Create New Pybind11 Context Constructor That Takes in Capsule (#1165)

* Create a custom constructor for `Context` that takes in a Python
  object. Use `keep_alive<1, 2>` to increase the refcount of the
  `tiledb.Ctx` object so that it not garbage collected prior to
  the `Group` object.
* Previously, the `Group` constructor was using a constructor
  for `Context` that took in a capsule object. Because the Pybind11
  `Group` has no knowledge of the Cython `Ctx`, the `tiledb_ctx_t *`
  pointer would be freed prior to `~Group` despite the usage of
  `keep_alive<1, 2>`. This would cause a segfault.

Author: nguyenv

HISTORY.md

@@ -4,6 +4,9 @@
 * Use `bool` instead of `uint8` for Boolean dtype in `dataframe_.py` [#1154](https://github.com/TileDB-Inc/TileDB-Py/pull/1154)
 * Support QueryCondition OR operator [#1146](https://github.com/TileDB-Inc/TileDB-Py/pull/1146)
 
+## Bug Fixes
+* Fix error where passing a `Context` to `Group` would segfault intermittenly [#1165](https://github.com/TileDB-Inc/TileDB-Py/pull/1165)
+
 # TileDB-Py 0.15.3 Release Notes
 
 ## TileDB Embedded updates:

tiledb/cc/context.cc

@@ -15,8 +15,12 @@ void init_context(py::module &m) {
       .def(py::init())
       .def(py::init<Config>())
       .def(py::init<py::capsule, bool>())
+      .def(py::init([](py::object ctx, bool own) {
+             return Context(py::capsule(ctx.attr("__capsule__")()), own);
+           }),
+           py::keep_alive<1, 2>())
 
-      .def_property_readonly("config", &Context::config)
+      .def("config", &Context::config)
       .def("set_tag", &Context::set_tag)
       .def("get_stats", &Context::stats)
       .def("is_supported_fs", &Context::is_supported_fs);

tiledb/group.py

@@ -245,7 +245,7 @@ def clear(self):
 
     def __init__(self, uri: str, mode: str = "r", ctx: "Ctx" = None):
         self._ctx = ctx or default_ctx()
-        cctx = lt.Context(self._ctx.__capsule__(), False)
+        cctx = lt.Context(self._ctx, False)
 
         if mode not in Group._mode_to_query_type:
             raise ValueError(f"invalid mode {mode}")
@@ -266,7 +266,7 @@ def create(uri: str, ctx: "Ctx" = None):
         :type ctx: tiledb.Ctx
         """
         _ctx = ctx or default_ctx()
-        cctx = lt.Context(_ctx.__capsule__(), False)
+        cctx = lt.Context(_ctx, False)
         lt.Group._create(cctx, uri)
 
     def open(self, mode: str = "r"):

tiledb/tests/test_group.py

@@ -479,3 +479,17 @@ def test_basic(self, test_vals):
         grp = tiledb.Group(path, "r")
         self.assert_metadata_roundtrip(grp.meta, test_vals)
         grp.close()
+
+    def test_pass_context(self):
+        foo = self.path("foo")
+        bar = self.path("foo/bar")
+
+        tiledb.group_create(foo)
+        tiledb.group_create(bar)
+
+        ctx = tiledb.Ctx()
+        with tiledb.Group(foo, mode="w", ctx=ctx) as G:
+            G.add(bar, name="bar")
+
+        with tiledb.Group(foo, mode="r", ctx=ctx) as G:
+            assert "bar" in G