From 7754655a075440da4e46307f2e401b25512d8bb5 Mon Sep 17 00:00:00 2001
From: Ken Kroenlein <kkroenlein@citrine.io>
Date: Mon, 18 Dec 2023 06:59:34 -0700
Subject: [PATCH 01/10] Boost max testing version to 3.12

---
 .travis.yml | 3 ++-
 setup.py    | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index a608294d..8330fa6e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,10 +1,11 @@
 language: python
-dist: bionic
+dist: jammy
 python:
 - '3.8'
 - '3.9'
 - '3.10'
 - '3.11'
+- '3.12'
 env:
   - UPGRADES="-U pint pandas"
   - UPGRADES=""
diff --git a/setup.py b/setup.py
index b753863c..8159dd1e 100644
--- a/setup.py
+++ b/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',
       ],
       )

From 55e930f216e212a3e4d179e54320ccfd1a94ca9c Mon Sep 17 00:00:00 2001
From: Ken Kroenlein <kkroenlein@citrine.io>
Date: Mon, 18 Dec 2023 07:14:17 -0700
Subject: [PATCH 02/10] Correct minimum Pandas version in testing

---
 test_requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test_requirements.txt b/test_requirements.txt
index 4264feee..23cab842 100644
--- a/test_requirements.txt
+++ b/test_requirements.txt
@@ -2,7 +2,7 @@ flake8==3.7.8
 flake8-docstrings==1.3.1
 pytest==7.3.1
 pytest-cov==4.0.0
-pandas==1.5.0
+pandas==1.5.3
 toolz==0.12.0
 derp==0.1.1
 sphinx==4.3.0

From 9c49dddecf6335564233f5d39c1c00f4f525fc49 Mon Sep 17 00:00:00 2001
From: Ken Kroenlein <kkroenlein@citrine.io>
Date: Mon, 18 Dec 2023 07:29:23 -0700
Subject: [PATCH 03/10] Swap from Jammy to Focal because of Python 3.10 version

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 8330fa6e..f03d9a9a 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,5 +1,5 @@
 language: python
-dist: jammy
+dist: focal
 python:
 - '3.8'
 - '3.9'

From dc85d903c947bb7b660cdb0df2c3bc05ac0c2d32 Mon Sep 17 00:00:00 2001
From: Ken Kroenlein <kkroenlein@citrine.io>
Date: Mon, 18 Dec 2023 08:20:52 -0700
Subject: [PATCH 04/10] Skip low-version build w/ 3.12 (pandas issues)

---
 .travis.yml           | 7 ++++++-
 test_requirements.txt | 2 +-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index f03d9a9a..9f917901 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -9,10 +9,15 @@ python:
 env:
   - UPGRADES="-U pint pandas"
   - UPGRADES=""
+jobs:
+  exclude:
+    - python: '3.12'
+      env: UPGRADES=""
 install:
   - pip install --only-binary ':all:' -r requirements.txt
+  - test $TRAVIS_PYTHON_VERSION == "3.12" || perl -pi -E 's/^.*pandas.*$//' test_requirements.txt
   - pip install --only-binary ':all:' -r test_requirements.txt
-  - pip install $UPGRADES -e .
+  - pip install $UPGRADES -e .d
 script:
 - bash scripts/run_tests.sh
 - test "$UPGRADES" != "" || test $TRAVIS_PYTHON_VERSION != "3.10" || bash scripts/build_docs.sh
diff --git a/test_requirements.txt b/test_requirements.txt
index 23cab842..3a3eebe3 100644
--- a/test_requirements.txt
+++ b/test_requirements.txt
@@ -2,7 +2,7 @@ flake8==3.7.8
 flake8-docstrings==1.3.1
 pytest==7.3.1
 pytest-cov==4.0.0
-pandas==1.5.3
+
 toolz==0.12.0
 derp==0.1.1
 sphinx==4.3.0

From 2d8603cd91598a813701c2fe1b0ff1315f4d3684 Mon Sep 17 00:00:00 2001
From: Ken Kroenlein <kkroenlein@citrine.io>
Date: Mon, 18 Dec 2023 08:26:03 -0700
Subject: [PATCH 05/10] Enforce that upgraded libraries are still binaries

---
 .travis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 9f917901..c1450e5f 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,7 +7,7 @@ python:
 - '3.11'
 - '3.12'
 env:
-  - UPGRADES="-U pint pandas"
+  - UPGRADES="-U '--only-binary=pint,pandas' pint pandas"
   - UPGRADES=""
 jobs:
   exclude:
@@ -17,7 +17,7 @@ install:
   - pip install --only-binary ':all:' -r requirements.txt
   - test $TRAVIS_PYTHON_VERSION == "3.12" || perl -pi -E 's/^.*pandas.*$//' test_requirements.txt
   - pip install --only-binary ':all:' -r test_requirements.txt
-  - pip install $UPGRADES -e .d
+  - pip install $UPGRADES -e .
 script:
 - bash scripts/run_tests.sh
 - test "$UPGRADES" != "" || test $TRAVIS_PYTHON_VERSION != "3.10" || bash scripts/build_docs.sh

From add7f50c7526e7d62b26f99c39e361d4a90780c4 Mon Sep 17 00:00:00 2001
From: Ken Kroenlein <kkroenlein@citrine.io>
Date: Mon, 18 Dec 2023 08:33:27 -0700
Subject: [PATCH 06/10] Correct typo

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index c1450e5f..db1f067a 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,7 +7,7 @@ python:
 - '3.11'
 - '3.12'
 env:
-  - UPGRADES="-U '--only-binary=pint,pandas' pint pandas"
+  - UPGRADES="-U '--only-binary==pint,pandas' pint pandas"
   - UPGRADES=""
 jobs:
   exclude:

From 6fdfe997028560b4529eba3dbec0c57fa1ebaa46 Mon Sep 17 00:00:00 2001
From: Ken Kroenlein <kkroenlein@citrine.io>
Date: Mon, 18 Dec 2023 08:38:33 -0700
Subject: [PATCH 07/10] Correct typo

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index db1f067a..95fbc4e5 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,7 +7,7 @@ python:
 - '3.11'
 - '3.12'
 env:
-  - UPGRADES="-U '--only-binary==pint,pandas' pint pandas"
+  - UPGRADES="-U --only-binary 'pint,pandas' pint pandas"
   - UPGRADES=""
 jobs:
   exclude:

From ea38da8a28559e2affcc8ba52180631f2568b6e1 Mon Sep 17 00:00:00 2001
From: Ken Kroenlein <kkroenlein@citrine.io>
Date: Mon, 18 Dec 2023 10:18:36 -0700
Subject: [PATCH 08/10] travis configuration

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 95fbc4e5..f0609cbb 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -15,7 +15,7 @@ jobs:
       env: UPGRADES=""
 install:
   - pip install --only-binary ':all:' -r requirements.txt
-  - test $TRAVIS_PYTHON_VERSION == "3.12" || perl -pi -E 's/^.*pandas.*$//' test_requirements.txt
+  - test $TRAVIS_PYTHON_VERSION != "3.12" || perl -pi -E 's/^.*pandas.*$//' test_requirements.txt
   - pip install --only-binary ':all:' -r test_requirements.txt
   - pip install $UPGRADES -e .
 script:

From e2141e620eef998c2bc2bbd9f4cbd67d4a209085 Mon Sep 17 00:00:00 2001
From: Ken Kroenlein <kkroenlein@citrine.io>
Date: Mon, 18 Dec 2023 10:27:53 -0700
Subject: [PATCH 09/10] Repair test_requirements.txt

---
 test_requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test_requirements.txt b/test_requirements.txt
index 3a3eebe3..4264feee 100644
--- a/test_requirements.txt
+++ b/test_requirements.txt
@@ -2,7 +2,7 @@ flake8==3.7.8
 flake8-docstrings==1.3.1
 pytest==7.3.1
 pytest-cov==4.0.0
-
+pandas==1.5.0
 toolz==0.12.0
 derp==0.1.1
 sphinx==4.3.0

From 94b3f5833afdf561c55cfb20ae7982d9438c5ad6 Mon Sep 17 00:00:00 2001
From: Ken Kroenlein <kkroenlein@citrine.io>
Date: Mon, 18 Dec 2023 15:02:54 -0700
Subject: [PATCH 10/10] Upgrade flake8 for python 3.12 support

---
 .travis.yml                                      | 2 +-
 gemd/demo/strehlow_and_cook.py                   | 4 ++--
 gemd/entity/base_entity.py                       | 2 +-
 gemd/entity/bounds/base_bounds.py                | 6 +++---
 gemd/entity/bounds/categorical_bounds.py         | 8 ++++----
 gemd/entity/bounds/composition_bounds.py         | 8 ++++----
 gemd/entity/bounds/integer_bounds.py             | 8 +++++---
 gemd/entity/bounds/molecular_structure_bounds.py | 8 ++++----
 gemd/entity/bounds/real_bounds.py                | 6 +++---
 gemd/entity/dict_serializable.py                 | 4 ++--
 gemd/entity/has_dependencies.py                  | 2 +-
 gemd/entity/object/has_conditions.py             | 2 +-
 gemd/entity/object/has_material.py               | 2 +-
 gemd/entity/object/has_parameters.py             | 2 +-
 gemd/entity/object/has_process.py                | 2 +-
 gemd/entity/object/has_properties.py             | 2 +-
 gemd/entity/object/has_spec.py                   | 2 +-
 gemd/entity/object/has_template.py               | 2 +-
 gemd/entity/object/material_run.py               | 2 +-
 gemd/entity/object/process_run.py                | 4 ++--
 gemd/entity/object/process_spec.py               | 2 +-
 gemd/entity/template/has_condition_templates.py  | 2 +-
 gemd/entity/template/has_parameter_templates.py  | 2 +-
 gemd/entity/template/has_property_templates.py   | 6 ++++--
 gemd/util/impl.py                                | 2 +-
 test_requirements.txt                            | 4 ++--
 26 files changed, 50 insertions(+), 46 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index f0609cbb..ab4cb1ea 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -15,7 +15,7 @@ jobs:
       env: UPGRADES=""
 install:
   - pip install --only-binary ':all:' -r requirements.txt
-  - test $TRAVIS_PYTHON_VERSION != "3.12" || perl -pi -E 's/^.*pandas.*$//' test_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:
diff --git a/gemd/demo/strehlow_and_cook.py b/gemd/demo/strehlow_and_cook.py
index e89d6f59..389b9ab9 100644
--- a/gemd/demo/strehlow_and_cook.py
+++ b/gemd/demo/strehlow_and_cook.py
@@ -289,7 +289,7 @@ 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,
@@ -297,7 +297,7 @@ def real_mapper(prop):
                                  origin=origin,
                                  notes=method
                                  ))
-                elif type(template) == ConditionTemplate:
+                elif isinstance(template, ConditionTemplate):
                     msr.conditions.append(
                         Condition(name=template.name,
                                   template=template,
diff --git a/gemd/entity/base_entity.py b/gemd/entity/base_entity.py
index 40a1bd23..c1d72289 100644
--- a/gemd/entity/base_entity.py
+++ b/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)]
diff --git a/gemd/entity/bounds/base_bounds.py b/gemd/entity/bounds/base_bounds.py
index 0453e817..fb6b4236 100644
--- a/gemd/entity/bounds/base_bounds.py
+++ b/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.
 
diff --git a/gemd/entity/bounds/categorical_bounds.py b/gemd/entity/bounds/categorical_bounds.py
index c2c8caa4..bad59205 100644
--- a/gemd/entity/bounds/categorical_bounds.py
+++ b/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.
 
diff --git a/gemd/entity/bounds/composition_bounds.py b/gemd/entity/bounds/composition_bounds.py
index e00de515..db399d5c 100644
--- a/gemd/entity/bounds/composition_bounds.py
+++ b/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.
 
diff --git a/gemd/entity/bounds/integer_bounds.py b/gemd/entity/bounds/integer_bounds.py
index 3f37f8c8..7c8f0ef3 100644
--- a/gemd/entity/bounds/integer_bounds.py
+++ b/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.
 
diff --git a/gemd/entity/bounds/molecular_structure_bounds.py b/gemd/entity/bounds/molecular_structure_bounds.py
index 43838c81..de08b369 100644
--- a/gemd/entity/bounds/molecular_structure_bounds.py
+++ b/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.
 
diff --git a/gemd/entity/bounds/real_bounds.py b/gemd/entity/bounds/real_bounds.py
index db8981e6..c49c9455 100644
--- a/gemd/entity/bounds/real_bounds.py
+++ b/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.
 
diff --git a/gemd/entity/dict_serializable.py b/gemd/entity/dict_serializable.py
index 0994222b..02ff6290 100644
--- a/gemd/entity/dict_serializable.py
+++ b/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):
diff --git a/gemd/entity/has_dependencies.py b/gemd/entity/has_dependencies.py
index 14ab166b..87b6f4e0 100644
--- a/gemd/entity/has_dependencies.py
+++ b/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."""
diff --git a/gemd/entity/object/has_conditions.py b/gemd/entity/object/has_conditions.py
index f37e3560..e0287407 100644
--- a/gemd/entity/object/has_conditions.py
+++ b/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}
diff --git a/gemd/entity/object/has_material.py b/gemd/entity/object/has_material.py
index 5ba58c7d..7a9d5f5b 100644
--- a/gemd/entity/object/has_material.py
+++ b/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()
diff --git a/gemd/entity/object/has_parameters.py b/gemd/entity/object/has_parameters.py
index d6168a42..28a18e67 100644
--- a/gemd/entity/object/has_parameters.py
+++ b/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}
diff --git a/gemd/entity/object/has_process.py b/gemd/entity/object/has_process.py
index 5f029483..d26b05d8 100644
--- a/gemd/entity/object/has_process.py
+++ b/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()
diff --git a/gemd/entity/object/has_properties.py b/gemd/entity/object/has_properties.py
index 307c4808..d247db9e 100644
--- a/gemd/entity/object/has_properties.py
+++ b/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}
diff --git a/gemd/entity/object/has_spec.py b/gemd/entity/object/has_spec.py
index 6e50cc53..d91ca213 100644
--- a/gemd/entity/object/has_spec.py
+++ b/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()
diff --git a/gemd/entity/object/has_template.py b/gemd/entity/object/has_template.py
index f69d684f..c968f9fa 100644
--- a/gemd/entity/object/has_template.py
+++ b/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()
diff --git a/gemd/entity/object/material_run.py b/gemd/entity/object/material_run.py
index 3531af0e..5d4a5348 100644
--- a/gemd/entity/object/material_run.py
+++ b/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
 
diff --git a/gemd/entity/object/process_run.py b/gemd/entity/object/process_run.py
index 47209d91..eb72cfca 100644
--- a/gemd/entity/object/process_run.py
+++ b/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
 
diff --git a/gemd/entity/object/process_spec.py b/gemd/entity/object/process_spec.py
index 2943ce84..ac5039ac 100644
--- a/gemd/entity/object/process_spec.py
+++ b/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
 
diff --git a/gemd/entity/template/has_condition_templates.py b/gemd/entity/template/has_condition_templates.py
index 98cc54c0..927b6795 100644
--- a/gemd/entity/template/has_condition_templates.py
+++ b/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}
diff --git a/gemd/entity/template/has_parameter_templates.py b/gemd/entity/template/has_parameter_templates.py
index 3d5f062e..29288b41 100644
--- a/gemd/entity/template/has_parameter_templates.py
+++ b/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}
diff --git a/gemd/entity/template/has_property_templates.py b/gemd/entity/template/has_property_templates.py
index 2e15cd89..5cb6810e 100644
--- a/gemd/entity/template/has_property_templates.py
+++ b/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}
diff --git a/gemd/util/impl.py b/gemd/util/impl.py
index b06c3862..64f64acb 100644
--- a/gemd/util/impl.py
+++ b/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))
 
 
diff --git a/test_requirements.txt b/test_requirements.txt
index 4264feee..8d88ee33 100644
--- a/test_requirements.txt
+++ b/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