From 41670f0663dd0286bb030354599acc9daf49716a Mon Sep 17 00:00:00 2001
From: Ryan Ly <rly@lbl.gov>
Date: Fri, 7 Feb 2025 22:41:44 -0800
Subject: [PATCH 01/14] Update ruff action

---
 .github/workflows/ruff.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml
index 1933fa75e..078a243cc 100644
--- a/.github/workflows/ruff.yml
+++ b/.github/workflows/ruff.yml
@@ -8,4 +8,4 @@ jobs:
       - name: Checkout repo
         uses: actions/checkout@v4
       - name: Run ruff
-        uses: chartboost/ruff-action@v1
+        uses: astral-sh/ruff-action@v1

From 61853c7fe2e11ef3615e00ca1f966df76193c85b Mon Sep 17 00:00:00 2001
From: Ryan Ly <rly@lbl.gov>
Date: Fri, 7 Feb 2025 22:47:29 -0800
Subject: [PATCH 02/14] Move min reqs testing info to pyproject.toml

---
 .github/PULL_REQUEST_TEMPLATE/release.md |  3 +--
 .github/dependabot.yml                   | 11 -----------
 docs/source/software_process.rst         |  6 +++---
 pyproject.toml                           | 24 ++++++++++++++++--------
 requirements-min.txt                     | 10 ----------
 tox.ini                                  |  4 +---
 6 files changed, 21 insertions(+), 37 deletions(-)
 delete mode 100644 requirements-min.txt

diff --git a/.github/PULL_REQUEST_TEMPLATE/release.md b/.github/PULL_REQUEST_TEMPLATE/release.md
index 82f987164..569c694da 100644
--- a/.github/PULL_REQUEST_TEMPLATE/release.md
+++ b/.github/PULL_REQUEST_TEMPLATE/release.md
@@ -2,8 +2,7 @@ Prepare for release of HDMF [version]
 
 ### Before merging:
 - [ ] Make sure all PRs to be included in this release have been merged to `dev`.
-- [ ] Major and minor releases: Update dependency ranges in `pyproject.toml` and minimums in
-  `requirements-min.txt` as needed.
+- [ ] Major and minor releases: Update dependency ranges in `pyproject.toml` as needed.
 - [ ] Check legal file dates and information in `Legal.txt`, `license.txt`, `README.rst`, `docs/source/conf.py`,
   and any other locations as needed
 - [ ] Update `pyproject.toml` as needed
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
index 24615639c..d202a332d 100644
--- a/.github/dependabot.yml
+++ b/.github/dependabot.yml
@@ -1,16 +1,5 @@
 version: 2
 updates:
-  # disable checking python requirements files because there are too
-  # many updates and dependabot will not ignore requirements-min.txt
-  # until https://github.com/dependabot/dependabot-core/issues/2883 is resolved
-  # workaround is to continue updating these files manually
-
-  # - package-ecosystem: "pip"
-  #   directory: "/"
-  #   schedule:
-  #     # Check for updates to requirements files and pyproject.toml every week
-  #     interval: "weekly"
-
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
diff --git a/docs/source/software_process.rst b/docs/source/software_process.rst
index f3a6c7457..bf765a062 100644
--- a/docs/source/software_process.rst
+++ b/docs/source/software_process.rst
@@ -45,8 +45,9 @@ pyproject.toml_ contains a list of package dependencies and their version ranges
 running HDMF. As a library, upper bound version constraints create more harm than good in the long term (see this
 `blog post`_) so we avoid setting upper bounds on requirements.
 
-When setting lower bounds, make sure to specify the lower bounds in both pyproject.toml_ and
-requirements-min.txt_. The latter is used in automated testing to ensure that the package runs
+When setting lower bounds, make sure to specify the lower bounds in the ``[project] dependencies`` key and 
+``[project.optional-dependencies] min-reqs`` key in pyproject.toml_. 
+The latter is used in automated testing to ensure that the package runs
 correctly using the minimum versions of dependencies.
 
 Minimum requirements should be updated manually if a new feature or bug fix is added in a dependency that is required
@@ -56,7 +57,6 @@ minimum version to be as high as it is.
 
 .. _pyproject.toml: https://github.com/hdmf-dev/hdmf/blob/dev/pyproject.toml
 .. _blog post: https://iscinumpy.dev/post/bound-version-constraints/
-.. _requirements-min.txt: https://github.com/hdmf-dev/hdmf/blob/dev/requirements-min.txt
 
 --------------------
 Testing Requirements
diff --git a/pyproject.toml b/pyproject.toml
index 5a58b6cef..7ccdfa2f2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -14,7 +14,7 @@ authors = [
 description = "A hierarchical data modeling framework for modern science data standards"
 readme = "README.rst"
 requires-python = ">=3.9"
-license = {text = "BSD-3-Clause"}
+license = "BSD-3-Clause"
 classifiers = [
     "Programming Language :: Python",
     "Programming Language :: Python :: 3.9",
@@ -29,6 +29,7 @@ classifiers = [
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: Medical Science Apps.",
 ]
+# make sure to update min-reqs dependencies below when these lower bounds change
 dependencies = [
     "h5py>=3.1.0",
     "jsonschema>=3.2.0",
@@ -39,6 +40,7 @@ dependencies = [
 dynamic = ["version"]
 
 [project.optional-dependencies]
+# make sure to update min-reqs dependencies below when these lower bounds change
 tqdm = ["tqdm>=4.41.0"]
 zarr = ["zarr>=2.12.0,<3"]
 sparse = ["scipy>=1.7"]
@@ -72,6 +74,18 @@ docs = [
 # all possible dependencies
 all = ["hdmf[tqdm,zarr,sparse,termset,test,docs]"]
 
+# minimum requirements of project dependencies for testing (see .github/workflows/run_all_tests.yml)
+min-reqs = [
+    "h5py==3.1.0",
+    "jsonschema==3.2.0",
+    "numpy==1.19.3",
+    "pandas==1.2.0",
+    "ruamel.yaml==0.16.0",
+    "scipy==1.7.0",
+    "tqdm==4.41.0",
+    "zarr==2.12.0",
+]
+
 [project.urls]
 "Homepage" = "https://github.com/hdmf-dev/hdmf"
 "Bug Tracker" = "https://github.com/hdmf-dev/hdmf/issues"
@@ -141,13 +155,8 @@ omit = [
 # force-exclude = "src/hdmf/common/hdmf-common-schema|docs/gallery"
 
 [tool.ruff]
-lint.select = ["E", "F", "T100", "T201", "T203"]
+lint.select = ["E", "F", "T100", "T201", "T203", "C901"]
 exclude = [
-  ".git",
-  ".tox",
-  "__pycache__",
-  "build/",
-  "dist/",
   "src/hdmf/common/hdmf-common-schema",
   "docs/source/conf.py",
   "src/hdmf/_due.py",
@@ -160,7 +169,6 @@ line-length = 120
 [tool.ruff.lint.per-file-ignores]
 "docs/gallery/*" = ["E402", "T201"]
 "src/*/__init__.py" = ["F401"]
-"setup.py" = ["T201"]
 "test_gallery.py" = ["T201"]
 
 [tool.ruff.lint.mccabe]
diff --git a/requirements-min.txt b/requirements-min.txt
deleted file mode 100644
index a9fbeb93e..000000000
--- a/requirements-min.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-# minimum versions of package dependencies for installing HDMF
-# NOTE: these should match the minimum bound for dependencies in pyproject.toml
-h5py==3.1.0
-jsonschema==3.2.0
-numpy==1.19.3
-pandas==1.2.0
-ruamel.yaml==0.16.0
-scipy==1.7.0
-tqdm==4.41.0
-zarr==2.12.0
diff --git a/tox.ini b/tox.ini
index 4caa68a4b..37171acb1 100644
--- a/tox.ini
+++ b/tox.ini
@@ -22,14 +22,12 @@ install_command =
     minimum, wheelinstall: python -I -m pip install {opts} {packages}
     upgraded:              python -I -m pip install -U {opts} {packages}
     prerelease:            python -I -m pip install -U --pre {opts} {packages}
-deps =
-    # which requirements files to use (default: none)
-    minimum:         -r requirements-min.txt
 extras =
     # which optional dependency set(s) to use (default: none)
     pytest:    test
     gallery:   doc
     optional:  tqdm,sparse,zarr,termset
+    minimum:   min-reqs
 commands =
     # commands to run for every environment
     python --version     # print python version for debugging

From 1d5322910dc82eff0a0d744a4351f413f338d886 Mon Sep 17 00:00:00 2001
From: Ryan Ly <rly@lbl.gov>
Date: Fri, 7 Feb 2025 22:47:49 -0800
Subject: [PATCH 03/14] Update github-app-token action

---
 .github/workflows/project_action.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/project_action.yml b/.github/workflows/project_action.yml
index 6037bd4ab..148d4d41d 100644
--- a/.github/workflows/project_action.yml
+++ b/.github/workflows/project_action.yml
@@ -12,10 +12,10 @@ jobs:
     steps:
       - name: GitHub App token
         id: generate_token
-        uses: tibdex/github-app-token@v2
+        uses: actions/create-github-app-token@v1
         with:
-          app_id: ${{ secrets.APP_ID }}
-          private_key: ${{ secrets.APP_PEM }}
+          app-id: ${{ secrets.APP_ID }}
+          private-key: ${{ secrets.APP_PEM }}
 
       - name: Add to Developer Board
         env:

From 59e60193814bc3e090a3d296937b03b9ffcd342d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 8 Feb 2025 07:08:47 +0000
Subject: [PATCH 04/14] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 docs/source/software_process.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/source/software_process.rst b/docs/source/software_process.rst
index bf765a062..96bf470e7 100644
--- a/docs/source/software_process.rst
+++ b/docs/source/software_process.rst
@@ -45,8 +45,8 @@ pyproject.toml_ contains a list of package dependencies and their version ranges
 running HDMF. As a library, upper bound version constraints create more harm than good in the long term (see this
 `blog post`_) so we avoid setting upper bounds on requirements.
 
-When setting lower bounds, make sure to specify the lower bounds in the ``[project] dependencies`` key and 
-``[project.optional-dependencies] min-reqs`` key in pyproject.toml_. 
+When setting lower bounds, make sure to specify the lower bounds in the ``[project] dependencies`` key and
+``[project.optional-dependencies] min-reqs`` key in pyproject.toml_.
 The latter is used in automated testing to ensure that the package runs
 correctly using the minimum versions of dependencies.
 

From 82294d80f1116e38c84f55994ec977e11e58ec4d Mon Sep 17 00:00:00 2001
From: Ryan Ly <rly@lbl.gov>
Date: Fri, 7 Feb 2025 23:37:54 -0800
Subject: [PATCH 05/14] Reduce complexity of DynamicTable.add_row

---
 src/hdmf/common/table.py | 52 +++++++++++++++++++++++-----------------
 1 file changed, 30 insertions(+), 22 deletions(-)

diff --git a/src/hdmf/common/table.py b/src/hdmf/common/table.py
index 2f6401672..d4697f487 100644
--- a/src/hdmf/common/table.py
+++ b/src/hdmf/common/table.py
@@ -638,26 +638,9 @@ def __len__(self):
         """Number of rows in the table"""
         return len(self.id)
 
-    @docval({'name': 'data', 'type': dict, 'doc': 'the data to put in this row', 'default': None},
-            {'name': 'id', 'type': int, 'doc': 'the ID for the row', 'default': None},
-            {'name': 'enforce_unique_id', 'type': bool, 'doc': 'enforce that the id in the table must be unique',
-             'default': False},
-            {'name': 'check_ragged', 'type': bool, 'default': True,
-             'doc': ('whether or not to check for ragged arrays when adding data to the table. '
-                     'Set to False to avoid checking every element if performance issues occur.')},
-            allow_extra=True)
-    def add_row(self, **kwargs):
-        """
-        Add a row to the table. If *id* is not provided, it will auto-increment.
-        """
-        data, row_id, enforce_unique_id, check_ragged = popargs('data', 'id', 'enforce_unique_id', 'check_ragged',
-                                                                kwargs)
-        data = data if data is not None else kwargs
-
+    def _validate_new_row(self, data: dict):
+        """Validate a row of new data to be added."""
         bad_data = []
-        extra_columns = set(list(data.keys())) - set(list(self.__colids.keys()))
-        missing_columns = set(list(self.__colids.keys())) - set(list(data.keys()))
-
         for colname, colnum in self.__colids.items():
             if colname not in data:
                 raise ValueError("column '%s' missing" % colname)
@@ -675,7 +658,12 @@ def add_row(self, **kwargs):
             msg = ('"%s" is not in the term set.' % ', '.join([str(item) for item in bad_data]))
             raise ValueError(msg)
 
-        # check to see if any of the extra columns just need to be added
+    def _add_extra_predefined_columns(self, data: dict):
+        """Add columns that are predefined, have not been added, and are present in the new row data.
+        Also check to see if all extra row data keys have corresponding columns in the table.
+        """
+        extra_columns = set(list(data.keys())) - set(list(self.__colids.keys()))
+
         if extra_columns:
             for col in self.__columns__:
                 if col['name'] in extra_columns:
@@ -691,14 +679,34 @@ def add_row(self, **kwargs):
                                            if k not in DynamicTable.__reserved_colspec_keys})
                     extra_columns.remove(col['name'])
 
-        if extra_columns or missing_columns:
+        if extra_columns:
             raise ValueError(
                 '\n'.join([
                     'row data keys don\'t match available columns',
                     'you supplied {} extra keys: {}'.format(len(extra_columns), extra_columns),
-                    'and were missing {} keys: {}'.format(len(missing_columns), missing_columns)
                 ])
             )
+
+    @docval({'name': 'data', 'type': dict, 'doc': 'the data to put in this row', 'default': None},
+            {'name': 'id', 'type': int, 'doc': 'the ID for the row', 'default': None},
+            {'name': 'enforce_unique_id', 'type': bool, 'doc': 'enforce that the id in the table must be unique',
+             'default': False},
+            {'name': 'check_ragged', 'type': bool, 'default': True,
+             'doc': ('whether or not to check for ragged arrays when adding data to the table. '
+                     'Set to False to avoid checking every element if performance issues occur.')},
+            allow_extra=True)
+    def add_row(self, **kwargs):
+        """
+        Add a row to the table. If *id* is not provided, it will auto-increment.
+        """
+        data, row_id, enforce_unique_id, check_ragged = popargs('data', 'id', 'enforce_unique_id', 'check_ragged',
+                                                                kwargs)
+        data = data if data is not None else kwargs
+
+        self._validate_new_row(data)
+        self._add_extra_predefined_columns(data)
+
+        
         if row_id is None:
             row_id = data.pop('id', None)
         if row_id is None:

From 1071f54601d51f2a8cdb3b95ece811027a9afb63 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 8 Feb 2025 07:38:01 +0000
Subject: [PATCH 06/14] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/hdmf/common/table.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/hdmf/common/table.py b/src/hdmf/common/table.py
index d4697f487..8b57bd569 100644
--- a/src/hdmf/common/table.py
+++ b/src/hdmf/common/table.py
@@ -706,7 +706,7 @@ def add_row(self, **kwargs):
         self._validate_new_row(data)
         self._add_extra_predefined_columns(data)
 
-        
+
         if row_id is None:
             row_id = data.pop('id', None)
         if row_id is None:

From 5e6a4b3749652e4c482d9aa97fcbf54fbf7b6d26 Mon Sep 17 00:00:00 2001
From: Ryan Ly <rly@lbl.gov>
Date: Fri, 7 Feb 2025 23:48:44 -0800
Subject: [PATCH 07/14] Reduce complexity of is_inherited_spec

---
 src/hdmf/spec/spec.py | 28 ++++++++++++----------------
 1 file changed, 12 insertions(+), 16 deletions(-)

diff --git a/src/hdmf/spec/spec.py b/src/hdmf/spec/spec.py
index bbd97b592..0e15cb92c 100644
--- a/src/hdmf/spec/spec.py
+++ b/src/hdmf/spec/spec.py
@@ -1045,24 +1045,20 @@ def is_inherited_spec(self, **kwargs):
             return self.is_inherited_type(spec_name)
         elif spec_name in self.__target_types:
             return self.is_inherited_target_type(spec_name)
+        elif super().is_inherited_spec(spec):  # attribute spec
+            return True
         else:
-            # attribute spec
-            if super().is_inherited_spec(spec):
-                return True
+            parent_name = spec.parent.name
+            if parent_name is None:
+                parent_name = spec.parent.data_type
+            if isinstance(spec.parent, DatasetSpec):
+                if (parent_name in self.__datasets and self.is_inherited_dataset(parent_name) and 
+                    self.__datasets[parent_name].get_attribute(spec_name) is not None):
+                        return True
             else:
-                parent_name = spec.parent.name
-                if parent_name is None:
-                    parent_name = spec.parent.data_type
-                if isinstance(spec.parent, DatasetSpec):
-                    if parent_name in self.__datasets:
-                        if self.is_inherited_dataset(parent_name):
-                            if self.__datasets[parent_name].get_attribute(spec_name) is not None:
-                                return True
-                else:
-                    if parent_name in self.__groups:
-                        if self.is_inherited_group(parent_name):
-                            if self.__groups[parent_name].get_attribute(spec_name) is not None:
-                                return True
+                if (parent_name in self.__groups and self.is_inherited_group(parent_name) and :
+                    self.__groups[parent_name].get_attribute(spec_name) is not None):
+                        return True
         return False
 
     @docval({'name': 'spec', 'type': Spec, 'doc': 'the specification to check'})

From 672d91c5f35319765c31225f3b81deec72c06311 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 8 Feb 2025 07:48:51 +0000
Subject: [PATCH 08/14] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/hdmf/spec/spec.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/hdmf/spec/spec.py b/src/hdmf/spec/spec.py
index 0e15cb92c..67969181b 100644
--- a/src/hdmf/spec/spec.py
+++ b/src/hdmf/spec/spec.py
@@ -1052,7 +1052,7 @@ def is_inherited_spec(self, **kwargs):
             if parent_name is None:
                 parent_name = spec.parent.data_type
             if isinstance(spec.parent, DatasetSpec):
-                if (parent_name in self.__datasets and self.is_inherited_dataset(parent_name) and 
+                if (parent_name in self.__datasets and self.is_inherited_dataset(parent_name) and
                     self.__datasets[parent_name].get_attribute(spec_name) is not None):
                         return True
             else:

From d1f699bd895a04996a5fd35434c10fbbf706463e Mon Sep 17 00:00:00 2001
From: Ryan Ly <rly@lbl.gov>
Date: Sat, 8 Feb 2025 00:01:59 -0800
Subject: [PATCH 09/14] Reduce complexity of add_ref

---
 src/hdmf/common/resources.py | 110 ++++++++++++++++++-----------------
 1 file changed, 56 insertions(+), 54 deletions(-)

diff --git a/src/hdmf/common/resources.py b/src/hdmf/common/resources.py
index 1fc731ef5..8ada6cf78 100644
--- a/src/hdmf/common/resources.py
+++ b/src/hdmf/common/resources.py
@@ -544,6 +544,52 @@ def add_ref_termset(self, **kwargs):
         if len(missing_terms)>0:
             return {"missing_terms": missing_terms}
 
+    def _validate_object(self, container, attribute, field):
+        if attribute is None:  # Trivial Case
+            relative_path = ''
+            object_field = self._check_object_field(file=file,
+                                                    container=container,
+                                                    relative_path=relative_path,
+                                                    field=field)
+        else:  # DataType Attribute Case
+            attribute_object = getattr(container, attribute)  # returns attribute object
+            if isinstance(attribute_object, AbstractContainer):
+                relative_path = ''
+                object_field = self._check_object_field(file=file,
+                                                        container=attribute_object,
+                                                        relative_path=relative_path,
+                                                        field=field)
+            else:  # Non-DataType Attribute Case:
+                obj_mapper = self.type_map.get_map(container)
+                spec = obj_mapper.get_attr_spec(attr_name=attribute)
+                parent_spec = spec.parent  # return the parent spec of the attribute
+                if parent_spec.data_type is None:
+                    while parent_spec.data_type is None:
+                        parent_spec = parent_spec.parent  # find the closest parent with a data_type
+                    parent_cls = self.type_map.get_dt_container_cls(data_type=parent_spec.data_type, autogen=False)
+                    if isinstance(container, parent_cls):
+                        parent = container
+                        # We need to get the path of the spec for relative_path
+                        absolute_path = spec.path
+                        relative_path = absolute_path[absolute_path.find('/')+1:]
+                        object_field = self._check_object_field(file=file,
+                                                                container=parent,
+                                                                relative_path=relative_path,
+                                                                field=field)
+                    else:
+                        msg = 'Container not the nearest data_type'
+                        raise ValueError(msg)
+                else:
+                    parent = container  # container needs to be the parent
+                    absolute_path = spec.path
+                    relative_path = absolute_path[absolute_path.find('/')+1:]
+                    # this regex removes everything prior to the container on the absolute_path
+                    object_field = self._check_object_field(file=file,
+                                                            container=parent,
+                                                            relative_path=relative_path,
+                                                            field=field)
+
+
     @docval({'name': 'container', 'type': (str, AbstractContainer), 'default': None,
              'doc': ('The Container/Data object that uses the key or '
                      'the object_id for the Container/Data object that uses the key.')},
@@ -630,52 +676,7 @@ def add_ref(self, **kwargs):
                 msg = 'This entity already exists. Ignoring new entity uri'
                 warn(msg, stacklevel=3)
 
-        #################
-        # Validate Object
-        #################
-        if attribute is None:  # Trivial Case
-            relative_path = ''
-            object_field = self._check_object_field(file=file,
-                                                    container=container,
-                                                    relative_path=relative_path,
-                                                    field=field)
-        else:  # DataType Attribute Case
-            attribute_object = getattr(container, attribute)  # returns attribute object
-            if isinstance(attribute_object, AbstractContainer):
-                relative_path = ''
-                object_field = self._check_object_field(file=file,
-                                                        container=attribute_object,
-                                                        relative_path=relative_path,
-                                                        field=field)
-            else:  # Non-DataType Attribute Case:
-                obj_mapper = self.type_map.get_map(container)
-                spec = obj_mapper.get_attr_spec(attr_name=attribute)
-                parent_spec = spec.parent  # return the parent spec of the attribute
-                if parent_spec.data_type is None:
-                    while parent_spec.data_type is None:
-                        parent_spec = parent_spec.parent  # find the closest parent with a data_type
-                    parent_cls = self.type_map.get_dt_container_cls(data_type=parent_spec.data_type, autogen=False)
-                    if isinstance(container, parent_cls):
-                        parent = container
-                        # We need to get the path of the spec for relative_path
-                        absolute_path = spec.path
-                        relative_path = absolute_path[absolute_path.find('/')+1:]
-                        object_field = self._check_object_field(file=file,
-                                                                container=parent,
-                                                                relative_path=relative_path,
-                                                                field=field)
-                    else:
-                        msg = 'Container not the nearest data_type'
-                        raise ValueError(msg)
-                else:
-                    parent = container  # container needs to be the parent
-                    absolute_path = spec.path
-                    relative_path = absolute_path[absolute_path.find('/')+1:]
-                    # this regex removes everything prior to the container on the absolute_path
-                    object_field = self._check_object_field(file=file,
-                                                            container=parent,
-                                                            relative_path=relative_path,
-                                                            field=field)
+        object_field = self._validate_object(container, attribute, field)
 
         #######################################
         # Validate Parameters and Populate HERD
@@ -998,7 +999,7 @@ def get_zip_directory(cls, path):
         directory = os.path.dirname(os.path.realpath(path))
         return directory
 
-    @classmethod
+    @classmethod  # noqa: C901
     @docval({'name': 'path', 'type': str, 'doc': 'The path to the zip file.'})
     def from_zip(cls, **kwargs):
         """
@@ -1075,11 +1076,12 @@ def from_zip(cls, **kwargs):
                 msg = "Key Index out of range in EntityKeyTable. Please check for alterations."
                 raise ValueError(msg)
 
-
-        er = HERD(files=files,
-                               keys=keys,
-                               entities=entities,
-                               entity_keys=entity_keys,
-                               objects=objects,
-                               object_keys=object_keys)
+        er = HERD(
+            files=files,
+            keys=keys,
+            entities=entities,
+            entity_keys=entity_keys,
+            objects=objects,
+            object_keys=object_keys
+        )
         return er

From eb41dda30d8b8a6c1101f5f8cc5431b9f1dca5e4 Mon Sep 17 00:00:00 2001
From: Ryan Ly <rly@lbl.gov>
Date: Sat, 8 Feb 2025 00:03:50 -0800
Subject: [PATCH 10/14] Fix

---
 src/hdmf/common/resources.py | 5 +++--
 src/hdmf/spec/spec.py        | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/hdmf/common/resources.py b/src/hdmf/common/resources.py
index 8ada6cf78..e93ccc135 100644
--- a/src/hdmf/common/resources.py
+++ b/src/hdmf/common/resources.py
@@ -544,7 +544,7 @@ def add_ref_termset(self, **kwargs):
         if len(missing_terms)>0:
             return {"missing_terms": missing_terms}
 
-    def _validate_object(self, container, attribute, field):
+    def _validate_object(self, container, attribute, field, file):
         if attribute is None:  # Trivial Case
             relative_path = ''
             object_field = self._check_object_field(file=file,
@@ -588,6 +588,7 @@ def _validate_object(self, container, attribute, field):
                                                             container=parent,
                                                             relative_path=relative_path,
                                                             field=field)
+        return object_field
 
 
     @docval({'name': 'container', 'type': (str, AbstractContainer), 'default': None,
@@ -676,7 +677,7 @@ def add_ref(self, **kwargs):
                 msg = 'This entity already exists. Ignoring new entity uri'
                 warn(msg, stacklevel=3)
 
-        object_field = self._validate_object(container, attribute, field)
+        object_field = self._validate_object(container, attribute, field, file)
 
         #######################################
         # Validate Parameters and Populate HERD
diff --git a/src/hdmf/spec/spec.py b/src/hdmf/spec/spec.py
index 67969181b..cf29c8b0e 100644
--- a/src/hdmf/spec/spec.py
+++ b/src/hdmf/spec/spec.py
@@ -1056,7 +1056,7 @@ def is_inherited_spec(self, **kwargs):
                     self.__datasets[parent_name].get_attribute(spec_name) is not None):
                         return True
             else:
-                if (parent_name in self.__groups and self.is_inherited_group(parent_name) and :
+                if (parent_name in self.__groups and self.is_inherited_group(parent_name) and
                     self.__groups[parent_name].get_attribute(spec_name) is not None):
                         return True
         return False

From f18b9c4bd5d54042f38372ce05308fe005d6128c Mon Sep 17 00:00:00 2001
From: Ryan Ly <rly@lbl.gov>
Date: Sat, 8 Feb 2025 00:06:27 -0800
Subject: [PATCH 11/14] Cleanup

---
 src/hdmf/backends/hdf5/h5tools.py |  2 +-
 src/hdmf/build/objectmapper.py    |  4 ++--
 src/hdmf/common/resources.py      |  4 ++--
 src/hdmf/common/table.py          |  4 ++--
 src/hdmf/spec/spec.py             | 29 +++++++++++++----------------
 src/hdmf/validate/validator.py    |  4 ++--
 6 files changed, 22 insertions(+), 25 deletions(-)

diff --git a/src/hdmf/backends/hdf5/h5tools.py b/src/hdmf/backends/hdf5/h5tools.py
index d30cef06c..493c4057f 100644
--- a/src/hdmf/backends/hdf5/h5tools.py
+++ b/src/hdmf/backends/hdf5/h5tools.py
@@ -1086,7 +1086,7 @@ def write_link(self, **kwargs):
         self.__set_written(builder)
         return link_obj
 
-    @docval({'name': 'parent', 'type': Group, 'doc': 'the parent HDF5 object'},  # noqa: C901
+    @docval({'name': 'parent', 'type': Group, 'doc': 'the parent HDF5 object'},
             {'name': 'builder', 'type': DatasetBuilder, 'doc': 'the DatasetBuilder to write'},
             {'name': 'link_data', 'type': bool,
              'doc': 'If not specified otherwise link (True) or copy (False) HDF5 Datasets', 'default': True},
diff --git a/src/hdmf/build/objectmapper.py b/src/hdmf/build/objectmapper.py
index 176de322c..e683e60bf 100644
--- a/src/hdmf/build/objectmapper.py
+++ b/src/hdmf/build/objectmapper.py
@@ -184,7 +184,7 @@ def no_convert(cls, obj_type):
         """
         cls.__no_convert.add(obj_type)
 
-    @classmethod  # noqa: C901
+    @classmethod
     def convert_dtype(cls, spec, value, spec_dtype=None):  # noqa: C901
         """
         Convert values to the specified dtype. For example, if a literal int
@@ -276,7 +276,7 @@ def __check_convert_numeric(cls, value_type):
                 np.issubdtype(value_dtype, np.integer)):
             raise ValueError("Cannot convert from %s to 'numeric' specification dtype." % value_type)
 
-    @classmethod  # noqa: C901
+    @classmethod
     def __check_edgecases(cls, spec, value, spec_dtype):  # noqa: C901
         """
         Check edge cases in converting data to a dtype
diff --git a/src/hdmf/common/resources.py b/src/hdmf/common/resources.py
index e93ccc135..2071415a0 100644
--- a/src/hdmf/common/resources.py
+++ b/src/hdmf/common/resources.py
@@ -1000,9 +1000,9 @@ def get_zip_directory(cls, path):
         directory = os.path.dirname(os.path.realpath(path))
         return directory
 
-    @classmethod  # noqa: C901
+    @classmethod
     @docval({'name': 'path', 'type': str, 'doc': 'The path to the zip file.'})
-    def from_zip(cls, **kwargs):
+    def from_zip(cls, **kwargs):  # noqa: C901
         """
         Method to read in zipped tsv files to populate HERD.
         """
diff --git a/src/hdmf/common/table.py b/src/hdmf/common/table.py
index 8b57bd569..40380b46e 100644
--- a/src/hdmf/common/table.py
+++ b/src/hdmf/common/table.py
@@ -304,7 +304,7 @@ def __gather_columns(cls, name, bases, classdict):
                     except AttributeError:   # raises error when "__columns__" is not an attr of item
                         continue
 
-    @docval({'name': 'name', 'type': str, 'doc': 'the name of this table'},  # noqa: C901
+    @docval({'name': 'name', 'type': str, 'doc': 'the name of this table'},
             {'name': 'description', 'type': str, 'doc': 'a description of what is in this table'},
             {'name': 'id', 'type': ('array_data', 'data', ElementIdentifiers), 'doc': 'the identifiers for this table',
              'default': None},
@@ -749,7 +749,7 @@ def __eq__(self, other):
             return False
         return self.to_dataframe().equals(other.to_dataframe())
 
-    @docval({'name': 'name', 'type': str, 'doc': 'the name of this VectorData'},  # noqa: C901
+    @docval({'name': 'name', 'type': str, 'doc': 'the name of this VectorData'},
             {'name': 'description', 'type': str, 'doc': 'a description for this column'},
             {'name': 'data', 'type': ('array_data', 'data'),
              'doc': 'a dataset where the first dimension is a concatenation of multiple vectors', 'default': list()},
diff --git a/src/hdmf/spec/spec.py b/src/hdmf/spec/spec.py
index cf29c8b0e..665be4a34 100644
--- a/src/hdmf/spec/spec.py
+++ b/src/hdmf/spec/spec.py
@@ -1062,7 +1062,7 @@ def is_inherited_spec(self, **kwargs):
         return False
 
     @docval({'name': 'spec', 'type': Spec, 'doc': 'the specification to check'})
-    def is_overridden_spec(self, **kwargs):  # noqa: C901
+    def is_overridden_spec(self, **kwargs):
         ''' Returns 'True' if specification overrides a specification from the parent type '''
         spec = getargs('spec', kwargs)
         spec_name = spec.name
@@ -1086,23 +1086,20 @@ def is_overridden_spec(self, **kwargs):  # noqa: C901
             return self.is_overridden_dataset(spec_name)
         elif spec_name in self.__data_types:
             return self.is_overridden_type(spec_name)
+        elif super().is_overridden_spec(spec):  # attribute spec
+            return True
         else:
-            if super().is_overridden_spec(spec):  # check if overridden attribute
-                return True
+            parent_name = spec.parent.name
+            if parent_name is None:
+                parent_name = spec.parent.data_type
+            if isinstance(spec.parent, DatasetSpec):
+                if (parent_name in self.__datasets and self.is_overridden_dataset(parent_name) and
+                    self.__datasets[parent_name].is_overridden_spec(spec)):
+                        return True
             else:
-                parent_name = spec.parent.name
-                if parent_name is None:
-                   parent_name = spec.parent.data_type
-                if isinstance(spec.parent, DatasetSpec):
-                    if parent_name in self.__datasets:
-                        if self.is_overridden_dataset(parent_name):
-                            if self.__datasets[parent_name].is_overridden_spec(spec):
-                                return True
-                else:
-                    if parent_name in self.__groups:
-                        if self.is_overridden_group(parent_name):
-                            if self.__groups[parent_name].is_overridden_spec(spec):
-                                return True
+                if (parent_name in self.__groups and self.is_overridden_group(parent_name) and
+                    self.__groups[parent_name].is_overridden_spec(spec)):
+                        return True
         return False
 
     @docval({'name': 'spec', 'type': (BaseStorageSpec, str), 'doc': 'the specification to check'})
diff --git a/src/hdmf/validate/validator.py b/src/hdmf/validate/validator.py
index d7ec78eaa..1a0be981d 100644
--- a/src/hdmf/validate/validator.py
+++ b/src/hdmf/validate/validator.py
@@ -472,9 +472,9 @@ class GroupValidator(BaseStorageValidator):
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
 
-    @docval({"name": "builder", "type": GroupBuilder, "doc": "the builder to validate"},  # noqa: C901
+    @docval({"name": "builder", "type": GroupBuilder, "doc": "the builder to validate"},
             returns='a list of Errors', rtype=list)
-    def validate(self, **kwargs):  # noqa: C901
+    def validate(self, **kwargs):
         builder = getargs('builder', kwargs)
         errors = super().validate(builder)
         errors.extend(self.__validate_children(builder))

From 63030e3eed41e132bc3b35a6ae858ce68ccf710b Mon Sep 17 00:00:00 2001
From: Ryan Ly <rly@lbl.gov>
Date: Sat, 8 Feb 2025 00:07:28 -0800
Subject: [PATCH 12/14] add c901 exception

---
 src/hdmf/common/resources.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/hdmf/common/resources.py b/src/hdmf/common/resources.py
index 2071415a0..ff333caac 100644
--- a/src/hdmf/common/resources.py
+++ b/src/hdmf/common/resources.py
@@ -605,7 +605,7 @@ def _validate_object(self, container, attribute, field, file):
             {'name': 'file',  'type': HERDManager, 'doc': 'The file associated with the container.',
              'default': None},
             )
-    def add_ref(self, **kwargs):
+    def add_ref(self, **kwargs):  # noqa: C901
         """
         Add information about an external reference used in this file.
 

From c81d99fad0926f17949131a6340b15dbc8600061 Mon Sep 17 00:00:00 2001
From: Ryan Ly <rly@lbl.gov>
Date: Sat, 8 Feb 2025 00:35:24 -0800
Subject: [PATCH 13/14] Update changelog

---
 CHANGELOG.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8e3f480c8..34da87402 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,11 @@
 # HDMF Changelog
 
+## [Unreleased]
+
+### Changed
+- Removed `requirements-min.txt` in favor of the `min-reqs` optional dependency group in `pyproject.toml`. @rly [#1246](https://github.com/hdmf-dev/hdmf/pull/1246)
+- Updated GitHub actions and ruff configuration. @rly [#1246](https://github.com/hdmf-dev/hdmf/pull/1246)
+
 ## HDMF 4.0.0 (January 22, 2025)
 
 ### Breaking changes

From 722a772f59c4d528dbc3d676958683afec0330c4 Mon Sep 17 00:00:00 2001
From: Ryan Ly <rly@lbl.gov>
Date: Sat, 8 Feb 2025 11:18:01 -0800
Subject: [PATCH 14/14] Update ruff.yml

---
 .github/workflows/ruff.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml
index 078a243cc..da9b4327c 100644
--- a/.github/workflows/ruff.yml
+++ b/.github/workflows/ruff.yml
@@ -8,4 +8,4 @@ jobs:
       - name: Checkout repo
         uses: actions/checkout@v4
       - name: Run ruff
-        uses: astral-sh/ruff-action@v1
+        uses: astral-sh/ruff-action@v3