Use typeguard==4.4.0, somacore==1.0.22` (#3250)

fixes #3216

.pre-commit-config.yaml

@@ -18,7 +18,7 @@ repos:
         # Pandas 2.x types (e.g. `pd.Series[Any]`). See `_types.py` or https://github.com/single-cell-data/TileDB-SOMA/issues/2839
         # for more info.
         - "pandas-stubs>=2"
-        - "somacore==1.0.21"
+        - "somacore==1.0.22"
         - types-setuptools
       args: ["--config-file=apis/python/pyproject.toml", "apis/python/src", "apis/python/devtools"]
       pass_filenames: false

apis/python/requirements_dev.txt

@@ -1,11 +1,7 @@
 black
-ruff
 pytest
 pytest-cov
+ruff
 sparse
-# Python 3.12 support requires https://github.com/agronholm/typeguard/pull/490, which landed between 4.3.0 and 4.4.0.
-# However, 4.4.0 also included https://github.com/agronholm/typeguard/pull/496, which causes errors in Python 3.9 (e.g.
-# https://github.com/single-cell-data/TileDB-SOMA/actions/runs/11545217103/job/32131849817), so we are pinning to the
-# last useful commit here. See also: https://github.com/single-cell-data/TileDB-SOMA/issues/3216.
-typeguard @ git+https://github.com/agronholm/typeguard@afad2c7
+typeguard==4.4.0
 types-setuptools

apis/python/setup.py

@@ -335,8 +335,8 @@ def run(self):
         "pyarrow",
         "scanpy>=1.9.2",
         "scipy",
-        # Note: the somacore version is in .pre-commit-config.yaml too
-        "somacore==1.0.21",
+        # Note: the somacore version is also pinned in .pre-commit-config.yaml
+        "somacore==1.0.22",
         "typing-extensions",  # Note "-" even though `import typing_extensions`
     ],
     extras_require={