Revert #439 (#443)

apis/python/src/tiledbsoma/query_condition.py

@@ -111,6 +111,7 @@ class QueryCondition:
     """
 
     expression: str
+    ctx: tiledb.Ctx = field(default_factory=tiledb.default_ctx, repr=False)
     tree: ast.Expression = field(init=False, repr=False)
     c_obj: PyQueryCondition = field(init=False, repr=False)
 
@@ -130,7 +131,7 @@ def __post_init__(self):
             )
 
     def init_query_condition(self, schema: tiledb.ArraySchema, query_attrs: List[str]):
-        qctree = QueryConditionTree(schema, query_attrs)
+        qctree = QueryConditionTree(self.ctx, schema, query_attrs)
         self.c_obj = qctree.visit(self.tree.body)
 
         if not isinstance(self.c_obj, PyQueryCondition):
@@ -142,6 +143,7 @@ def init_query_condition(self, schema: tiledb.ArraySchema, query_attrs: List[str
 
 @dataclass
 class QueryConditionTree(ast.NodeVisitor):
+    ctx: tiledb.Ctx
     schema: tiledb.ArraySchema
     query_attrs: List[str]
 
@@ -239,7 +241,7 @@ def aux_visit_Compare(
         dtype = "string" if dt.kind in "SUa" else dt.name
         val = self.cast_val_to_dtype(val, dtype)
 
-        pyqc = PyQueryCondition()
+        pyqc = PyQueryCondition(self.ctx)
         self.init_pyqc(pyqc, dtype)(att, val, op)
 
         return pyqc

apis/python/src/tiledbsoma/soma_sparse_nd_array.py

@@ -6,8 +6,6 @@
 import scipy.sparse as sp
 import tiledb
 
-import tiledbsoma.libtiledbsoma as clib
-
 from . import util_arrow
 from .soma_collection import SOMACollectionBase
 from .tiledb_array import TileDBArray
@@ -144,7 +142,7 @@ def nnz(self) -> int:
         """
         Return the number of stored values in the array, including explicitly stored zeros.
         """
-        return cast(int, clib.SOMAReader(self.uri).nnz())
+        raise NotImplementedError("SOMASparseNdArray.nnz is not implemented.")
 
     def read_sparse_tensor(
         self,

apis/python/tests/test_soma_sparse_nd_array.py

@@ -371,13 +371,15 @@ def test_soma_sparse_nd_array_nnz(tmp_path):
     """
     a = soma.SOMASparseNdArray(tmp_path.as_posix())
     a.create(type=pa.int32(), shape=(10, 10, 10))
-    assert a.nnz == 0
+    with pytest.raises(NotImplementedError):
+        assert a.nnz == 0
 
     t: pa.SparseCOOTensor = create_random_tensor(
         "coo", a.shape, pa.int32().to_pandas_dtype(), 0.1
     )
     a.write_sparse_tensor(t)
-    assert t.non_zero_length == a.nnz
+    with pytest.raises(NotImplementedError):
+        assert t.non_zero_length == a.nnz
 
 
 def test_soma_sparse_nd_array_reshape(tmp_path):

libtiledbsoma/CMakeLists.txt

@@ -46,9 +46,7 @@ option(SUPERBUILD "If true, perform a superbuild (builds all missing dependencie
 option(CMAKE_IDE "(Used for CLion builds). Disables superbuild and sets the EP install dir." OFF)
 option(FORCE_BUILD_TILEDB "Forces a local build of TileDB instead of searching system paths." ON)
 option(TILEDB_FORCE_ALL_DEPS "Forces a local build of TileDB instead of searching system paths." OFF)
-# TODO: keep this until the next TileDB core release
-# option(DOWNLOAD_TILEDB_PREBUILT "If tiledb is being super built, this controls downloading prebuilt artifacts or building from source" ON)
-option(DOWNLOAD_TILEDB_PREBUILT "If tiledb is being super built, this controls downloading prebuilt artifacts or building from source" OFF)
+option(DOWNLOAD_TILEDB_PREBUILT "If tiledb is being super built, this controls downloading prebuilt artifacts or building from source" ON)
 
 # TileDB BUILD Options
 option(TILEDB_S3 "Enables S3/minio support using aws-cpp-sdk" ON)
@@ -154,7 +152,7 @@ if (MSVC)
   #   C4996: deprecation warning about e.g. sscanf.
   add_compile_options(/W4 /wd4101 /wd4146 /wd4244 /wd4251 /wd4456 /wd4457 /wd4702 /wd4800 /wd4996)
   # Warnings as errors:
-  if (TILEDBSOMA_ENABLE_WERROR)
+  if (ENABLE_TILEDBSOMA_WERROR)
     add_compile_options(/WX)
   endif()
   # Disable GDI (which we don't need, and causes some macro

libtiledbsoma/cmake/Modules/FindTileDB_EP.cmake

@@ -86,11 +86,8 @@ else()
     else() # Build from source
         ExternalProject_Add(ep_tiledb
           PREFIX "externals"
-          # TODO: keep this until the next TileDB core release
-          # URL "https://github.com/TileDB-Inc/TileDB/archive/2.11.1.zip"
-          # URL_HASH SHA1=98505ca9924b0fe703feb0da08c0918e675b2a8f
-          GIT_REPOSITORY "https://github.com/TileDB-Inc/TileDB/"
-          GIT_TAG "yt/ch22464/make_logger_prefix_unique-2.12"
+          URL "https://github.com/TileDB-Inc/TileDB/archive/2.11.1.zip"
+          URL_HASH SHA1=98505ca9924b0fe703feb0da08c0918e675b2a8f
           DOWNLOAD_NAME "tiledb.zip"
           CMAKE_ARGS
             -DCMAKE_INSTALL_PREFIX=${EP_INSTALL_PREFIX}

libtiledbsoma/src/pyapi/query_condition.cc

@@ -68,11 +68,8 @@ class PyQueryCondition {
   PyQueryCondition() = delete;
 
   PyQueryCondition(py::object ctx) {
-    (void)ctx;
     try {
-      // create one global context for all query conditions
-      static Context context = Context();
-      ctx_ = context;
+      set_ctx(ctx);
       qc_ = shared_ptr<QueryCondition>(new QueryCondition(ctx_));
     } catch (TileDBError &e) {
       TPY_ERROR_LOC(e.what());

libtiledbsoma/src/soma_reader.cc

@@ -148,12 +148,6 @@ uint64_t SOMAReader::nnz() {
     //===============================================================
     // If only one fragment, return total_cell_num
     auto fragment_count = fragment_info.fragment_num();
-
-    if (fragment_count == 0) {
-        // Array schema has been created but no data have been written
-        return 0;
-    }
-
     if (fragment_count == 1) {
         return fragment_info.total_cell_num();
     }

scripts/bld

@@ -77,8 +77,6 @@ else
   # non-trivial cmake debugging.
   if [ ! -z "$LIBTILEDBSOMA_DEBUG_BUILD" ]; then
     EXTRA_OPTS="-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON"
-    # TILEDB_WERROR=OFF is necessary to build core with XCode 14; doesn't hurt for XCode 13.
-    # EXTRA_OPTS="-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DTILEDB_WERROR=OFF _DENABLE_TILEDBSOMA_WERROR=OFF"
   fi
   # Also (pro-tip), set nproc=1 to get a more deterministic ordering of output lines.
   if [ ! -z "$LIBTILEDBSOMA_NO_PARALLEL_BUILD" ]; then