Remove Cython Dependency (#2118)

* Move version method to pybind11
* Delete libtiledb.pyx, libtiledb.pxd, and common.pxi
* Add __iter__ for FragmentsInfoIterator

.gitignore

@@ -7,9 +7,6 @@ __pycache__/
 *.so
 *.dylib
 
-# Cython extensions
-*.cpp
-
 # Distribution / packaging
 .Python
 env/

pyproject.toml

@@ -2,7 +2,6 @@
 requires = [
     "scikit-build-core",
     "pybind11",
-    "Cython>=3",
     "numpy>=2.0.1"
 ]
 build-backend = "scikit_build_core.build"

tiledb/CMakeLists.txt

@@ -1,33 +1,3 @@
-# Cython
-
-add_custom_command(
-  OUTPUT libtiledb.cc
-  COMMAND Python::Interpreter -m cython
-          "${CMAKE_CURRENT_SOURCE_DIR}/libtiledb.pyx" --output-file libtiledb.cc
-  DEPENDS libtiledb.pyx
-  VERBATIM
-)
-
-python_add_library(
-    libtiledb
-    MODULE
-    libtiledb.cc
-    WITH_SOABI
-)
-
-target_link_libraries(
-    libtiledb
-    PUBLIC
-    Python::NumPy
-    TileDB::tiledb_shared
-)
-
-target_compile_features(
-    libtiledb
-    PUBLIC
-    cxx_std_20
-)
-
 # Pybind11
 
 pybind11_add_module(
@@ -64,7 +34,7 @@ if (TILEDB_SERIALIZATION)
     )
 endif()
 
-install(TARGETS main libtiledb DESTINATION tiledb)
+install(TARGETS main DESTINATION tiledb)
 
 if(TILEDB_DOWNLOADED)
     message(STATUS "Adding \"libtiledb\" into install group")
@@ -73,18 +43,15 @@ if(TILEDB_DOWNLOADED)
 
     if (APPLE)
         set_target_properties(main PROPERTIES INSTALL_RPATH "@loader_path")
-        set_target_properties(libtiledb PROPERTIES INSTALL_RPATH "@loader_path")
     elseif(UNIX)
         set_target_properties(main PROPERTIES INSTALL_RPATH "\$ORIGIN")
-        set_target_properties(libtiledb PROPERTIES INSTALL_RPATH "\$ORIGIN")
     endif()
 else()
     # If using external TileDB core library force it to be linked at runtime using RPATH
     get_property(TILEDB_LOCATION TARGET TileDB::tiledb_shared PROPERTY LOCATION)
     get_filename_component(TILEDB_LOCATION ${TILEDB_LOCATION} DIRECTORY)
     message(STATUS "Setting RPATH for targets \"main\" and \"libtiledb\" to ${TILEDB_LOCATION}")
     set_target_properties(main PROPERTIES INSTALL_RPATH ${TILEDB_LOCATION})
-    set_target_properties(libtiledb PROPERTIES INSTALL_RPATH ${TILEDB_LOCATION})
 endif()
 
-add_subdirectory(cc)
+add_subdirectory(libtiledb)

tiledb/__init__.py

@@ -2,15 +2,6 @@
 import os
 import sys
 
-# un-comment this section to fix Cython backtrace line-numbers in
-# IPython/Jupyter. see https://bugs.python.org/issue32797#msg323167
-# ---
-# try:
-#    from importlib.machinery import ExtensionFileLoader
-# else:
-#    del ExtensionFileLoader.get_source
-# ---
-
 if os.name == "posix":
     if sys.platform == "darwin":
         lib_name = "libtiledb.dylib"
@@ -19,6 +10,14 @@
 else:
     lib_name = "tiledb"
 
+import numpy as np
+
+# TODO: get rid of this - It is currently used for unified numpy printing accross numpy versions
+np.set_printoptions(
+    legacy="1.21" if np.lib.NumpyVersion(np.__version__) >= "1.22.0" else False
+)
+del np
+
 from tiledb.libtiledb import version as libtiledb_version
 
 if libtiledb_version()[0] == 2 and libtiledb_version()[1] >= 26:
@@ -30,7 +29,6 @@
 from .array import Array
 from .array_schema import ArraySchema
 from .attribute import Attr
-from .cc import TileDBError
 from .consolidation_plan import ConsolidationPlan
 from .ctx import Config, Ctx, default_ctx, scope_ctx
 from .dataframe_ import from_csv, from_pandas, open_dataframe
@@ -88,7 +86,7 @@
     vacuum,
     walk,
 )
-from .libtiledb import Ctx
+from .libtiledb import TileDBError
 from .multirange_indexing import EmptyRange
 from .object import Object
 from .parquet_ import from_parquet

tiledb/aggregation.py

@@ -1,4 +1,4 @@
-import tiledb.cc as lt
+import tiledb.libtiledb as lt
 
 
 class Aggregation:

tiledb/array.py

@@ -4,7 +4,7 @@
 import numpy as np
 
 import tiledb
-import tiledb.cc as lt
+import tiledb.libtiledb as lt
 
 from .ctx import Config, Ctx, default_ctx
 from .datatypes import DataType

tiledb/array_schema.py

@@ -5,16 +5,15 @@
 
 import numpy as np
 
-import tiledb.cc as lt
-from tiledb.libtiledb import version as libtiledb_version
+import tiledb.libtiledb as lt
 
 from .attribute import Attr
 from .ctx import Ctx, CtxMixin, default_ctx
 from .dimension_label import DimLabel
 from .domain import Domain
 from .filter import Filter, FilterList
 
-if libtiledb_version()[0] == 2 and libtiledb_version()[1] >= 26:
+if lt.version()[0] == 2 and lt.version()[1] >= 25:
     from .current_domain import CurrentDomain
 
 _tiledb_order_to_string = {
@@ -388,7 +387,7 @@ def has_dim_label(self, name: str) -> bool:
         """
         return self._has_dim_label(self._ctx, name)
 
-    if libtiledb_version()[0] == 2 and libtiledb_version()[1] >= 26:
+    if lt.version()[0] == 2 and lt.version()[1] >= 25:
 
         @property
         def current_domain(self) -> CurrentDomain:

tiledb/attribute.py

@@ -4,7 +4,7 @@
 
 import numpy as np
 
-import tiledb.cc as lt
+import tiledb.libtiledb as lt
 
 from .ctx import Ctx, CtxMixin
 from .datatypes import DataType

tiledb/consolidation_plan.py

@@ -1,6 +1,6 @@
 import pprint
 
-import tiledb.cc as lt
+import tiledb.libtiledb as lt
 
 from .array import Array
 from .ctx import Ctx, CtxMixin, default_ctx

tiledb/ctx.py

@@ -5,7 +5,7 @@
 from typing import Union
 
 import tiledb
-import tiledb.cc as lt
+import tiledb.libtiledb as lt
 
 _ctx_var = ContextVar("ctx")
 

tiledb/current_domain.py

@@ -1,4 +1,4 @@
-import tiledb.cc as lt
+import tiledb.libtiledb as lt
 
 from .ctx import Ctx, CtxMixin
 from .domain import Domain

tiledb/data_order.py

@@ -1,6 +1,6 @@
 from enum import Enum
 
-import tiledb.cc as lt
+import tiledb.libtiledb as lt
 
 
 class DataOrder(Enum):

tiledb/datatypes.py

@@ -6,7 +6,7 @@
 
 import numpy as np
 
-import tiledb.cc as lt
+import tiledb.libtiledb as lt
 
 
 @dataclass(frozen=True)

tiledb/dense_array.py

@@ -3,7 +3,7 @@
 import numpy as np
 
 import tiledb
-import tiledb.cc as lt
+import tiledb.libtiledb as lt
 
 from .array import (
     Array,

tiledb/dimension.py

@@ -3,7 +3,7 @@
 
 import numpy as np
 
-import tiledb.cc as lt
+import tiledb.libtiledb as lt
 
 from .ctx import Ctx, CtxMixin
 from .datatypes import DataType

tiledb/dimension_label.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 
-import tiledb.cc as lt
+import tiledb.libtiledb as lt
 
 from .ctx import CtxMixin
 from .data_order import DataOrder

tiledb/dimension_label_schema.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 
-import tiledb.cc as lt
+import tiledb.libtiledb as lt
 
 from .ctx import Ctx, default_ctx
 from .data_order import DataOrder

tiledb/domain.py

@@ -3,7 +3,7 @@
 
 import numpy as np
 
-import tiledb.cc as lt
+import tiledb.libtiledb as lt
 
 from .ctx import Ctx, CtxMixin
 from .datatypes import DataType

tiledb/domain_indexer.py

@@ -3,7 +3,7 @@
 import numpy as np
 
 import tiledb
-import tiledb.cc as lt
+import tiledb.libtiledb as lt
 
 
 def _index_as_tuple(idx):

tiledb/enumeration.py

@@ -6,7 +6,7 @@
 import numpy as np
 from numpy.typing import NDArray
 
-import tiledb.cc as lt
+import tiledb.libtiledb as lt
 
 from .ctx import Ctx, CtxMixin
 from .datatypes import DataType

tiledb/filestore.py

@@ -1,7 +1,7 @@
 import warnings
 from typing import ByteString, Optional
 
-import tiledb.cc as lt
+import tiledb.libtiledb as lt
 
 from .ctx import Ctx, default_ctx
 

tiledb/filter.py

@@ -3,7 +3,7 @@
 
 import numpy as np
 
-import tiledb.cc as lt
+import tiledb.libtiledb as lt
 
 from .ctx import Ctx, CtxMixin
 from .datatypes import DataType

tiledb/fragment.py

@@ -5,8 +5,6 @@
 import tiledb
 from tiledb.libtiledb import version as libtiledb_version
 
-from .main import PyFragmentInfo
-
 """
 Classes and functions relating to TileDB fragments.
 """
@@ -105,6 +103,8 @@ def __init__(self, array_uri, include_mbrs=False, ctx=None):
 
         self.array_uri = array_uri
 
+        from .main import PyFragmentInfo
+
         fi = PyFragmentInfo(self.array_uri, schema, include_mbrs, ctx)
 
         self.__nums = fi.get_num_fragments()
@@ -188,6 +188,9 @@ def __init__(self, fragments):
         self._fragments = fragments
         self._index = 0
 
+    def __iter__(self):
+        return self
+
     def __next__(self):
         if self._index < len(self._fragments):
             fi = FragmentInfo(self._fragments, self._index)