Merge remote-tracking branch 'origin/dev' into db/scikit-build-core

Author: dudoslav

.pre-commit-config.yaml

@@ -4,6 +4,6 @@ repos:
     hooks:
     - id: black
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.284
+    rev: v0.4.4
     hooks:
     - id: ruff

HISTORY.md

@@ -1,3 +1,20 @@
+# Release 0.29.1
+
+## Improvements
+
+* Expose WebP enums by @kounelisagis in https://github.com/TileDB-Inc/TileDB-Py/pull/1974
+* Add Array.query in docs and improve docs in general by @kounelisagis in https://github.com/TileDB-Inc/TileDB-Py/pull/1965
+* Add support for creating WKB/WKT attributes by @jp-dark in https://github.com/TileDB-Inc/TileDB-Py/pull/1912
+* Add wrapping for ls recursive by @kounelisagis in https://github.com/TileDB-Inc/TileDB-Py/pull/1968
+* Fix compatibility for delete_fragments by @kounelisagis in https://github.com/TileDB-Inc/TileDB-Py/pull/1966
+
+## Build system changes
+
+* Fix ModuleNotFoundError: No module named 'numpy' on build by @kounelisagis in https://github.com/TileDB-Inc/TileDB-Py/pull/1979
+* Add support for numpy2 by @kounelisagis in https://github.com/TileDB-Inc/TileDB-Py/pull/1969
+* Fix syntax error in nightly build workflow by @ihnorton in https://github.com/TileDB-Inc/TileDB-Py/pull/1970
+* Set an upper bound for numpy to dodge 2.0 by @sgillies in https://github.com/TileDB-Inc/TileDB-Py/pull/1963
+
 # Release 0.29.0
 
 * TileDB-Py 0.29.0 includes TileDB Embedded [2.23.0](https://github.com/TileDB-Inc/TileDB/releases/tag/2.23.0)

doc/source/conf.py

@@ -75,7 +75,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

doc/source/python-api.rst

@@ -68,7 +68,7 @@ Filters
    .. automethod:: __getitem__(idx)
    .. automethod:: __len__
 
-.. autoclass:: tiledb.libtiledb.CompressionFilter
+.. autoclass:: tiledb.CompressionFilter
    :members:
 .. autoclass:: tiledb.GzipFilter
    :members:
@@ -116,22 +116,21 @@ Dense Array
 -----------
 
 .. autoclass:: tiledb.DenseArray
-   :members:
-
-   .. automethod:: __getitem__(selection)
-   .. automethod:: __setitem__(selection, value)
-   .. automethod:: query
-   .. automethod:: from_numpy(uri, array, ctx=None, **kwargs)
+   :members: query
+   :special-members: __getitem__, __setitem__
 
 Sparse Array
 ------------
 
 .. autoclass:: tiledb.SparseArray
-   :members:
+   :members: query
+   :special-members: __getitem__, __setitem__
 
-   .. automethod:: __getitem__(selection)
-   .. automethod:: __setitem__(selection, value)
-   .. automethod:: query
+Query
+---------------
+
+.. autoclass:: tiledb.libtiledb.Query
+   :members:
 
 Query Condition
 ---------------

pyproject.toml

@@ -80,6 +80,9 @@ extend-select = ["I001"]
 extend-exclude = ["doc"]
 fix = true
 
+[tool.ruff.lint]
+select = ["NPY201"]
+
 [tool.ruff.per-file-ignores]
 "tiledb/__init__.py" = ["F401"]
 

tiledb/__init__.py

@@ -39,6 +39,7 @@
     Bzip2Filter,
     ChecksumMD5Filter,
     ChecksumSHA256Filter,
+    CompressionFilter,
     DeltaFilter,
     DictionaryFilter,
     DoubleDeltaFilter,
@@ -73,6 +74,8 @@
 )
 from .libtiledb import (
     Array,
+    DenseArrayImpl,
+    SparseArrayImpl,
     consolidate,
     ls,
     move,
@@ -85,8 +88,6 @@
     vacuum,
     walk,
 )
-from .libtiledb import DenseArrayImpl as DenseArray
-from .libtiledb import SparseArrayImpl as SparseArray
 from .multirange_indexing import EmptyRange
 from .object import Object
 from .parquet_ import from_parquet
@@ -116,13 +117,19 @@
 try:
     from tiledb.cloud.cloudarray import CloudArray
 except ImportError:
-    pass
+
+    class DenseArray(DenseArrayImpl):
+        pass
+
+    class SparseArray(SparseArrayImpl):
+        pass
+
 else:
 
-    class DenseArray(DenseArray, CloudArray):
+    class DenseArray(DenseArrayImpl, CloudArray):
         pass
 
-    class SparseArray(SparseArray, CloudArray):
+    class SparseArray(SparseArrayImpl, CloudArray):
         pass
 
     del CloudArray

tiledb/array_schema.py

@@ -322,7 +322,7 @@ def version(self) -> int:
         """The array's schema (storage) version.
 
         :rtype: int
-        :raises :py:exc:`tiledb.TileDBError`
+        :raises: :py:exc:`tiledb.TileDBError`
         """
         return self._version
 

tiledb/ctx.py

@@ -209,7 +209,7 @@ def dict(self, prefix: str = ""):
 
         :param str prefix: return only parameters with a given prefix
         :rtype: dict
-        :return: Config parameter / values as a a Python dict
+        :return: Config parameter / values as a Python dict
 
         """
         return dict(ConfigItems(self, prefix=prefix))

tiledb/filter.py

@@ -79,7 +79,7 @@ class CompressionFilter(Filter):
     >>> with tempfile.TemporaryDirectory() as tmp:
     ...     dom = tiledb.Domain(tiledb.Dim(domain=(0, 9), tile=2, dtype=np.uint64))
     ...     a1 = tiledb.Attr(name="a1", dtype=np.int64,
-    ...                      filters=tiledb.FilterList([tiledb.GzipFilter(level=10)]))
+    ...                      filters=tiledb.FilterList([tiledb.CompressionFilter(level=10)]))
     ...     schema = tiledb.ArraySchema(domain=dom, attrs=(a1,))
     ...     tiledb.DenseArray.create(tmp + "/array", schema)
 
@@ -326,8 +326,7 @@ class DoubleDeltaFilter(CompressionFilter):
 
     :param level: -1 (default) sets the compressor level to the default level as specified in TileDB core. Otherwise, sets the compressor level to the given value.
     :type level: int
-    :param reinterp_dtype: (optional) sets the compressor to compress the data treating
-    as the new datatype.
+    :param reinterp_dtype: (optional) sets the compressor to compress the data treating as the new datatype.
 
     **Example:**
 
@@ -501,7 +500,8 @@ class PositiveDeltaFilter(Filter):
     :param ctx: A TileDB Context
     :type ctx: tiledb.Ctx
     :param window: -1 (default) sets the max window size for the filter to the default window size as specified in TileDB core. Otherwise, sets the compressor level to the given value.
-     :type window: int
+    :type window: int
+
     **Example:**
 
     >>> import tiledb, numpy as np, tempfile
@@ -754,6 +754,9 @@ class WebpFilter(Filter):
         lt.FilterOption.WEBP_LOSSLESS,
     )
 
+    # Expose WebP enums at the top level
+    WebpInputFormat = lt.WebpInputFormat
+
     def __init__(
         self,
         input_format: lt.WebpInputFormat = None,

tiledb/highlevel.py

@@ -224,7 +224,7 @@ def is_ndarray_like(arr):
     elif shape and dtype:
         if np.issubdtype(np.bytes_, dtype):
             dtype = np.dtype("S")
-        elif np.issubdtype(dtype, np.unicode_):
+        elif np.issubdtype(dtype, np.str_):
             dtype = np.dtype("U")
 
         ndim = len(shape)