BiocPy · jkanche · Feb 29, 2024 · Feb 29, 2024 · Feb 29, 2024 · Feb 29, 2024
diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml
@@ -48,4 +48,4 @@ jobs:
       uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
       with:
         user: __token__
-        password: ${{ secrets.PYPI_PASSWORD }}
+        password: ${{ secrets.PYPI_PASSWORD }}
diff --git a/.github/workflows/pypi-test.yml b/.github/workflows/pypi-test.yml
@@ -5,21 +5,26 @@ name: Test the library
 
 on:
   push:
-    branches:
-      - master
+    branches: [ master ]
   pull_request:
+    branches: [ master ]
 
 jobs:
   build:
 
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ '3.8', '3.9', '3.10', '3.11', '3.12' ]
 
+    name: Python ${{ matrix.python-version }}
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.9
+    - name: Setup Python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

diff --git a/.pre-commit-config.yml → .pre-commit-config.yaml b/.pre-commit-config.yml → .pre-commit-config.yaml
@@ -49,4 +49,4 @@ repos:
 # - repo: https://github.com/codespell-project/codespell
 #   rev: v2.2.5
 #   hooks:
-#   - id: codespell
+#   - id: codespell
diff --git a/pyproject.toml b/pyproject.toml
@@ -21,4 +21,4 @@ convention = "google"
 "__init__.py" = ["E402", "F401"]
 
 [tool.black]
-force-exclude = "__init__.py"
+force-exclude = "__init__.py"
diff --git a/setup.py b/setup.py
@@ -1,10 +1,8 @@
-"""
-    Setup file for tiledbarray.
-    Use setup.cfg to configure your project.
+"""Setup file for tiledbarray. Use setup.cfg to configure your project.
 
-    This file was generated with PyScaffold 4.5.
-    PyScaffold helps you to put up the scaffold of your new Python project.
-    Learn more under: https://pyscaffold.org/
+This file was generated with PyScaffold 4.5.
+PyScaffold helps you to put up the scaffold of your new Python project.
+Learn more under: https://pyscaffold.org/
 """
 from setuptools import setup
 

diff --git a/src/tiledbarray/TileDBArraySeed.py b/src/tiledbarray/TileDBArraySeed.py
@@ -112,11 +112,9 @@ def dimnames(self) -> List[str]:
 
 @chunk_grid.register
 def chunk_grid_TileDbArraySeed(x: TileDbArraySeed):
-    """
-    See :py:meth:`~delayedarray.chunk_grid.chunk_grid`.
+    """See :py:meth:`~delayedarray.chunk_grid.chunk_grid`.
 
-    The cost factor is set to 20 to reflect the computational work involved in
-    extracting data from disk.
+    The cost factor is set to 20 to reflect the computational work involved in extracting data from disk.
     """
     return chunk_shape_to_grid(x._tiles, x._shape, cost_factor=20)
 
@@ -142,7 +140,7 @@ def _sanitize_subset(subset, dimlength):
     elif isinstance(subset, range):
         subset = list(subset)
 
-    return subset
+    return sorted(subset)
 
 
 def _extract_array(x: TileDbArraySeed, subset: Tuple[Sequence[int], ...]):
@@ -241,18 +239,17 @@ def extract_sparse_array_TileDbArraySeed(
 
 
 class TileDbArray(DelayedArray):
-    """Sparse or Dense arrays from TileDB file as a ``DelayedArray``. This
-    subclass allows developers to implement custom methods for tiledb-backed
-    sparse or dense matrices."""
+    """Sparse or Dense arrays from TileDB file as a ``DelayedArray``.
+
+    This subclass allows developers to implement custom methods for tiledb-backed sparse or dense matrices.
+    """
 
     def __init__(
         self,
         path: Union[str, TileDbArraySeed],
         attribute_name: Optional[str],
     ):
-        """
-        To construct a ``TileDbArray`` from an existing
-        :py:class:`~TileDbArraySeed`, use
+        """To construct a ``TileDbArray`` from an existing :py:class:`~TileDbArraySeed`, use
         :py:meth:`~delayedarray.wrap.wrap` instead.
 
         Args:

diff --git a/src/tiledbarray/__init__.py b/src/tiledbarray/__init__.py
@@ -15,4 +15,4 @@
 finally:
     del version, PackageNotFoundError
 
-from .TileDBArraySeed import TileDbArraySeed, TileDbArray
+from .TileDBArraySeed import TileDbArraySeed, TileDbArray
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -1,10 +1,9 @@
-"""
-    Dummy conftest.py for tiledbarray.
+"""Dummy conftest.py for tiledbarray.
 
-    If you don't know what this is for, just leave it empty.
-    Read more about conftest.py under:
-    - https://docs.pytest.org/en/stable/fixture.html
-    - https://docs.pytest.org/en/stable/writing_plugins.html
+If you don't know what this is for, just leave it empty.
+Read more about conftest.py under:
+- https://docs.pytest.org/en/stable/fixture.html
+- https://docs.pytest.org/en/stable/writing_plugins.html
 """
 
 # import pytest
diff --git a/tests/test_tiledbarray.py b/tests/test_tiledbarray.py
@@ -86,4 +86,4 @@ def test_TileDbArray():
         is True
     )
 
-    assert np.allclose(delayedarray.to_dense_array(roundtrip), y) is True
+    assert np.allclose(delayedarray.to_dense_array(roundtrip), y) is True
-Original file line number
+Diff line change
@@ Expand Up / @@ -86,4 +86,4 @@ def test_TileDbArray(): @@
             is True
         )
-        assert np.allclose(delayedarray.to_dense_array(roundtrip), y) is True
+        assert np.allclose(delayedarray.to_dense_array(roundtrip), y) is True