Fixes for TileDB-Py 0.33.2 (#147)

* Rename tiledb.cc references to tiledb.libtiledb

Author: kounelisagis

tests/__init__.py

@@ -6,7 +6,7 @@
 
 import tiledb
 from tiledb.bioimg import ATTR_NAME
-from tiledb.cc import WebpInputFormat
+from tiledb.libtiledb import WebpInputFormat
 from tiledb.bioimg.helpers import merge_ned_ranges
 import xml.etree.ElementTree as ET
 

tests/integration/converters/test_ome_tiff.py

@@ -12,7 +12,7 @@
 from tiledb.bioimg.converters.ome_tiff import OMETiffConverter
 from tiledb.bioimg.helpers import open_bioimg
 from tiledb.bioimg.openslide import TileDBOpenSlide
-from tiledb.cc import WebpInputFormat
+from tiledb.libtiledb import WebpInputFormat
 
 
 def test_ome_tiff_converter(tmp_path):

tests/integration/converters/test_ome_tiff_experimental.py

@@ -7,7 +7,7 @@
 from tiledb.bioimg.converters.ome_tiff import OMETiffConverter
 from tiledb.bioimg.helpers import open_bioimg
 from tiledb.bioimg.openslide import TileDBOpenSlide
-from tiledb.cc import WebpInputFormat
+from tiledb.libtiledb import WebpInputFormat
 
 
 # We need to expand on the test files. Most of the test files we have currently are not memory

tests/integration/converters/test_ome_zarr.py

@@ -11,7 +11,7 @@
 from tiledb.bioimg.converters.ome_zarr import OMEZarrConverter
 from tiledb.bioimg.helpers import iter_color, open_bioimg
 from tiledb.bioimg.openslide import TileDBOpenSlide
-from tiledb.cc import WebpInputFormat
+from tiledb.libtiledb import WebpInputFormat
 
 schemas = (get_schema(2220, 2967), get_schema(387, 463), get_schema(1280, 431))
 

tests/integration/converters/test_openslide.py

@@ -10,7 +10,7 @@
 from tiledb.bioimg.converters.openslide import OpenSlideConverter
 from tiledb.bioimg.helpers import open_bioimg
 from tiledb.bioimg.openslide import TileDBOpenSlide
-from tiledb.cc import WebpInputFormat
+from tiledb.libtiledb import WebpInputFormat
 
 
 @pytest.mark.parametrize("preserve_axes", [False, True])

tests/integration/converters/test_png.py

@@ -10,7 +10,7 @@
 from tiledb.bioimg.converters.png import PNGConverter
 from tiledb.bioimg.helpers import open_bioimg
 from tiledb.bioimg.openslide import TileDBOpenSlide
-from tiledb.cc import WebpInputFormat
+from tiledb.libtiledb import WebpInputFormat
 
 
 def create_synthetic_image(

tiledb/bioimg/converters/base.py

@@ -37,7 +37,7 @@
     register_group = None
 
 import tiledb
-from tiledb.cc import WebpInputFormat
+from tiledb.libtiledb import WebpInputFormat
 
 from .. import ATTR_NAME
 from ..helpers import (

tiledb/bioimg/converters/ome_tiff.py

@@ -30,8 +30,8 @@
     raise err
 
 from tiledb import VFS, Config, Ctx
-from tiledb.cc import WebpInputFormat
 from tiledb.highlevel import _get_ctx
+from tiledb.libtiledb import WebpInputFormat
 
 from .. import ATTR_NAME, EXPORT_TILE_SIZE, WHITE_RGBA
 from ..helpers import (

tiledb/bioimg/converters/ome_zarr.py

@@ -32,8 +32,8 @@
     raise err
 
 from tiledb import Config, Ctx
-from tiledb.cc import WebpInputFormat
 from tiledb.highlevel import _get_ctx
+from tiledb.libtiledb import WebpInputFormat
 
 from .. import WHITE_RGB
 from ..helpers import get_logger_wrapper, get_rgba, translate_config_to_s3fs

tiledb/bioimg/converters/openslide.py

@@ -8,8 +8,8 @@
 from numpy._typing import NDArray
 
 from tiledb import Config, Ctx
-from tiledb.cc import WebpInputFormat
 from tiledb.highlevel import _get_ctx
+from tiledb.libtiledb import WebpInputFormat
 
 from ..helpers import cache_filepath, get_logger_wrapper, is_remote_protocol, iter_color
 from . import DEFAULT_SCRATCH_SPACE

tiledb/bioimg/converters/png.py

@@ -18,8 +18,8 @@
 from PIL import Image
 
 from tiledb import VFS, Config, Ctx
-from tiledb.cc import WebpInputFormat
 from tiledb.highlevel import _get_ctx
+from tiledb.libtiledb import WebpInputFormat
 
 from ..helpers import get_logger_wrapper, iter_color
 from .axes import Axes

tiledb/bioimg/helpers.py

@@ -24,7 +24,7 @@
 
 import tiledb
 from tiledb import Config, Ctx
-from tiledb.cc import WebpInputFormat
+from tiledb.libtiledb import WebpInputFormat
 
 from . import ATTR_NAME
 from .converters.axes import Axes, AxesMapper
@@ -215,7 +215,7 @@ def iter_levels_meta(
     for o in group:
         with open_bioimg(o.uri, config=config, ctx=ctx) as array:
             try:
-                level = array.meta["level"]
+                level = int(array.meta["level"])
             except KeyError as exc:
                 raise RuntimeError(
                     "Key: 'level' not found in array metadata. Make sure that levels have been "