Move vacuum to pure Python (#2067)

tiledb/__init__.py

@@ -83,14 +83,14 @@
     remove,
     save,
     schema_like,
+    vacuum,
     walk,
 )
 from .libtiledb import (
     Array,
     Ctx,
     DenseArrayImpl,
     SparseArrayImpl,
-    vacuum,
 )
 from .multirange_indexing import EmptyRange
 from .object import Object

tiledb/highlevel.py

@@ -269,6 +269,70 @@ def consolidate(uri, config=None, ctx=None, fragment_uris=None, timestamp=None):
         return arr.consolidate(ctx, config)
 
 
+def vacuum(uri, config=None, ctx=None, timestamp=None):
+    """
+    Vacuum underlying array fragments after consolidation.
+
+    :param str uri: URI of array to be vacuumed
+    :param config: Override the context configuration for vacuuming.
+        Defaults to None, inheriting the context parameters.
+    :param (ctx: tiledb.Ctx, optional): Context. Defaults to
+        `tiledb.default_ctx()`.
+    :raises TypeError: cannot convert `uri` to unicode string
+    :raises: :py:exc:`tiledb.TileDBError`
+
+    This operation of this function is controlled by
+    the `"sm.vacuum.mode"` parameter, which accepts the values ``fragments``,
+    ``fragment_meta``, and ``array_meta``. Rather than passing the timestamp
+    into this function, it may be set by using `"sm.vacuum.timestamp_start"`and
+    `"sm.vacuum.timestamp_end"` which takes in a time in UNIX seconds. If both
+    are set then this function's `timestamp` argument will be used.
+
+    **Example:**
+
+    >>> import tiledb, numpy as np
+    >>> import tempfile
+    >>> path = tempfile.mkdtemp()
+    >>> with tiledb.from_numpy(path, np.random.rand(4)) as A:
+    ...     pass # make sure to close
+    >>> with tiledb.open(path, 'w') as A:
+    ...     for i in range(4):
+    ...         A[:] = np.ones(4, dtype=np.int64) * i
+    >>> paths = tiledb.VFS().ls(path)
+    >>> # should be 12 (2 base files + 2*5 fragment+ok files)
+    >>> (); len(paths); () # doctest:+ELLIPSIS
+    (...)
+    >>> () ; tiledb.consolidate(path) ; () # doctest:+ELLIPSIS
+    (...)
+    >>> tiledb.vacuum(path)
+    >>> paths = tiledb.VFS().ls(path)
+    >>> # should now be 4 ( base files + 2 fragment+ok files)
+    >>> (); len(paths); () # doctest:+ELLIPSIS
+    (...)
+
+    """
+    ctx = _get_ctx(ctx)
+    if config is None:
+        config = tiledb.Config()
+
+    if timestamp is not None:
+        warnings.warn(
+            "Partial vacuuming via timestamp will be deprecrated in "
+            "a future release and replaced by passing in fragment URIs.",
+            DeprecationWarning,
+        )
+
+        if not isinstance(timestamp, tuple) and len(timestamp) != 2:
+            raise TypeError("'timestamp' argument expects tuple(start: int, end: int)")
+
+        if timestamp[0] is not None:
+            config["sm.vacuum.timestamp_start"] = timestamp[0]
+        if timestamp[1] is not None:
+            config["sm.vacuum.timestamp_end"] = timestamp[1]
+
+    lt.Array.vacuum(ctx, uri, config)
+
+
 def schema_like(*args, shape=None, dtype=None, ctx=None, **kwargs):
     """
     Return an ArraySchema corresponding to a NumPy-like object or

tiledb/libtiledb.pyx

@@ -3156,76 +3156,3 @@ cdef class SparseArrayImpl(Array):
                 dim_values[dim] = tuple(np.unique(query[dim]))
 
         return dim_values
-
-
-def vacuum(uri, config=None, ctx=None, timestamp=None):
-    """
-    Vacuum underlying array fragments after consolidation.
-
-    :param str uri: URI of array to be vacuumed
-    :param config: Override the context configuration for vacuuming.
-        Defaults to None, inheriting the context parameters.
-    :param (ctx: tiledb.Ctx, optional): Context. Defaults to
-        `tiledb.default_ctx()`.
-    :raises TypeError: cannot convert `uri` to unicode string
-    :raises: :py:exc:`tiledb.TileDBError`
-
-    This operation of this function is controlled by
-    the `"sm.vacuum.mode"` parameter, which accepts the values ``fragments``,
-    ``fragment_meta``, and ``array_meta``. Rather than passing the timestamp
-    into this function, it may be set by using `"sm.vacuum.timestamp_start"`and
-    `"sm.vacuum.timestamp_end"` which takes in a time in UNIX seconds. If both
-    are set then this function's `timestamp` argument will be used.
-
-    **Example:**
-
-    >>> import tiledb, numpy as np
-    >>> import tempfile
-    >>> path = tempfile.mkdtemp()
-    >>> with tiledb.from_numpy(path, np.random.rand(4)) as A:
-    ...     pass # make sure to close
-    >>> with tiledb.open(path, 'w') as A:
-    ...     for i in range(4):
-    ...         A[:] = np.ones(4, dtype=np.int64) * i
-    >>> paths = tiledb.VFS().ls(path)
-    >>> # should be 12 (2 base files + 2*5 fragment+ok files)
-    >>> (); len(paths); () # doctest:+ELLIPSIS
-    (...)
-    >>> () ; tiledb.consolidate(path) ; () # doctest:+ELLIPSIS
-    (...)
-    >>> tiledb.vacuum(path)
-    >>> paths = tiledb.VFS().ls(path)
-    >>> # should now be 4 ( base files + 2 fragment+ok files)
-    >>> (); len(paths); () # doctest:+ELLIPSIS
-    (...)
-
-    """
-    cdef tiledb_ctx_t* ctx_ptr = NULL
-    cdef tiledb_config_t* config_ptr = NULL
-
-    if not ctx:
-        ctx = default_ctx()
-
-    if timestamp is not None:
-        warnings.warn("Partial vacuuming via timestamp will be deprecrated in "
-                      "a future release and replaced by passing in fragment URIs.",
-                      DeprecationWarning)
-
-        if config is None:
-            config = Config()
-
-        if not isinstance(timestamp, tuple) and len(timestamp) != 2:
-            raise TypeError("'timestamp' argument expects tuple(start: int, end: int)")
-
-        if timestamp[0] is not None:
-            config["sm.vacuum.timestamp_start"] = timestamp[0]
-        if timestamp[1] is not None:
-            config["sm.vacuum.timestamp_end"] = timestamp[1]
-
-    ctx_ptr = safe_ctx_ptr(ctx)
-    config_ptr = <tiledb_config_t*>PyCapsule_GetPointer(
-        config.__capsule__(), "config") if config is not None else NULL
-    cdef bytes buri = unicode_path(uri)
-    cdef const char* uri_ptr = PyBytes_AS_STRING(buri)
-
-    check_error(ctx, tiledb_array_vacuum(ctx_ptr, uri_ptr, config_ptr))