[python] verify_core_versions() during import tiledbsoma (#2437) (#…

…2443)

* verify_core_versions() during `import tiledbsoma`

* add comment

Co-authored-by: Ryan Williams <[email protected]>

apis/python/src/tiledbsoma/__init__.py

@@ -156,6 +156,7 @@
     get_SOMA_version,
     get_storage_engine,
     show_package_versions,
+    verify_core_versions,
 )
 from ._indexer import IntIndexer, tiledbsoma_build_index
 from ._measurement import Measurement
@@ -168,6 +169,11 @@
     tiledbsoma_stats_reset,
 )
 
+# Ensure TileDB-Py and libtiledbsoma have matching core versions; if they don't, undefined behavior
+# / segfaults may ensue. Once libtiledbsoma is the only "path to core" (cf. #1632), this can be
+# removed.
+verify_core_versions()
+
 __version__ = get_implementation_version()
 
 __all__ = [

apis/python/src/tiledbsoma/_general_utilities.py

@@ -5,13 +5,14 @@
 
 """General utility functions.
 """
-
+import os
 import platform
 import sys
+from re import fullmatch
 
 import tiledb
 
-from .pytiledbsoma import version as libtiledbsoma_version
+from .pytiledbsoma import version as libtiledbsoma_core_version_str
 
 
 def get_SOMA_version() -> str:
@@ -59,19 +60,75 @@ def get_storage_engine() -> str:
     return "tiledb"
 
 
+def get_tiledb_py_core_version() -> str:
+    """Returns the version of libtiledb ("core") used by the `tiledb` Python library.
+
+    Lifecycle: maturing
+    """
+    return ".".join(str(ijk) for ijk in list(tiledb.libtiledb.version()))
+
+
+def get_libtiledbsoma_core_version() -> str:
+    """Returns the version of libtiledb ("core") used by libtiledbsoma.
+
+    Lifecycle: maturing
+    """
+    v = libtiledbsoma_core_version_str()
+    m = fullmatch(r"libtiledb=(\d+\.\d+\.\d+)", v)
+    if m is None:
+        raise ValueError(f"Unexpected libtiledbsoma_core_version: {v}")
+    return m.group(1)
+
+
+# Set this env var to "err" to print an error to stderr when TileDB-Py's and libtiledbsoma's core
+# versions mismatch (by default, an AssertionError is raised).
+TILEDB_CORE_MISMATCHED_VERSIONS_ERROR_LEVEL_VAR = (
+    "TILEDB_CORE_MISMATCHED_VERSIONS_ERROR_LEVEL"
+)
+
+
+def verify_core_versions() -> None:
+    """Verify that the versions of libtiledb used by the `tiledb` Python library and
+    libtiledbsoma are the same.
+
+    See discussion on https://github.com/single-cell-data/TileDB-SOMA/issues/1837; this
+    will be unnecessary when libtiledbsoma is the only "path to core" (cf.
+    https://github.com/single-cell-data/TileDB-SOMA/issues/1632).
+
+    Lifecycle: maturing
+    """
+    tiledb_py_core_version = get_tiledb_py_core_version()
+    libtiledbsoma_core_version = get_libtiledbsoma_core_version()
+    if tiledb_py_core_version != libtiledbsoma_core_version:
+        msg = "libtiledb versions used by tiledb and libtiledbsoma differ: %s != %s" % (
+            tiledb_py_core_version,
+            libtiledbsoma_core_version,
+        )
+        if os.environ.get(TILEDB_CORE_MISMATCHED_VERSIONS_ERROR_LEVEL_VAR) == "err":
+            print(msg, file=sys.stderr)
+            print(
+                f"Continuing, since ${TILEDB_CORE_MISMATCHED_VERSIONS_ERROR_LEVEL_VAR} is set, but it is highly recommended you fix the core version mismatch, as undefined behavior and segfaults can result.",
+                file=sys.stderr,
+            )
+        else:
+            raise AssertionError(
+                f"libtiledb versions used by tiledb and libtiledbsoma differ: {tiledb_py_core_version} != {libtiledbsoma_core_version}"
+            )
+
+
 def show_package_versions() -> None:
     """Nominal use is for bug reports, so issue filers and issue fixers can be on
     the same page.
 
     Lifecycle: maturing
     """
-    print("tiledbsoma.__version__       ", get_implementation_version())
-    print("TileDB-Py tiledb.version()   ", tiledb.version())
-    print(
-        "TileDB core version          ",
-        ".".join(str(ijk) for ijk in list(tiledb.libtiledb.version())),
-    )
-    print("libtiledbsoma version()      ", libtiledbsoma_version())
-    print("python version               ", ".".join(str(v) for v in sys.version_info))
     u = platform.uname()
-    print("OS version                   ", u.system, u.release)
+    # fmt: off
+    print("tiledbsoma.__version__             ", get_implementation_version())
+    print("TileDB-Py version                  ", ".".join(str(v) for v in tiledb.version()))
+    print("TileDB core version (tiledb)       ", get_tiledb_py_core_version())
+    print("TileDB core version (libtiledbsoma)", get_libtiledbsoma_core_version())
+    print("python version                     ", ".".join(str(v) for v in sys.version_info))
+    print("OS version                         ", u.system, u.release)
+    # fmt: on
+    verify_core_versions()