cellarr-array 0.0.1__py3-none-any.whl → 0.0.2__py3-none-any.whl

cellarr_array/CellArray.py

@@ -42,7 +42,8 @@ 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 +54,15 @@ 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

{cellarr_array-0.0.1.dist-info → cellarr_array-0.0.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: cellarr-array
-Version: 0.0.1
+Version: 0.0.2
 Summary: Base class for handling TileDB backed arrays.
 Home-page: https://github.com/cellarr/cellarr-array
 Author: Jayaram Kancherla
@@ -26,7 +26,7 @@ Requires-Dist: pytest-cov; extra == "testing"
 
 # 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 +116,43 @@ 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 +163,7 @@ array.consolidate()
 
 # Custom consolidation
 config = ConsolidationConfig(
-    steps=["fragment"],
+    steps=2,
     vacuum_after=True
 )
 array.consolidate(config)

{cellarr_array-0.0.1.dist-info → cellarr_array-0.0.2.dist-info}/RECORD

@@ -1,11 +1,11 @@
-cellarr_array/CellArray.py,sha256=vOaq-0FbVKeuS31992oc_N5IOBXclcVkczPNIbua5Ws,7498
+cellarr_array/CellArray.py,sha256=sFD258mPp4w-8-xmjAgoicKo0Nbu0GGa-1gMXxt5cZ0,7570
 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,,
+cellarr_array-0.0.2.dist-info/LICENSE.txt,sha256=qI2hRZobcUlj8gqFqXwqt522HeYyWvHLF00zCSZofHA,1084
+cellarr_array-0.0.2.dist-info/METADATA,sha256=-VmLQZQmbUhNkD_Y9ZLeZkBgLf4H5YIXgO_rDj7zKmw,4098
+cellarr_array-0.0.2.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+cellarr_array-0.0.2.dist-info/top_level.txt,sha256=oErp0D8ABZV-QPtTiXT8_F2z36Ic7ykuDg_1Y84HLZM,14
+cellarr_array-0.0.2.dist-info/RECORD,,