New blosc2.concat that overrides blosc2.concatenate (now deprecated)

Author: FrancescAlted

bench/ndarray/concatenate.py

@@ -73,15 +73,15 @@ def run_benchmark(num_arrays=10, size=500, aligned_chunks=False, axis=0,
 
     # Time the concatenation
     start_time = time.time()
-    result = blosc2.concatenate(arrays, axis=axis, cparams=blosc2.CParams(codec=codec))
+    result = blosc2.concat(arrays, axis=axis, cparams=blosc2.CParams(codec=codec))
     duration = time.time() - start_time
 
     return duration, result.shape, data_size_gb
 
 
 def run_numpy_benchmark(num_arrays=10, size=500, axis=0, dtype=np.float64, datadist="linspace"):
     """
-    Benchmark numpy.concatenate performance for comparison.
+    Benchmark numpy.concat performance for comparison.
 
     Parameters:
     - num_arrays: Number of arrays to concatenate
@@ -120,7 +120,7 @@ def run_numpy_benchmark(num_arrays=10, size=500, axis=0, dtype=np.float64, datad
 
     # Time the concatenation
     start_time = time.time()
-    result = np.concatenate(numpy_arrays, axis=axis)
+    result = np.concat(numpy_arrays, axis=axis)
     duration = time.time() - start_time
 
     return duration, result.shape, data_size_gb
@@ -200,11 +200,11 @@ def autolabel(rects, ax):
 
     # Save the plot
     plt.tight_layout()
-    plt.savefig(os.path.join(output_dir, 'concatenate_benchmark_combined.png'), dpi=100)
+    plt.savefig(os.path.join(output_dir, 'concat_benchmark_combined.png'), dpi=100)
     plt.show()
     plt.close()
 
-    print(f"Combined plot saved to {os.path.join(output_dir, 'concatenate_benchmark_combined.png')}")
+    print(f"Combined plot saved to {os.path.join(output_dir, 'concat_benchmark_combined.png')}")
 
 
 def main():

doc/reference/ndarray.rst

@@ -72,7 +72,7 @@ Constructors
 
     asarray
     copy
-    concatenate
+    concat
     empty
     expand_dims
     frombuffer

src/blosc2/__init__.py

@@ -243,6 +243,7 @@ class Tuner(Enum):
     sort,
     reshape,
     copy,
+    concat,
     concatenate,
     expand_dims,
     empty,

src/blosc2/blosc2_ext.pyx

@@ -2872,7 +2872,7 @@ def schunk_get_slice_nchunks(schunk: SChunk, key):
     return res
 
 
-def concatenate(arr1: NDArray, arr2: NDArray, axis: int, **kwargs):
+def concat(arr1: NDArray, arr2: NDArray, axis: int, **kwargs):
     """
     Concatenate two NDArray objects along a specified axis.
     """

src/blosc2/ndarray.py

@@ -3523,7 +3523,7 @@ def copy(array: NDArray, dtype: np.dtype | str = None, **kwargs: Any) -> NDArray
     return array.copy(dtype, **kwargs)
 
 
-def concatenate(arrays: list[NDArray], /, axis=0, **kwargs: Any) -> NDArray:  # noqa: C901
+def concat(arrays: list[NDArray], /, axis=0, **kwargs: Any) -> NDArray:  # noqa: C901
     """Concatenate a list of arrays along a specified axis.
 
     Parameters
@@ -3549,7 +3549,7 @@ def concatenate(arrays: list[NDArray], /, axis=0, **kwargs: Any) -> NDArray:  #
     >>> import numpy as np
     >>> arr1 = blosc2.arange(0, 5, dtype=np.int32)
     >>> arr2 = blosc2.arange(5, 10, dtype=np.int32)
-    >>> result = blosc2.concatenate([arr1, arr2])
+    >>> result = blosc2.concat([arr1, arr2])
     >>> print(result[:])
     [0 1 2 3 4 5 6 7 8 9]
     """
@@ -3583,7 +3583,7 @@ def concatenate(arrays: list[NDArray], /, axis=0, **kwargs: Any) -> NDArray:  #
     # When provided urlpath coincides with an array
     mode = kwargs.pop("mode", "a")  # default mode for blosc2 is "a"
     for arr2 in arrays[1:]:
-        arr1 = blosc2_ext.concatenate(arr1, arr2, axis, copy=copy, mode=mode, **kwargs)
+        arr1 = blosc2_ext.concat(arr1, arr2, axis, copy=copy, mode=mode, **kwargs)
         # Have now overwritten existing file (if mode ='w'), need to change mode
         # for concatenating to the same file
         mode = "r" if mode == "r" else "a"
@@ -3593,6 +3593,20 @@ def concatenate(arrays: list[NDArray], /, axis=0, **kwargs: Any) -> NDArray:  #
     return arr1
 
 
+# Previous concatenate function was renamed to concat.  Keep it with a DeprecationWarning
+def concatenate(arrays: list[NDArray], /, axis=0, **kwargs: Any) -> NDArray:
+    """Concatenate a list of arrays along a specified axis.
+
+    This is an alias for :func:`concat`.  It is kept for backward compatibility.
+    """
+    warnings.warn(
+        "blosc2.concatenate is deprecated, use blosc2.concat instead.",
+        DeprecationWarning,
+        stacklevel=2,
+    )
+    return concat(arrays, axis, **kwargs)
+
+
 def expand_dims(array: NDArray, axis=0) -> NDArray:
     if not isinstance(array, blosc2.NDArray):
         raise TypeError("Argument array must be instance of blosc2.NDArray")
@@ -3638,7 +3652,7 @@ def stack(arrays: list[NDArray], axis=0, **kwargs: Any) -> NDArray:
     newarrays = []
     for arr in arrays:
         newarrays += [blosc2.expand_dims(arr, axis=axis)]
-    return blosc2.concatenate(newarrays, axis, **kwargs)
+    return blosc2.concat(newarrays, axis, **kwargs)
 
 
 def save(array: NDArray, urlpath: str, contiguous=True, **kwargs: Any) -> None:

tests/ndarray/test_concatenate.py

@@ -33,8 +33,8 @@ def test_concat2(shape1, shape2, dtype, axis):
     ndarr1 = blosc2.arange(0, int(np.prod(shape1)), 1, dtype=dtype, shape=shape1)
     ndarr2 = blosc2.arange(0, int(np.prod(shape2)), 1, dtype=dtype, shape=shape2)
     cparams = blosc2.CParams(clevel=1)
-    result = blosc2.concatenate([ndarr1, ndarr2], axis=axis, cparams=cparams)
-    nparray = np.concatenate([ndarr1[:], ndarr2[:]], axis=axis)
+    result = blosc2.concat([ndarr1, ndarr2], axis=axis, cparams=cparams)
+    nparray = np.concat([ndarr1[:], ndarr2[:]], axis=axis)
     np.testing.assert_almost_equal(result[:], nparray)
 
 
@@ -59,8 +59,8 @@ def test_concat3(shape1, shape2, shape3, dtype, axis):
     ndarr2 = blosc2.arange(0, int(np.prod(shape2)), 1, dtype=dtype, shape=shape2)
     ndarr3 = blosc2.arange(0, int(np.prod(shape3)), 1, dtype=dtype, shape=shape3)
     cparams = blosc2.CParams(codec=blosc2.Codec.BLOSCLZ)
-    result = blosc2.concatenate([ndarr1, ndarr2, ndarr3], axis=axis, cparams=cparams)
-    nparray = np.concatenate([ndarr1[:], ndarr2[:], ndarr3[:]], axis=axis)
+    result = blosc2.concat([ndarr1, ndarr2, ndarr3], axis=axis, cparams=cparams)
+    nparray = np.concat([ndarr1[:], ndarr2[:], ndarr3[:]], axis=axis)
     np.testing.assert_almost_equal(result[:], nparray)