[python] Work around pyarrow>=13 issue on MacOS, 1.10 branch

single-cell-data · Jun 14, 2024 · 2fdac1d · 2fdac1d
1 parent babb931
commit 2fdac1d
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Showing 3 changed files with 15 additions and 12 deletions.
diff --git a/apis/python/setup.py b/apis/python/setup.py
@@ -320,13 +320,7 @@ def run(self):
         "attrs>=22.2",
         "numba>=0.58.0",
         "pandas",
-        # TODO: once we no longer support Python 3.7, remove this and pin to pyarrow >= 14.0.1
-        # https://github.com/single-cell-data/TileDB-SOMA/issues/1926
-        "pyarrow_hotfix",
-        # MacOS issue with import pyarrow before import tiledb at >= 13.0:
-        # https://github.com/single-cell-data/TileDB-SOMA/issues/1926#issuecomment-1834695149
-        "pyarrow>=9.0.0,<13.0.0; platform_system=='Darwin'",
-        "pyarrow>=9.0.0; platform_system!='Darwin'",
+        "pyarrow>=14.0.0",
         "scanpy>=1.9.2",
         "scipy",
         # Note: the somacore version is in .pre-commit-config.yaml too

diff --git a/apis/python/src/tiledbsoma/__init__.py b/apis/python/src/tiledbsoma/__init__.py
@@ -89,6 +89,13 @@
 :class:`ValueError`.
 """
 
+# This ABSOLUTELY MUST be imported before pyarrow to avoid abort-traps on MacOS
+# with any pyarrow >= 13.  And the pre-commit hook, isort, et al. MUST NOT be
+# allowed to reorder this.  See also
+# https://github.com/single-cell-data/TileDB-SOMA/issues/1926
+# https://github.com/single-cell-data/TileDB-SOMA/issues/1849
+import tiledb  # noqa E402
+
 # ^^ the rest is autogen whether viewed from Python on-line help, Sphinx/readthedocs, etc.  It's
 # crucial that we include a separator (e.g. "Classes and functions") to make an entry in the
 # readthedocs table of contents.
@@ -138,11 +145,6 @@
 from somacore import AxisColumnNames, AxisQuery, ExperimentAxisQuery
 from somacore.options import ResultOrder
 
-# TODO: once we no longer support Python 3.7, remove this and pin to pyarrow >= 14.0.1
-# https://github.com/single-cell-data/TileDB-SOMA/issues/1926
-# ruff: noqa
-import pyarrow_hotfix
-
 from ._collection import Collection
 from ._constants import SOMA_JOINID
 from ._dataframe import DataFrame

diff --git a/apis/python/tests/__init__.py b/apis/python/tests/__init__.py
@@ -1,3 +1,10 @@
+# This ABSOLUTELY MUST be imported before pyarrow to avoid abort-traps on MacOS
+# with any pyarrow >= 13.  And the pre-commit hook, isort, et al. MUST NOT be
+# allowed to reorder this.  See also
+# https://github.com/single-cell-data/TileDB-SOMA/issues/1926
+# https://github.com/single-cell-data/TileDB-SOMA/issues/1849
+import tiledb  # noqa E402
+
 import pyarrow as pa
 from typeguard import install_import_hook