TILEDB_STRING_ASCII Now Displaying As UTF-8 / str Everywhere

* Previously `TILEDB_STRING_ASCII` data was inconsistently displayed
  as `bytes`
* There is a need to coerce to `str` everywhere because (1) previously
  the resulting dataframe displayed ASCII as bytes with Pyarrow disabled
  but as str with Pyarrow enabled, and (2) this fix would remove the
  need to copy large amounts of data to convert back and forth in the
  TileDB-SingleCell Python API
* Warning now emitted to the user to pass `dtype="ascii"` for string dim
  types in lieu of `np.bytes_` or `np.str_` for clarity. All three still
  work and under the hood use `np.str_` and `TILEDB_STRING_ASCII`
* `repr` of string dimensions is now always displayed as `dtype="ascii"`.
  Calling `.dtype()` will return `np.dtype('U')` as the return signature
  of `dtype` requires a Numpy dtype

Author: nguyenv

HISTORY.md

@@ -1,5 +1,8 @@
 # In Progress
 
+## API Changes
+* `TILEDB_STRING_ASCII` displaying as `str` instead of `bytes` [#1304](https://github.com/TileDB-Inc/TileDB-Py/pull/1304)
+
 ## Misc Updates
 * Wheels will no longer be supported for macOS 10.15 Catalina; the minimum supported macOS version is now 11 Big Sur [#1300](https://github.com/TileDB-Inc/TileDB-Py/pull/1300)
 * Wheels will no longer supported for Python 3.6 [#1300](https://github.com/TileDB-Inc/TileDB-Py/pull/1300)

tiledb/core.cc

@@ -246,10 +246,10 @@ py::dtype tiledb_dtype(tiledb_datatype_t type, uint32_t cell_val_num) {
     std::string base_str;
     switch (type) {
     case TILEDB_CHAR:
-    case TILEDB_STRING_ASCII:
       base_str = "|S";
       break;
     case TILEDB_STRING_UTF8:
+    case TILEDB_STRING_ASCII:
       base_str = "|U";
       break;
     default:

tiledb/dataframe_.py

@@ -273,9 +273,8 @@ def dim_for_column(name, values, dtype, tile, full_domain=False, dim_filters=Non
     return tiledb.Dim(
         name=name,
         domain=(dim_min, dim_max),
-        # libtiledb only supports TILEDB_ASCII dimensions, so we must use
-        # nb.bytes_ which will force encoding on write
-        dtype=np.bytes_ if dtype == np.str_ else dtype,
+        # TileDB only supports TILEDB_STRING_ASCII dimensions for strings
+        dtype="ascii" if dtype in (np.bytes_, np.str_) else dtype,
         tile=tile,
         filters=dim_filters,
     )

tiledb/libmetadata.pyx

@@ -82,10 +82,10 @@ cdef object unpack_metadata_val(
     ):
     assert value_num != 0, "internal error: unexpected value_num==0"
 
-    if value_type == TILEDB_STRING_UTF8:
+    if value_type == TILEDB_STRING_UTF8 or value_type == TILEDB_STRING_ASCII:
         return value_ptr[:value_num].decode('UTF-8')  if value_ptr != NULL else ''
 
-    if value_type == TILEDB_CHAR or value_type == TILEDB_STRING_ASCII:
+    if value_type == TILEDB_CHAR:
         return value_ptr[:value_num] if value_ptr != NULL else b''
 
     if value_ptr == NULL:

tiledb/libtiledb.pyx

@@ -110,7 +110,7 @@ _tiledb_dtype_to_numpy_typeid_convert ={
     TILEDB_INT16: np.NPY_INT16,
     TILEDB_UINT16: np.NPY_UINT16,
     TILEDB_CHAR: np.NPY_STRING,
-    TILEDB_STRING_ASCII: np.NPY_STRING,
+    TILEDB_STRING_ASCII: np.NPY_UNICODE,
     TILEDB_STRING_UTF8: np.NPY_UNICODE,
 }
 IF LIBTILEDB_VERSION_MAJOR >= 2:
@@ -133,7 +133,7 @@ _tiledb_dtype_to_numpy_dtype_convert = {
     TILEDB_INT16: np.int16,
     TILEDB_UINT16: np.uint16,
     TILEDB_CHAR: np.dtype('S1'),
-    TILEDB_STRING_ASCII: np.dtype('S'),
+    TILEDB_STRING_ASCII: np.dtype('U'),
     TILEDB_STRING_UTF8: np.dtype('U1'),
 }
 IF LIBTILEDB_VERSION_MAJOR >= 2:
@@ -1824,10 +1824,8 @@ cdef class Attr(object):
                 filters_str +=  repr(f) + ", "
             filters_str += "])"
 
-        attr_dtype = "ascii" if self.isascii else self.dtype
-
         # filters_str must be last with no spaces
-        return (f"""Attr(name={repr(self.name)}, dtype='{attr_dtype!s}', """
+        return (f"""Attr(name={repr(self.name)}, dtype='{self.dtype!s}', """
                 f"""var={self.isvar!s}, nullable={self.isnullable!s}"""
                 f"""{filters_str})""")
 
@@ -1852,7 +1850,7 @@ cdef class Attr(object):
 
         output.write("<tr>")
         output.write(f"<td>{self.name}</td>")
-        output.write(f"<td>{'ascii' if self.isascii else self.dtype}</td>")
+        output.write(f"<td>{self.isascii}</td>")
         output.write(f"<td>{self.isvar}</td>")
         output.write(f"<td>{self.isnullable}</td>")
         output.write(f"<td>{self.filters._repr_html_()}</td>")
@@ -1903,8 +1901,12 @@ cdef class Dim(object):
         if not ctx:
             ctx = default_ctx()
 
+        is_string = (
+            isinstance(dtype, str) and dtype == "ascii"
+        ) or np.dtype(dtype) in (np.str_, np.bytes_)
+
         if var is not None:
-            if var and np.dtype(dtype) not in (np.str_, np.bytes_):
+            if var and not is_string:
                 raise TypeError("'var=True' specified for non-str/bytes dtype")
 
         if domain is not None and len(domain) != 2:
@@ -1919,12 +1921,14 @@ cdef class Dim(object):
         cdef void* tile_size_ptr = NULL
         cdef np.dtype domain_dtype
 
-        if ((isinstance(dtype, str) and dtype == "ascii") or
-                dtype == np.dtype('S')):
+        if is_string:
             # Handle var-len domain type
             #  (currently only TILEDB_STRING_ASCII)
             # The dimension's domain is implicitly formed as
             # coordinates are written.
+            if dtype != "ascii":
+                warnings.warn("Use 'ascii' for string dimensions.")
+            dtype = np.dtype("|U0")
             dim_datatype = TILEDB_STRING_ASCII
         else:
             if domain is None or len(domain) != 2:
@@ -1985,17 +1989,19 @@ cdef class Dim(object):
         self.ptr = dim_ptr
 
     def __repr__(self):
-        filters_str = ""
+        filters = ""
         if self.filters:
-            filters_str = ", filters=FilterList(["
+            filters = ", filters=FilterList(["
             for f in self.filters:
-                filters_str +=  repr(f) + ", "
-            filters_str += "])"
+                filters +=  repr(f) + ", "
+            filters += "])"
+
+        dtype = "ascii" if self._get_type() == TILEDB_STRING_ASCII else self.dtype
 
         # for consistency, print `var=True` for string-like types
-        varlen = "" if not self.dtype in (np.str_, np.bytes_) else ", var=True"
-        return "Dim(name={0!r}, domain={1!s}, tile={2!r}, dtype='{3!s}'{4}{5})" \
-            .format(self.name, self.domain, self.tile, self.dtype, varlen, filters_str)
+        varlen = "" if dtype != "ascii" else ", var=True"
+        return f"Dim(name={self.name!r}, domain={self.domain}, tile={self.tile!r}, dtype='{dtype}'{varlen}{filters})"
+
 
     def _repr_html_(self) -> str:
         output = io.StringIO()
@@ -2022,7 +2028,7 @@ cdef class Dim(object):
         output.write(f"<td>{self.domain}</td>")
         output.write(f"<td>{self.tile}</td>")
         output.write(f"<td>{self.dtype}</td>")
-        output.write(f"<td>{self.dtype in (np.str_, np.bytes_)}</td>")
+        output.write(f"<td>{self.dtype == 'ascii'}</td>")
         output.write(f"<td>{self.filters._repr_html_()}</td>")
         output.write("</tr>")
 
@@ -2222,7 +2228,7 @@ cdef class Dim(object):
         :rtype: tuple(numpy scalar, numpy scalar)
 
         """
-        if self.dtype == np.dtype('S'):
+        if self.dtype == np.dtype('U'):
             return None, None
         cdef const void* domain_ptr = NULL
         check_error(self.ctx,
@@ -3864,9 +3870,8 @@ cdef class Array(object):
                     results.append((None, None))
                     continue
 
-                buf_dtype = 'S'
-                start_buf = np.empty(start_size, 'S' + str(start_size))
-                end_buf = np.empty(end_size, 'S' + str(end_size))
+                start_buf = np.empty(start_size, f"S{start_size}")
+                end_buf = np.empty(end_size, f"S{end_size}")
                 start_buf_ptr = np.PyArray_DATA(start_buf)
                 end_buf_ptr = np.PyArray_DATA(end_buf)
             else:
@@ -3884,7 +3889,8 @@ cdef class Array(object):
                     return None
 
                 if start_size > 0 and end_size > 0:
-                    results.append((start_buf.item(0), end_buf.item(0)))
+                    results.append((start_buf.item(0).decode("UTF-8"), 
+                                    end_buf.item(0).decode("UTF-8")))
                 else:
                     results.append((None, None))
             else:
@@ -4918,7 +4924,7 @@ def index_domain_coords(dom: Domain, idx: tuple, check_ndim: bool):
                 # ensure strings contain only ASCII characters
                 domain_coords.append(np.array(sel, dtype=np.bytes_, ndmin=1))
             except Exception as exc:
-                raise TileDBError(f'Dim\' strings may only contain ASCII characters')
+                raise TileDBError('Dimension strings may only contain ASCII characters')
         else:
             domain_coords.append(np.array(sel, dtype=dim.dtype, ndmin=1))
 

tiledb/tests/test_filters.py

@@ -97,7 +97,7 @@ def test_dictionary_encoding(self):
         schema = tiledb.ArraySchema(domain=dom, attrs=[attr], sparse=True)
         tiledb.Array.create(path, schema)
 
-        data = [b"x" * i for i in np.random.randint(1, 10, size=10)]
+        data = ["x" * i for i in np.random.randint(1, 10, size=10)]
 
         with tiledb.open(path, "w") as A:
             A[np.arange(10)] = data

tiledb/tests/test_fragments.py

@@ -75,7 +75,7 @@ def test_array_fragments_var(self):
 
         uri = self.path("test_array_fragments_var")
         dom = tiledb.Domain(
-            tiledb.Dim(name="dim", domain=(None, None), tile=None, dtype=np.bytes_)
+            tiledb.Dim(name="dim", domain=(None, None), tile=None, dtype="ascii")
         )
         schema = tiledb.ArraySchema(
             domain=dom,
@@ -285,22 +285,22 @@ def test_nonempty_domain_date(self):
     def test_nonempty_domain_strings(self):
         uri = self.path("test_nonempty_domain_strings")
         dom = tiledb.Domain(
-            tiledb.Dim(name="x", domain=(None, None), dtype=np.bytes_),
-            tiledb.Dim(name="y", domain=(None, None), dtype=np.bytes_),
+            tiledb.Dim(name="x", domain=(None, None), dtype="ascii"),
+            tiledb.Dim(name="y", domain=(None, None), dtype="ascii"),
         )
         att = tiledb.Attr()
         schema = tiledb.ArraySchema(sparse=True, domain=dom, attrs=(att,))
 
         tiledb.SparseArray.create(uri, schema)
 
         with tiledb.SparseArray(uri, mode="w") as T:
-            x_dims = [b"a", b"b", b"c", b"d"]
-            y_dims = [b"e", b"f", b"g", b"h"]
+            x_dims = ["a", "b", "c", "d"]
+            y_dims = ["e", "f", "g", "h"]
             T[x_dims, y_dims] = np.array([1, 2, 3, 4])
 
         with tiledb.SparseArray(uri, mode="w") as T:
-            x_dims = [b"a", b"b"]
-            y_dims = [b"e", b"f"]
+            x_dims = ["a", "b"]
+            y_dims = ["e", "f"]
             T[x_dims, y_dims] = np.array([1, 2])
 
         fragment_info = PyFragmentInfo(uri, schema, False, tiledb.default_ctx())