From 7a9a84fcfc028fc03682c6c64fe9f8b24e834aee Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Tue, 18 Nov 2025 16:52:48 -0800
Subject: [PATCH 01/10] minor changes

---
 src/biocutils/combine_rows.py    |  2 +-
 src/biocutils/package_utils.py   |  6 ++--
 src/biocutils/subset_rows.py     | 49 ++++++++++++++++++++++++-----
 src/biocutils/subset_sequence.py | 54 +++++++++++++++++++++++---------
 4 files changed, 86 insertions(+), 25 deletions(-)

diff --git a/src/biocutils/combine_rows.py b/src/biocutils/combine_rows.py
index 1783dcf..9102d1e 100644
--- a/src/biocutils/combine_rows.py
+++ b/src/biocutils/combine_rows.py
@@ -77,7 +77,7 @@ def _combine_rows_sparse_arrays(*x):
         _check_array_dimensions(x, 0)
         if is_list_of_type(x, sp.sparray):
             combined = sp.vstack(x)
-            return _coerce_sparse_array(first, combined, sp)
+            return _coerce_sparse_array(x[0], combined, sp)
 
         warn("not all elements are SciPy sparse arrays")
         x = [convert_to_dense(y) for y in x]
diff --git a/src/biocutils/package_utils.py b/src/biocutils/package_utils.py
index e6e4b3a..dcf03d1 100644
--- a/src/biocutils/package_utils.py
+++ b/src/biocutils/package_utils.py
@@ -4,13 +4,13 @@
 
 
 def is_package_installed(package_name: str) -> bool:
-    """Check if the package is installed.
+    """Check if a package is installed.
 
     Args:
-        package_name (str): Package name.
+        package_name: Package name.
 
     Returns:
-        bool: True if package is installed, otherwise False.
+        True if package is installed, otherwise False.
     """
     _installed = False
     try:
diff --git a/src/biocutils/subset_rows.py b/src/biocutils/subset_rows.py
index a09fadb..e5b31cb 100644
--- a/src/biocutils/subset_rows.py
+++ b/src/biocutils/subset_rows.py
@@ -1,19 +1,21 @@
 from functools import singledispatch
 from typing import Any, Sequence
 
+import numpy
+
+from .package_utils import is_package_installed
+
 
 @singledispatch
 def subset_rows(x: Any, indices: Sequence[int]) -> Any:
-    """
+    """Subset a high-dimensional object by indices on the first dimension.
+
     Subset ``x`` by ``indices`` on the first dimension. The default
-    method attempts to use ``x``'s ``__getitem__`` method,
+    method attempts to use ``x``'s ``__getitem__`` method.
 
     Args:
-        x:
-            Any high-dimensional object.
-
-        indices:
-            Sequence of non-negative integers specifying the integers of interest.
+        x: Any high-dimensional object.
+        indices: Sequence of non-negative integers specifying the rows of interest.
 
     Returns:
         The result of slicing ``x`` by ``indices``. The exact type
@@ -22,3 +24,36 @@ def subset_rows(x: Any, indices: Sequence[int]) -> Any:
     tmp = [slice(None)] * len(x.shape)
     tmp[0] = indices
     return x[(*tmp,)]
+
+
+@subset_rows.register
+def _subset_rows_numpy(x: numpy.ndarray, indices: Sequence[int]) -> numpy.ndarray:
+    """Subset a NumPy array by row indices.
+
+    Args:
+        x: NumPy array to subset.
+        indices: Sequence of non-negative integers specifying rows.
+
+    Returns:
+        Subsetted NumPy array.
+    """
+    tmp = [slice(None)] * len(x.shape)
+    tmp[0] = indices
+    return x[(*tmp,)]
+
+
+if is_package_installed("pandas"):
+    from pandas import DataFrame
+
+    @subset_rows.register(DataFrame)
+    def _subset_rows_dataframe(x: DataFrame, indices: Sequence[int]) -> DataFrame:
+        """Subset a pandas DataFrame by row indices.
+
+        Args:
+            x: DataFrame to subset.
+            indices: Sequence of non-negative integers specifying rows.
+
+        Returns:
+            Subsetted DataFrame.
+        """
+        return x.iloc[indices, :]
diff --git a/src/biocutils/subset_sequence.py b/src/biocutils/subset_sequence.py
index 609027e..1c39517 100644
--- a/src/biocutils/subset_sequence.py
+++ b/src/biocutils/subset_sequence.py
@@ -4,17 +4,15 @@
 
 @singledispatch
 def subset_sequence(x: Any, indices: Sequence[int]) -> Any:
-    """
+    """Subset a sequence-like object by indices.
+
     Subset ``x`` by ``indices`` to obtain a new object. The default method
     attempts to use ``x``'s ``__getitem__`` method.
 
     Args:
-        x:
-            Any object that supports ``__getitem__`` with an integer sequence.
-
-        indices:
-            Sequence of non-negative integers specifying the integers of interest.
-            All indices should be less than ``len(x)``.
+        x: Any object that supports ``__getitem__`` with an integer sequence.
+        indices: Sequence of non-negative integers specifying the positions of
+            interest. All indices should be less than ``len(x)``.
 
     Returns:
         The result of slicing ``x`` by ``indices``. The exact type
@@ -24,19 +22,47 @@ def subset_sequence(x: Any, indices: Sequence[int]) -> Any:
 
 
 @subset_sequence.register
-def _subset_sequence_list(x: list, indices: Sequence) -> list:
+def _subset_sequence_list(x: list, indices: Sequence[int]) -> list:
+    """Subset a list by indices.
+
+    Args:
+        x: List to subset.
+        indices: Sequence of non-negative integers specifying positions.
+
+    Returns:
+        A new list containing the specified elements.
+    """
     return type(x)(x[i] for i in indices)
 
 
 @subset_sequence.register
-def _subset_sequence_range(x: range, indices: Sequence) -> Union[list, range]:
+def _subset_sequence_range(x: range, indices: Sequence[int]) -> Union[list, range]:
+    """Subset a range by indices.
+
+    Args:
+        x: Range object to subset.
+        indices: Sequence of non-negative integers or a range object.
+
+    Returns:
+        A range if indices is a range, otherwise a list.
+    """
     if isinstance(indices, range):
         # We can just assume that all 'indices' are in [0, len(x)),
         # so no need to handle out-of-range indices.
-        return range(
-            x.start + x.step * indices.start,
-            x.start + x.step * indices.stop,
-            x.step * indices.step
-        )
+        return range(x.start + x.step * indices.start, x.start + x.step * indices.stop, x.step * indices.step)
     else:
         return [x[i] for i in indices]
+
+
+@subset_sequence.register
+def _subset_sequence_tuple(x: tuple, indices: Sequence[int]) -> tuple:
+    """Subset a tuple by indices.
+
+    Args:
+        x: Tuple to subset.
+        indices: Sequence of non-negative integers specifying positions.
+
+    Returns:
+        A new tuple containing the specified elements.
+    """
+    return tuple(x[i] for i in indices)

From ef1ca9678e7561c1654b88628d545d9d2e64502a Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Tue, 18 Nov 2025 16:55:18 -0800
Subject: [PATCH 02/10] update actions

---
 .github/workflows/publish-pypi.yml | 52 +++++++++++++++++++++
 .github/workflows/pypi-publish.yml | 51 ---------------------
 .github/workflows/pypi-test.yml    | 40 ----------------
 .github/workflows/run-tests.yml    | 73 ++++++++++++++++++++++++++++++
 4 files changed, 125 insertions(+), 91 deletions(-)
 create mode 100644 .github/workflows/publish-pypi.yml
 delete mode 100644 .github/workflows/pypi-publish.yml
 delete mode 100644 .github/workflows/pypi-test.yml
 create mode 100644 .github/workflows/run-tests.yml

diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/publish-pypi.yml
new file mode 100644
index 0000000..405fee0
--- /dev/null
+++ b/.github/workflows/publish-pypi.yml
@@ -0,0 +1,52 @@
+name: Publish to PyPI
+
+on:
+  push:
+    tags: "*"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      repository-projects: write
+      contents: write
+      pages: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox
+
+      - name: Test with tox
+        run: |
+          tox
+
+      - name: Build Project and Publish
+        run: |
+          python -m tox -e clean,build
+
+      # This uses the trusted publisher workflow so no token is required.
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+      - name: Build docs
+        run: |
+          tox -e docs
+
+      - run: touch ./docs/_build/html/.nojekyll
+
+      - name: GH Pages Deployment
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          branch: gh-pages # The branch the action should deploy to.
+          folder: ./docs/_build/html
+          clean: true # Automatically remove deleted files from the deploy branch
diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml
deleted file mode 100644
index 030cd10..0000000
--- a/.github/workflows/pypi-publish.yml
+++ /dev/null
@@ -1,51 +0,0 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
-name: Publish to PyPI
-
-on:
-  push:
-    tags: "*"
-
-jobs:
-  build:
-
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v5
-      with:
-        python-version: 3.11
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest tox
-    # - name: Lint with flake8
-    #   run: |
-    #     # stop the build if there are Python syntax errors or undefined names
-    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-    #     # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with tox
-      run: |
-        tox
-    - name: Build docs
-      run: |
-        tox -e docs
-    - run: touch ./docs/_build/html/.nojekyll
-    - name: GH Pages Deployment
-      uses: JamesIves/github-pages-deploy-action@4.1.3
-      with:
-        branch: gh-pages # The branch the action should deploy to.
-        folder: ./docs/_build/html
-        clean: true # Automatically remove deleted files from the deploy branch
-    - name: Build Project and Publish
-      run: |
-        python -m tox -e clean,build
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_PASSWORD }}
diff --git a/.github/workflows/pypi-test.yml b/.github/workflows/pypi-test.yml
deleted file mode 100644
index 22f6c4a..0000000
--- a/.github/workflows/pypi-test.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
-name: Test the library
-
-on:
-  push:
-    branches: [ master ]
-  pull_request:
-    branches: [ master ]
-
-jobs:
-  build:
-
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [ '3.9', '3.10', '3.11', '3.12', '3.13' ]
-
-    name: Python ${{ matrix.python-version }}
-    steps:
-    - uses: actions/checkout@v4
-    - name: Setup Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-        cache: 'pip'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest tox
-    # - name: Lint with flake8
-    #   run: |
-    #     # stop the build if there are Python syntax errors or undefined names
-    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-    #     # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with tox
-      run: |
-        tox
diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
new file mode 100644
index 0000000..e8ab6fa
--- /dev/null
+++ b/.github/workflows/run-tests.yml
@@ -0,0 +1,73 @@
+name: Test the library
+
+on:
+  push:
+    branches:
+      - master # for legacy repos
+      - main
+  pull_request:
+    branches:
+      - master # for legacy repos
+      - main
+  workflow_dispatch: # Allow manually triggering the workflow
+  schedule:
+    # Run roughly every 15 days at 00:00 UTC
+    # (useful to check if updates on dependencies break the package)
+    - cron: "0 0 1,16 * *"
+
+permissions:
+  contents: read
+
+concurrency:
+  group: >-
+    ${{ github.workflow }}-${{ github.ref_type }}-
+    ${{ github.event.pull_request.number || github.sha }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        python: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
+        platform:
+          - ubuntu-latest
+          - macos-latest
+          - windows-latest
+    runs-on: ${{ matrix.platform }}
+    name: Python ${{ matrix.python }}, ${{ matrix.platform }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        id: setup-python
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox coverage
+
+      - name: Run tests
+        run: >-
+          pipx run --python '${{ steps.setup-python.outputs.python-path }}'
+          tox
+          -- -rFEx --durations 10 --color yes --cov --cov-branch --cov-report=xml  # pytest args
+
+      - name: Check for codecov token availability
+        id: codecov-check
+        shell: bash
+        run: |
+          if [ ${{ secrets.CODECOV_TOKEN }} != '' ]; then
+            echo "codecov=true" >> $GITHUB_OUTPUT;
+          else
+            echo "codecov=false" >> $GITHUB_OUTPUT;
+          fi
+
+      - name: Upload coverage reports to Codecov with GitHub Action
+        uses: codecov/codecov-action@v5
+        if: ${{ steps.codecov-check.outputs.codecov == 'true' }}
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          slug: ${{ github.repository }}
+          flags: ${{ matrix.platform }} - py${{ matrix.python }}

From 43775ea197ddfbed0128eb5674f571e45bd80dd0 Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Tue, 18 Nov 2025 17:40:48 -0800
Subject: [PATCH 03/10] minor docstring updates

---
 src/biocutils/BooleanList.py          | 19 +++++++++++++++++--
 src/biocutils/FloatList.py            | 19 +++++++++++++++++--
 src/biocutils/IntegerList.py          | 19 +++++++++++++++++--
 src/biocutils/StringList.py           | 19 +++++++++++++++++--
 src/biocutils/extract_column_names.py |  2 +-
 src/biocutils/extract_row_names.py    |  2 +-
 src/biocutils/is_high_dimensional.py  |  9 +++++----
 src/biocutils/is_missing_scalar.py    | 10 ++++++----
 src/biocutils/match.py                |  2 +-
 src/biocutils/normalize_subscript.py  | 24 +++++++++++++-----------
 src/biocutils/print_wrapped_table.py  | 11 +++++++----
 src/biocutils/reverse_index.py        |  6 +++---
 src/biocutils/which.py                |  2 +-
 13 files changed, 106 insertions(+), 38 deletions(-)

diff --git a/src/biocutils/BooleanList.py b/src/biocutils/BooleanList.py
index 1e46826..f309322 100644
--- a/src/biocutils/BooleanList.py
+++ b/src/biocutils/BooleanList.py
@@ -10,10 +10,25 @@ def _coerce_to_bool(x: Any):
 
 
 class _SubscriptCoercer:
-    def __init__(self, data):
+    """Coercer for subscript operations on BooleanList."""
+
+    def __init__(self, data: Sequence) -> None:
+        """Initialize the coercer.
+
+        Args:
+            data: Sequence of values to coerce.
+        """
         self._data = data
 
-    def __getitem__(self, index):
+    def __getitem__(self, index: int) -> Optional[bool]:
+        """Get an item and coerce it to boolean.
+
+        Args:
+            index: Index of the item.
+
+        Returns:
+            Coerced boolean value.
+        """
         return _coerce_to_bool(self._data[index])
 
 
diff --git a/src/biocutils/FloatList.py b/src/biocutils/FloatList.py
index 3b587bd..3249da5 100644
--- a/src/biocutils/FloatList.py
+++ b/src/biocutils/FloatList.py
@@ -15,10 +15,25 @@ def _coerce_to_float(x: Any):
 
 
 class _SubscriptCoercer:
-    def __init__(self, data):
+    """Coercer for subscript operations on FloatList."""
+
+    def __init__(self, data: Sequence) -> None:
+        """Initialize the coercer.
+
+        Args:
+            data: Sequence of values to coerce.
+        """
         self._data = data
 
-    def __getitem__(self, index):
+    def __getitem__(self, index: int) -> Optional[float]:
+        """Get an item and coerce it to float.
+
+        Args:
+            index: Index of the item.
+
+        Returns:
+            Coerced float value.
+        """
         return _coerce_to_float(self._data[index])
 
 
diff --git a/src/biocutils/IntegerList.py b/src/biocutils/IntegerList.py
index c06e3e6..8f8f191 100644
--- a/src/biocutils/IntegerList.py
+++ b/src/biocutils/IntegerList.py
@@ -15,10 +15,25 @@ def _coerce_to_int(x: Any):
 
 
 class _SubscriptCoercer:
-    def __init__(self, data):
+    """Coercer for subscript operations on IntegerList."""
+
+    def __init__(self, data: Sequence) -> None:
+        """Initialize the coercer.
+
+        Args:
+            data: Sequence of values to coerce.
+        """
         self._data = data
 
-    def __getitem__(self, index):
+    def __getitem__(self, index: int) -> Optional[int]:
+        """Get an item and coerce it to integer.
+
+        Args:
+            index: Index of the item.
+
+        Returns:
+            Coerced integer value.
+        """
         return _coerce_to_int(self._data[index])
 
 
diff --git a/src/biocutils/StringList.py b/src/biocutils/StringList.py
index c16366b..518b729 100644
--- a/src/biocutils/StringList.py
+++ b/src/biocutils/StringList.py
@@ -10,10 +10,25 @@ def _coerce_to_str(x: Any):
 
 
 class _SubscriptCoercer:
-    def __init__(self, data):
+    """Coercer for subscript operations on StringList."""
+
+    def __init__(self, data: Sequence) -> None:
+        """Initialize the coercer.
+
+        Args:
+            data: Sequence of values to coerce.
+        """
         self._data = data
 
-    def __getitem__(self, index):
+    def __getitem__(self, index: int) -> Optional[str]:
+        """Get an item and coerce it to string.
+
+        Args:
+            index: Index of the item.
+
+        Returns:
+            Coerced string value.
+        """
         return _coerce_to_str(self._data[index])
 
 
diff --git a/src/biocutils/extract_column_names.py b/src/biocutils/extract_column_names.py
index 5b63683..6f98521 100644
--- a/src/biocutils/extract_column_names.py
+++ b/src/biocutils/extract_column_names.py
@@ -15,7 +15,7 @@ def extract_column_names(x: Any) -> numpy.ndarray:
     """Access column names from 2-dimensional representations.
 
     Args:
-        x: Any object.
+        x: Any object with column names.
 
     Returns:
         Array of strings containing column names.
diff --git a/src/biocutils/extract_row_names.py b/src/biocutils/extract_row_names.py
index 81b81fb..5ea3927 100644
--- a/src/biocutils/extract_row_names.py
+++ b/src/biocutils/extract_row_names.py
@@ -15,7 +15,7 @@ def extract_row_names(x: Any) -> numpy.ndarray:
     """Access row names from 2-dimensional representations.
 
     Args:
-        x: Any object.
+        x: Any object with row names.
 
     Returns:
         Array of strings containing row names.
diff --git a/src/biocutils/is_high_dimensional.py b/src/biocutils/is_high_dimensional.py
index 9d9d5d2..3bdfc6f 100644
--- a/src/biocutils/is_high_dimensional.py
+++ b/src/biocutils/is_high_dimensional.py
@@ -1,15 +1,16 @@
 from functools import singledispatch
+from typing import Any
 
 
 @singledispatch
-def is_high_dimensional(x):
-    """
+def is_high_dimensional(x: Any) -> bool:
+    """Check if an object is high-dimensional.
+
     Whether an object is high-dimensional, i.e., has a ``shape``
     attribute that is of length greater than 1.
 
     Args:
-        x:
-            Some kind of object.
+        x: Some kind of object.
 
     Returns:
         Whether ``x`` is high-dimensional.
diff --git a/src/biocutils/is_missing_scalar.py b/src/biocutils/is_missing_scalar.py
index 8392fdf..f32dd60 100644
--- a/src/biocutils/is_missing_scalar.py
+++ b/src/biocutils/is_missing_scalar.py
@@ -1,11 +1,13 @@
+from typing import Any
+
 import numpy
 
 
-def is_missing_scalar(x) -> bool:
-    """
+def is_missing_scalar(x: Any) -> bool:
+    """Check if a scalar value is missing.
+
     Args:
-        x:
-            Any scalar value.
+        x: Any scalar value.
 
     Returns:
         Whether ``x`` is None or a NumPy masked constant.
diff --git a/src/biocutils/match.py b/src/biocutils/match.py
index 2881bec..0e237c5 100644
--- a/src/biocutils/match.py
+++ b/src/biocutils/match.py
@@ -8,7 +8,7 @@ def match(
     x: Sequence,
     targets: Union[dict, Sequence],
     duplicate_method: DUPLICATE_METHOD = "first",
-    dtype: Optional[numpy.ndarray] = None,
+    dtype: Optional[numpy.dtype] = None,
     fail_missing: Optional[bool] = None,
 ) -> numpy.ndarray:
     """Find a matching value of each element of ``x`` in ``target``.
diff --git a/src/biocutils/normalize_subscript.py b/src/biocutils/normalize_subscript.py
index 890a9b3..da37a7e 100644
--- a/src/biocutils/normalize_subscript.py
+++ b/src/biocutils/normalize_subscript.py
@@ -23,11 +23,11 @@ class NormalizedSubscript:
     such that :py:func:`~normalize_subscript` is just a no-op.
     """
 
-    def __init__(self, subscript: Sequence[int]):
-        """
+    def __init__(self, subscript: Sequence[int]) -> None:
+        """Initialize a NormalizedSubscript.
+
         Args:
-            subscript:
-                Sequence of integers for a normalized subscript.
+            subscript: Sequence of integers for a normalized subscript.
         """
         self._subscript = subscript
 
@@ -40,11 +40,11 @@ def subscript(self) -> Sequence[int]:
         return self._subscript
 
     def __getitem__(self, index: Any) -> Any:
-        """
+        """Get an item from the subscript.
+
         Args:
-            index:
-                Any argument accepted by the ``__getitem__`` method of the
-                :py:attr:`~subscript`.
+            index: Any argument accepted by the ``__getitem__`` method of the
+                subscript.
 
         Returns:
             The same return value as the ``__getitem__`` method of the
@@ -53,7 +53,8 @@ def __getitem__(self, index: Any) -> Any:
         return self._subscript[index]
 
     def __len__(self) -> int:
-        """
+        """Get the length of the subscript.
+
         Returns:
             Length of the subscript.
         """
@@ -68,8 +69,9 @@ def normalize_subscript(
     length: int,
     names: Optional[Sequence[str]] = None,
     non_negative_only: bool = True,
-) -> Tuple:
-    """
+) -> Tuple[Sequence[int], bool]:
+    """Normalize a subscript into a sequence of integer indices.
+
     Normalize a subscript for ``__getitem__`` or friends into a sequence of
     integer indices, for consistent downstream use.
 
diff --git a/src/biocutils/print_wrapped_table.py b/src/biocutils/print_wrapped_table.py
index cbfcb36..12f602f 100644
--- a/src/biocutils/print_wrapped_table.py
+++ b/src/biocutils/print_wrapped_table.py
@@ -144,14 +144,17 @@ def truncate_strings(values: List[str], width: int = 40) -> List[str]:
     return replacement
 
 
-def print_type(x) -> str:
-    """Print the type of an object, with some special behavior for certain classes (e.g., to add the data type of NumPy
-    arrays). This is intended for display at the top of the columns of :py:meth:`~print_wrapped_table`.
+def print_type(x: Any) -> str:
+    """Print the type of an object.
+
+    Print the type of an object, with some special behavior for certain classes
+    (e.g., to add the data type of NumPy arrays). This is intended for display
+    at the top of the columns of :py:meth:`~print_wrapped_table`.
 
     Args:
         x: Some object.
 
-    Return:
+    Returns:
         String containing the class of the object.
     """
     cls = type(x).__name__
diff --git a/src/biocutils/reverse_index.py b/src/biocutils/reverse_index.py
index 3b64c9e..528f1ee 100644
--- a/src/biocutils/reverse_index.py
+++ b/src/biocutils/reverse_index.py
@@ -1,16 +1,16 @@
 from typing import Sequence
 
 
-def build_reverse_index(obj: Sequence[str]):
+def build_reverse_index(obj: Sequence[str]) -> dict:
     """Build a reverse index by name, for fast lookup operations.
 
-    Only contains the first occurence of a term.
+    Only contains the first occurrence of a term.
 
     Args:
         obj: List of names.
 
     Returns:
-        A map of keys and their index positions.
+        A dictionary mapping names to their index positions.
     """
     revmap = {}
     for i, n in enumerate(obj):
diff --git a/src/biocutils/which.py b/src/biocutils/which.py
index 2a0c0d1..87d2fdd 100644
--- a/src/biocutils/which.py
+++ b/src/biocutils/which.py
@@ -4,7 +4,7 @@
 
 def which(
     x: Sequence,
-    dtype: Optional[numpy.ndarray] = None,
+    dtype: Optional[numpy.dtype] = None,
 ) -> numpy.ndarray:
     """Report the indices of all elements of ``x`` that are truthy.
 

From 591af1f33975019007a47053e344359d20ac9bbf Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Tue, 18 Nov 2025 21:14:57 -0800
Subject: [PATCH 04/10] missing import

---
 src/biocutils/print_wrapped_table.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/biocutils/print_wrapped_table.py b/src/biocutils/print_wrapped_table.py
index 12f602f..583f583 100644
--- a/src/biocutils/print_wrapped_table.py
+++ b/src/biocutils/print_wrapped_table.py
@@ -1,4 +1,4 @@
-from typing import List, Optional, Sequence
+from typing import Any, List, Optional, Sequence
 
 import numpy
 

From 21b8bfcd530389de97e12527c30c83421656080a Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Thu, 18 Dec 2025 14:58:07 -0800
Subject: [PATCH 05/10] renaming to follow pep guidelines

---
 src/biocutils/Factor.py                           |  4 ++--
 src/biocutils/__init__.py                         | 14 +++++++-------
 src/biocutils/bioc_object.py                      |  2 +-
 src/biocutils/{BooleanList.py => boolean_list.py} |  4 ++--
 src/biocutils/{FloatList.py => float_list.py}     |  4 ++--
 src/biocutils/{IntegerList.py => integer_list.py} |  4 ++--
 src/biocutils/{NamedList.py => named_list.py}     |  2 +-
 src/biocutils/normalize_subscript.py              |  6 +++---
 src/biocutils/{StringList.py => string_list.py}   |  4 ++--
 tests/test_biocobject.py                          |  2 +-
 10 files changed, 23 insertions(+), 23 deletions(-)
 rename src/biocutils/{BooleanList.py => boolean_list.py} (98%)
 rename src/biocutils/{FloatList.py => float_list.py} (98%)
 rename src/biocutils/{IntegerList.py => integer_list.py} (98%)
 rename src/biocutils/{NamedList.py => named_list.py} (99%)
 rename src/biocutils/{StringList.py => string_list.py} (98%)

diff --git a/src/biocutils/Factor.py b/src/biocutils/Factor.py
index 374b34e..fedf75e 100644
--- a/src/biocutils/Factor.py
+++ b/src/biocutils/Factor.py
@@ -10,14 +10,14 @@
 from .is_list_of_type import is_list_of_type
 from .is_missing_scalar import is_missing_scalar
 from .match import match
-from .Names import Names, _combine_names, _name_to_position, _sanitize_names
+from .names import Names, _combine_names, _name_to_position, _sanitize_names
 from .normalize_subscript import (
     NormalizedSubscript,
     SubscriptTypes,
     normalize_subscript,
 )
 from .print_truncated import print_truncated_list
-from .StringList import StringList
+from .string_list import StringList
 from .subset_sequence import subset_sequence
 
 
diff --git a/src/biocutils/__init__.py b/src/biocutils/__init__.py
index 6f2326f..13fa31c 100644
--- a/src/biocutils/__init__.py
+++ b/src/biocutils/__init__.py
@@ -15,13 +15,13 @@
 finally:
     del version, PackageNotFoundError
 
-from .Factor import Factor
-from .StringList import StringList
-from .IntegerList import IntegerList
-from .FloatList import FloatList
-from .BooleanList import BooleanList
-from .Names import Names
-from .NamedList import NamedList
+from .factor import Factor
+from .string_list import StringList
+from .integer_list import IntegerList
+from .float_list import FloatList
+from .boolean_list import BooleanList
+from .names import Names
+from .named_list import NamedList
 
 from .factorize import factorize
 from .intersect import intersect
diff --git a/src/biocutils/bioc_object.py b/src/biocutils/bioc_object.py
index 1302663..ac40431 100644
--- a/src/biocutils/bioc_object.py
+++ b/src/biocutils/bioc_object.py
@@ -9,7 +9,7 @@
 except ImportError:
     Self = "BiocObject"
 
-from .NamedList import NamedList
+from .named_list import NamedList
 
 __author__ = "Jayaram Kancherla"
 __copyright__ = "jkanche"
diff --git a/src/biocutils/BooleanList.py b/src/biocutils/boolean_list.py
similarity index 98%
rename from src/biocutils/BooleanList.py
rename to src/biocutils/boolean_list.py
index f309322..6f19900 100644
--- a/src/biocutils/BooleanList.py
+++ b/src/biocutils/boolean_list.py
@@ -1,7 +1,7 @@
 from typing import Any, Iterable, Optional, Sequence, Union
 
-from .NamedList import NamedList
-from .Names import Names
+from .named_list import NamedList
+from .names import Names
 from .normalize_subscript import SubscriptTypes
 
 
diff --git a/src/biocutils/FloatList.py b/src/biocutils/float_list.py
similarity index 98%
rename from src/biocutils/FloatList.py
rename to src/biocutils/float_list.py
index 3249da5..ccf8bd4 100644
--- a/src/biocutils/FloatList.py
+++ b/src/biocutils/float_list.py
@@ -1,7 +1,7 @@
 from typing import Any, Iterable, Optional, Sequence, Union
 
-from .NamedList import NamedList
-from .Names import Names
+from .named_list import NamedList
+from .names import Names
 from .normalize_subscript import SubscriptTypes
 
 
diff --git a/src/biocutils/IntegerList.py b/src/biocutils/integer_list.py
similarity index 98%
rename from src/biocutils/IntegerList.py
rename to src/biocutils/integer_list.py
index 8f8f191..9ca9fbb 100644
--- a/src/biocutils/IntegerList.py
+++ b/src/biocutils/integer_list.py
@@ -1,7 +1,7 @@
 from typing import Any, Iterable, Optional, Sequence, Union
 
-from .NamedList import NamedList
-from .Names import Names
+from .named_list import NamedList
+from .names import Names
 from .normalize_subscript import SubscriptTypes
 
 
diff --git a/src/biocutils/NamedList.py b/src/biocutils/named_list.py
similarity index 99%
rename from src/biocutils/NamedList.py
rename to src/biocutils/named_list.py
index af4670a..0d971d0 100644
--- a/src/biocutils/NamedList.py
+++ b/src/biocutils/named_list.py
@@ -3,7 +3,7 @@
 
 from .assign_sequence import assign_sequence
 from .combine_sequences import combine_sequences
-from .Names import Names, _name_to_position, _sanitize_names
+from .names import Names, _name_to_position, _sanitize_names
 from .normalize_subscript import (
     NormalizedSubscript,
     SubscriptTypes,
diff --git a/src/biocutils/normalize_subscript.py b/src/biocutils/normalize_subscript.py
index da37a7e..d85c6d0 100644
--- a/src/biocutils/normalize_subscript.py
+++ b/src/biocutils/normalize_subscript.py
@@ -103,7 +103,7 @@ def normalize_subscript(
         names:
             List of names for each entry in the object. If not None, this
             should have length equal to ``length``. Some optimizations
-            are possible if this is a :py:class:`~Names.Names` object.
+            are possible if this is a :py:class:`~Names.names` object.
 
         non_negative_only:
             Whether negative indices must be converted into non-negative
@@ -138,7 +138,7 @@ def normalize_subscript(
                 + "' for vector-like object with no names"
             )
         i = -1
-        from .Names import Names
+        from .names import Names
 
         if isinstance(names, Names):
             i = names.map(sub)
@@ -197,7 +197,7 @@ def normalize_subscript(
     output = []
     has_strings = set()
     string_positions = []
-    from .Names import Names
+    from .names import Names
 
     are_names_indexed = isinstance(names, Names)
 
diff --git a/src/biocutils/StringList.py b/src/biocutils/string_list.py
similarity index 98%
rename from src/biocutils/StringList.py
rename to src/biocutils/string_list.py
index 518b729..8fe1d84 100644
--- a/src/biocutils/StringList.py
+++ b/src/biocutils/string_list.py
@@ -1,7 +1,7 @@
 from typing import Any, Iterable, Optional, Sequence, Union
 
-from .NamedList import NamedList
-from .Names import Names
+from .named_list import NamedList
+from .names import Names
 from .normalize_subscript import SubscriptTypes
 
 
diff --git a/tests/test_biocobject.py b/tests/test_biocobject.py
index 4315995..3645936 100644
--- a/tests/test_biocobject.py
+++ b/tests/test_biocobject.py
@@ -1,7 +1,7 @@
 import pytest
 from copy import copy
 from biocutils.bioc_object import BiocObject
-from biocutils.NamedList import NamedList
+from biocutils.named_list import NamedList
 
     
 def test_init_empty():

From dea34833f2949f67d32b3f1117427820713417d3 Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Thu, 18 Dec 2025 15:04:18 -0800
Subject: [PATCH 06/10] rename files

---
 src/biocutils/{Factor.py => factor.py} | 0
 src/biocutils/{Names.py => names.py}   | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename src/biocutils/{Factor.py => factor.py} (100%)
 rename src/biocutils/{Names.py => names.py} (100%)

diff --git a/src/biocutils/Factor.py b/src/biocutils/factor.py
similarity index 100%
rename from src/biocutils/Factor.py
rename to src/biocutils/factor.py
diff --git a/src/biocutils/Names.py b/src/biocutils/names.py
similarity index 100%
rename from src/biocutils/Names.py
rename to src/biocutils/names.py

From 5692f35342bbfe7cf57a83561e6107e3a0b656cc Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Thu, 18 Dec 2025 15:06:02 -0800
Subject: [PATCH 07/10] remove 3.9 from actions

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

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index e8ab6fa..e0f247d 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -28,7 +28,7 @@ jobs:
   test:
     strategy:
       matrix:
-        python: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
+        python: ["3.10", "3.11", "3.12", "3.13", "3.14"]
         platform:
           - ubuntu-latest
           - macos-latest

From 31bb62783dc16399bb19e74d48e0d0b783564d71 Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Thu, 18 Dec 2025 15:07:45 -0800
Subject: [PATCH 08/10] export biocobject

---
 src/biocutils/__init__.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/biocutils/__init__.py b/src/biocutils/__init__.py
index 13fa31c..ed683fd 100644
--- a/src/biocutils/__init__.py
+++ b/src/biocutils/__init__.py
@@ -60,3 +60,5 @@
 
 from .get_height import get_height
 from .is_high_dimensional import is_high_dimensional
+
+from .bioc_object import BiocObject
\ No newline at end of file

From c8aa74082d62afa12186bd4bf21dc287dc73d31f Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Thu, 18 Dec 2025 15:13:25 -0800
Subject: [PATCH 09/10] NamedList() refer to use from_dict instead

---
 src/biocutils/named_list.py | 32 +++++++++-----------------------
 1 file changed, 9 insertions(+), 23 deletions(-)

diff --git a/src/biocutils/named_list.py b/src/biocutils/named_list.py
index 0d971d0..f51b050 100644
--- a/src/biocutils/named_list.py
+++ b/src/biocutils/named_list.py
@@ -39,6 +39,9 @@ def __init__(
             _validate:
                 Internal use only.
         """
+        if isinstance(data, dict):
+            raise TypeError("'data' is a dictionary, use 'NamedList.from_dict' instead.")
+
         if _validate:
             if data is None:
                 data = []
@@ -86,14 +89,7 @@ def __str__(self) -> str:
             names if any exist.
         """
         if self._names is not None:
-            return (
-                "["
-                + ", ".join(
-                    repr(self._names[i]) + "=" + repr(x)
-                    for i, x in enumerate(self._data)
-                )
-                + "]"
-            )
+            return "[" + ", ".join(repr(self._names[i]) + "=" + repr(x) for i, x in enumerate(self._data)) + "]"
         else:
             return repr(self._data)
 
@@ -204,9 +200,7 @@ def __getitem__(self, index: SubscriptTypes) -> Union["NamedList", Any]:
         else:
             return self.get_slice(NormalizedSubscript(index))
 
-    def set_value(
-        self, index: Union[str, int], value: Any, in_place: bool = False
-    ) -> "NamedList":
+    def set_value(self, index: Union[str, int], value: Any, in_place: bool = False) -> "NamedList":
         """
         Args:
             index:
@@ -253,9 +247,7 @@ def set_value(
 
         return output
 
-    def set_slice(
-        self, index: SubscriptTypes, value: Sequence, in_place: bool = False
-    ) -> "NamedList":
+    def set_slice(self, index: SubscriptTypes, value: Sequence, in_place: bool = False) -> "NamedList":
         """
         Args:
             index:
@@ -324,9 +316,7 @@ def _define_output(self, in_place: bool) -> "NamedList":
         else:
             return self.copy()
 
-    def safe_insert(
-        self, index: Union[int, str], value: Any, in_place: bool = False
-    ) -> "NamedList":
+    def safe_insert(self, index: Union[int, str], value: Any, in_place: bool = False) -> "NamedList":
         """
         Args:
             index:
@@ -530,9 +520,7 @@ def _combine_sequences_NamedList(*x: NamedList) -> NamedList:
 
 
 @assign_sequence.register
-def _assign_sequence_NamedList(
-    x: NamedList, indices: Sequence[int], other: Sequence
-) -> NamedList:
+def _assign_sequence_NamedList(x: NamedList, indices: Sequence[int], other: Sequence) -> NamedList:
     if isinstance(other, NamedList):
         # Do NOT set the names if 'other' is a NamedList. Names don't change
         # during assignment/setting operations, as a matter of policy. This is
@@ -541,6 +529,4 @@ def _assign_sequence_NamedList(
         # of names, and it would be weird for the same sequence of names to
         # suddently become an invalid indexing vector after an assignment.
         other = other._data
-    return type(x)(
-        assign_sequence(x._data, NormalizedSubscript(indices), other), names=x._names
-    )
+    return type(x)(assign_sequence(x._data, NormalizedSubscript(indices), other), names=x._names)

From cd0fa74bc7f460ce77287eaa5a9ee0198e94cc18 Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Thu, 18 Dec 2025 15:17:16 -0800
Subject: [PATCH 10/10] switch to classmethod

---
 src/biocutils/named_list.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/biocutils/named_list.py b/src/biocutils/named_list.py
index f51b050..94918bd 100644
--- a/src/biocutils/named_list.py
+++ b/src/biocutils/named_list.py
@@ -482,28 +482,28 @@ def as_dict(self) -> Dict[str, Any]:
                 output[n] = self[i]
         return output
 
-    @staticmethod
-    def from_list(x: list) -> "NamedList":
+    @classmethod
+    def from_list(cls, x: list) -> "NamedList":
         """
         Args:
             x: List of data elements.
 
         Returns:
-            A ``NamedList`` instance with the contents of ``x`` and no names.
+            A instance with the contents of ``x`` and no names.
         """
-        return NamedList(x)
+        return cls(x)
 
-    @staticmethod
-    def from_dict(x: dict) -> "NamedList":
+    @classmethod
+    def from_dict(cls, x: dict) -> "NamedList":
         """
         Args:
             x: Dictionary where keys are strings (or can be coerced to them).
 
         Returns:
-            A ``NamedList`` instance where the list elements are the values of
+            A instance where the list elements are the values of
             ``x`` and the names are the stringified keys.
         """
-        return NamedList(list(x.values()), names=Names(str(y) for y in x.keys()))
+        return cls(list(x.values()), names=Names(str(y) for y in x.keys()))
 
 
 @subset_sequence.register