Merge branch 'main' into bkmartinjr/fastercsx

.pre-commit-config.yaml

@@ -1,16 +1,16 @@
 exclude: ^doc/source/
 repos:
   - repo: https://github.com/psf/black
-    rev: "24.4.2"
+    rev: "24.10.0"
     hooks:
     - id: black
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.5
+    rev: v0.7.4
     hooks:
     - id: ruff
       args: ["--config=apis/python/pyproject.toml"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.1
+    rev: v1.13.0
     hooks:
     - id: mypy
       additional_dependencies:

apis/python/notebooks/tutorial_exp_query.ipynb

@@ -53,6 +53,7 @@
    "source": [
     "import tarfile\n",
     "import tempfile\n",
+    "\n",
     "sparse_uri = tempfile.mktemp()\n",
     "with tarfile.open(\"data/pbmc3k-sparse.tgz\") as handle:\n",
     "    handle.extractall(sparse_uri)\n",

apis/python/notebooks/tutorial_soma_append_mode.ipynb

@@ -55,6 +55,7 @@
    ],
    "source": [
     "import scanpy as sc\n",
+    "\n",
     "import tiledbsoma\n",
     "import tiledbsoma.io\n",
     "import tiledbsoma.logging\n",

apis/python/notebooks/tutorial_soma_objects.ipynb

@@ -67,6 +67,7 @@
    "source": [
     "import tarfile\n",
     "import tempfile\n",
+    "\n",
     "dense_uri = tempfile.mktemp()\n",
     "with tarfile.open(\"data/pbmc3k-dense.tgz\") as handle:\n",
     "    handle.extractall(dense_uri)\n",
@@ -1459,6 +1460,7 @@
    "source": [
     "import tarfile\n",
     "import tempfile\n",
+    "\n",
     "sparse_uri = tempfile.mktemp()\n",
     "with tarfile.open(\"data/pbmc3k-sparse.tgz\") as handle:\n",
     "    handle.extractall(sparse_uri)\n",

apis/python/notebooks/tutorial_soma_reading.ipynb

@@ -92,6 +92,7 @@
    "source": [
     "import tarfile\n",
     "import tempfile\n",
+    "\n",
     "sparse_uri = tempfile.mktemp()\n",
     "with tarfile.open(\"data/pbmc3k-sparse.tgz\") as handle:\n",
     "    handle.extractall(sparse_uri)\n",

apis/python/notebooks/tutorial_soma_shape.ipynb

@@ -646,10 +646,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import tiledbsoma.io\n",
     "import tarfile\n",
     "import tempfile\n",
     "\n",
+    "import tiledbsoma.io\n",
+    "\n",
     "uri = tempfile.mktemp()\n",
     "with tarfile.open(\"data/pbmc3k-sparse-pre-1.15.tgz\") as handle:\n",
     "    handle.extractall(uri)\n",

apis/python/notebooks/tutorial_spatial.ipynb

@@ -20,27 +20,25 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import shlex\n",
     "from functools import partial\n",
-    "import numpy as np\n",
     "from os import makedirs, remove\n",
-    "from os.path import basename, exists, join\n",
-    "import shlex\n",
+    "from os.path import exists, join\n",
     "from shutil import rmtree\n",
     "from subprocess import check_call\n",
     "from sys import stderr\n",
-    "from urllib.parse import urlparse\n",
-    "err = partial(print, file=stderr)\n",
     "\n",
+    "import matplotlib.patches as mplp\n",
+    "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "import scanpy as sc\n",
+    "from matplotlib.collections import PatchCollection\n",
     "\n",
-    "from tiledbsoma.experimental import from_visium\n",
-    "from tiledbsoma import Experiment\n",
     "import tiledbsoma\n",
+    "from tiledbsoma import Experiment\n",
+    "from tiledbsoma.experimental import from_visium\n",
     "\n",
-    "import matplotlib as mpl\n",
-    "import matplotlib.pyplot as plt\n",
-    "import matplotlib.patches as mplp\n",
-    "from matplotlib.collections import PatchCollection"
+    "err = partial(print, file=stderr)\n"
    ]
   },
   {

apis/python/src/tiledbsoma/_util.py

@@ -165,7 +165,8 @@ def slice_to_numeric_range(
     start = domain_start if slc.start is None else max(slc.start, domain_start)
     stop = domain_stop if slc.stop is None else min(slc.stop, domain_stop)
 
-    if stop < start:
+    # Lint says the left-hand and right-hand sides are both unions
+    if stop < start:  # type: ignore[operator]
         # With the above, we have guaranteed that at least one bound will
         # include the domain.  If we get here, that means that the other bound
         # never included it (e.g. stop == slc.stop < domain_start == start).