       url='http://github.com/CitrineInformatics/gemd-python',
       description="Python binding for Citrine's GEMD data model",
@@ -43,5 +43,6 @@
           'Programming Language :: Python :: 3.9',
           'Programming Language :: Python :: 3.10',
           'Programming Language :: Python :: 3.11',
+          'Programming Language :: Python :: 3.12',
       ],
       )

test_requirements.txt

@@ -1,5 +1,5 @@
-flake8==3.7.8
-flake8-docstrings==1.3.1
+flake8==6.1.0
+flake8-docstrings==1.7.0
 pytest==7.3.1
 pytest-cov==4.0.0
 pandas==1.5.0