cellarr-array 0.0.1__py3-none-any.whl → 0.0.3__py3-none-any.whl

cellarr_array/CellArray.py

@@ -1,5 +1,11 @@
 from abc import ABC, abstractmethod
 from contextlib import contextmanager
+
+try:
+    from types import EllipsisType
+except ImportError:
+    # TODO: This is required for Python <3.10. Remove once Python 3.9 reaches EOL in October 2025
+    EllipsisType = type(...)
 from typing import List, Literal, Optional, Tuple, Union
 
 import numpy as np
@@ -42,7 +48,8 @@ class CellArray(ABC):
                 Defaults to None for automatic mode switching.
 
             config_or_context:
-                Config or context object.
+                Optional config or context object.
+
                 Defaults to None.
 
             validate:
@@ -53,14 +60,15 @@ class CellArray(ABC):
         self._mode = mode
 
         if config_or_context is None:
-            config_or_context = tiledb.Config()
-
-        if isinstance(config_or_context, tiledb.Config):
-            ctx = tiledb.Ctx(config_or_context)
-        elif isinstance(config_or_context, tiledb.Ctx):
-            ctx = config_or_context
+            # config_or_context = tiledb.Config()
+            ctx = None
         else:
-            raise TypeError("'config_or_context' must be either TileDB config or a context object.")
+            if isinstance(config_or_context, tiledb.Config):
+                ctx = tiledb.Ctx(config_or_context)
+            elif isinstance(config_or_context, tiledb.Ctx):
+                ctx = config_or_context
+            else:
+                raise TypeError("'config_or_context' must be either TileDB config or a context object.")
 
         self._ctx = ctx
         self._array = None
@@ -68,6 +76,7 @@ class CellArray(ABC):
         self._ndim = None
         self._dim_names = None
         self._attr_names = None
+        self._nonempty_domain = None
 
         if validate:
             self._validate(attr=attr)
@@ -157,7 +166,7 @@ class CellArray(ABC):
         finally:
             array.close()
 
-    def __getitem__(self, key: Union[slice, Tuple[Union[slice, List[int]], ...]]):
+    def __getitem__(self, key: Union[slice, EllipsisType, Tuple[Union[slice, List[int]], ...], EllipsisType]):
         """Get item implementation that routes to either direct slicing or multi_index
         based on the type of indices provided.
 
@@ -174,16 +183,22 @@ class CellArray(ABC):
         # Normalize all indices
         normalized_key = tuple(SliceHelper.normalize_index(idx, self.shape[i]) for i, idx in enumerate(key))
 
+        num_ellipsis = sum(isinstance(i, EllipsisType) for i in normalized_key)
+        if num_ellipsis > 1:
+            raise IndexError(f"Found more than 1 Ellipsis (...) in key: {normalized_key}")
+
         # Check if we can use direct slicing
-        use_direct = all(isinstance(idx, slice) for idx in normalized_key)
+        use_direct = all(isinstance(idx, (slice, EllipsisType)) for idx in normalized_key)
 
         if use_direct:
             return self._direct_slice(normalized_key)
         else:
+            if num_ellipsis > 0:
+                raise IndexError(f"tiledb does not support ellipsis in multi-index access: {normalized_key}")
             return self._multi_index(normalized_key)
 
     @abstractmethod
-    def _direct_slice(self, key: Tuple[slice, ...]) -> np.ndarray:
+    def _direct_slice(self, key: Tuple[Union[slice, EllipsisType], ...]) -> np.ndarray:
         """Implementation for direct slicing."""
         pass
 

cellarr_array/DenseCellArray.py

@@ -1,3 +1,8 @@
+try:
+    from types import EllipsisType
+except ImportError:
+    # TODO: This is required for Python <3.10. Remove once Python 3.9 reaches EOL in October 2025
+    EllipsisType = type(...)
 from typing import List, Tuple, Union
 
 import numpy as np
@@ -13,7 +18,7 @@ __license__ = "MIT"
 class DenseCellArray(CellArray):
     """Implementation for dense TileDB arrays."""
 
-    def _direct_slice(self, key: Tuple[slice, ...]) -> np.ndarray:
+    def _direct_slice(self, key: Tuple[Union[slice, EllipsisType], ...]) -> np.ndarray:
         """Implementation for direct slicing of dense arrays.
 
         Args:

cellarr_array/SparseCellArray.py

@@ -1,3 +1,8 @@
+try:
+    from types import EllipsisType
+except ImportError:
+    # TODO: This is required for Python <3.10. Remove once Python 3.9 reaches EOL in October 2025
+    EllipsisType = type(...)
 from typing import Dict, List, Optional, Tuple, Union
 
 import numpy as np
@@ -118,7 +123,7 @@ class SparseCellArray(CellArray):
 
         return sliced[key]
 
-    def _direct_slice(self, key: Tuple[slice, ...]) -> Union[np.ndarray, sparse.coo_matrix]:
+    def _direct_slice(self, key: Tuple[Union[slice, EllipsisType], ...]) -> Union[np.ndarray, sparse.coo_matrix]:
         """Implementation for direct slicing of sparse arrays."""
         with self.open_array(mode="r") as array:
             result = array[key]

cellarr_array/__init__.py

@@ -18,4 +18,4 @@ finally:
 from .config import CellArrConfig, ConsolidationConfig
 from .DenseCellArray import DenseCellArray
 from .SparseCellArray import SparseCellArray
-from .helpers import create_cellarray, SliceHelper
+from .helpers import create_cellarray, SliceHelper

cellarr_array/helpers.py

@@ -1,3 +1,8 @@
+try:
+    from types import EllipsisType
+except ImportError:
+    # TODO: This is required for Python <3.10. Remove once Python 3.9 reaches EOL in October 2025
+    EllipsisType = type(...)
 from typing import List, Optional, Tuple, Union
 
 import numpy as np
@@ -150,9 +155,12 @@ class SliceHelper:
         return None
 
     @staticmethod
-    def normalize_index(idx: Union[int, slice, List[int]], dim_size: int) -> Union[slice, List[int]]:
+    def normalize_index(idx: Union[int, slice, List[int]], dim_size: int) -> Union[slice, List[int], EllipsisType]:
         """Normalize index to handle negative indices and ensure consistency."""
 
+        if isinstance(idx, EllipsisType):
+            return idx
+
         # Convert ranges to slices
         if isinstance(idx, range):
             idx = slice(idx.start, idx.stop, idx.step)

{cellarr_array-0.0.1.dist-info → cellarr_array-0.0.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: cellarr-array
-Version: 0.0.1
+Version: 0.0.3
 Summary: Base class for handling TileDB backed arrays.
 Home-page: https://github.com/cellarr/cellarr-array
 Author: Jayaram Kancherla
@@ -20,13 +20,14 @@ Provides-Extra: testing
 Requires-Dist: setuptools; extra == "testing"
 Requires-Dist: pytest; extra == "testing"
 Requires-Dist: pytest-cov; extra == "testing"
+Dynamic: license-file
 
 [![PyPI-Server](https://img.shields.io/pypi/v/cellarr-array.svg)](https://pypi.org/project/cellarr-array/)
 ![Unit tests](https://github.com/cellarr/cellarr-array/actions/workflows/run-tests.yml/badge.svg)
 
 # cellarr-array
 
-This package provided high-level wrappers for TileDB arrays optimized for handling genomic data matrices.
+This package provided high-level wrappers for TileDB arrays, for handling genomic data matrices.
 
 ## Install
 
@@ -116,24 +117,43 @@ subset = dense_array[100:200, genes]
 ### Working with Sparse Arrays
 
 ```python
-# Create a sparse array with COO output format
-coo_array = SparseCellArray(
+from cellarr_array import SparseCellArray
+
+# Create a sparse array with CSR output format
+csr_array = SparseCellArray(
     uri="sparse_matrix.tdb",
-    return_coo=True
+    return_sparse=True
 )
 
-# Get result as COO matrix
-result = coo_array[100:200, 500:1000]
+# Get result as CSR matrix
+result = csr_array[100:200, 500:1000]
 
 # Result is scipy.sparse.coo_matrix
-assert sparse.isspmatrix_coo(result)
+assert sparse.isspmatrix_csr(result)
 
 # Perform sparse operations
 nnz = result.nnz
 density = result.nnz / (result.shape[0] * result.shape[1])
 
 # Convert to other sparse formats if needed
-result_csr = result.tocsr()
+result_csc = result.tocsc()
+```
+
+Likewise create a CSC output format
+
+```python
+from scipy import sparse
+
+# Create a sparse array with CSC output format
+csc_array = SparseCellArray(
+    uri="sparse_matrix.tdb",
+    return_sparse=True,
+    sparse_coerce=sparse.csc_matrix
+)
+
+# Get result as CSR matrix
+result = csc_array[100:200, 500:1000]
+print(result)
 ```
 
 ### Array Maintenance
@@ -144,7 +164,7 @@ array.consolidate()
 
 # Custom consolidation
 config = ConsolidationConfig(
-    steps=["fragment"],
+    steps=2,
     vacuum_after=True
 )
 array.consolidate(config)

cellarr_array-0.0.3.dist-info/RECORD

@@ -0,0 +1,11 @@
+cellarr_array/CellArray.py,sha256=vc_6oDLCpVgUaP8HsQz4vE0ZyJ1SPdX43s7VQyh7gF0,8204
+cellarr_array/DenseCellArray.py,sha256=rlu2xq8SONwIswqe0TzRNCwM5f0HYgxr4QBtvbBe8ro,3953
+cellarr_array/SparseCellArray.py,sha256=cOIbs_97j5u13FU7FfEfRNqAZi8rHUkypgLgRcubXrU,7304
+cellarr_array/__init__.py,sha256=IUE9wMDISgRkWp-Fc0KJpDiezCJ61kzuTqS9HdK-JeE,779
+cellarr_array/config.py,sha256=67zBxpYY9N_v6TMdyljUIZmckbwOBcuLC99aJooGmfA,2917
+cellarr_array/helpers.py,sha256=ZqK_josEzKzTMP62P9pb4qBiOTisFofTCnu1LETYJT4,6449
+cellarr_array-0.0.3.dist-info/licenses/LICENSE.txt,sha256=qI2hRZobcUlj8gqFqXwqt522HeYyWvHLF00zCSZofHA,1084
+cellarr_array-0.0.3.dist-info/METADATA,sha256=1KgSZEEF2i9aCr4mkkyAmuPXht4y5ZG2-YdH4dBELpQ,4120
+cellarr_array-0.0.3.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+cellarr_array-0.0.3.dist-info/top_level.txt,sha256=oErp0D8ABZV-QPtTiXT8_F2z36Ic7ykuDg_1Y84HLZM,14
+cellarr_array-0.0.3.dist-info/RECORD,,

{cellarr_array-0.0.1.dist-info → cellarr_array-0.0.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (78.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

cellarr_array-0.0.1.dist-info/RECORD

@@ -1,11 +0,0 @@
-cellarr_array/CellArray.py,sha256=vOaq-0FbVKeuS31992oc_N5IOBXclcVkczPNIbua5Ws,7498
-cellarr_array/DenseCellArray.py,sha256=iPrjFtGolnHB0BTi4A8ncEpoFI9FWe6oZHhA1Men3Wo,3745
-cellarr_array/SparseCellArray.py,sha256=8bajVOvUMaQhWU-_pZY0Cg9sD6kWRAJCu2G45uY-W4Q,7096
-cellarr_array/__init__.py,sha256=8m0_shRPKNNaNab5tGBL2l0K5XgkKCFuLAh7QGogfYo,778
-cellarr_array/config.py,sha256=67zBxpYY9N_v6TMdyljUIZmckbwOBcuLC99aJooGmfA,2917
-cellarr_array/helpers.py,sha256=O0RgDLIdYbWc01yp2Cw0EmjJ3g_uzlz2JnYE8W7PZEE,6182
-cellarr_array-0.0.1.dist-info/LICENSE.txt,sha256=qI2hRZobcUlj8gqFqXwqt522HeYyWvHLF00zCSZofHA,1084
-cellarr_array-0.0.1.dist-info/METADATA,sha256=UaSorFB0-5KuhVrM8pvdGuN98WQ6iSLgUUH6MtpJwXM,3747
-cellarr_array-0.0.1.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-cellarr_array-0.0.1.dist-info/top_level.txt,sha256=oErp0D8ABZV-QPtTiXT8_F2z36Ic7ykuDg_1Y84HLZM,14
-cellarr_array-0.0.1.dist-info/RECORD,,