Merge pull request #575 from Blosc/optimise_cumsum

Optimise cumsum

Author: lshaw8317

doc/conf.py

@@ -6,6 +6,7 @@
 import numpy as np
 
 import blosc2
+from blosc2.utils import constructors, elementwise_funcs, reducers
 
 
 def genbody(f, func_list, lib="blosc2"):
@@ -99,7 +100,7 @@ def genbody(f, func_list, lib="blosc2"):
 
 Their result is always a :ref:`LazyExpr` instance, which can be evaluated (with ``compute`` or ``__getitem__``) to get the actual values of the computation.
 
-Note: The functions ``conj``, ``real``, ``imag``, ``contains``, ``where`` are not technically ufuncs.
+Note: The functions ``real``, ``imag``, ``contains``, ``where`` are not technically ufuncs.
 
 .. currentmodule:: blosc2
 
@@ -110,7 +111,7 @@ def genbody(f, func_list, lib="blosc2"):
     genbody(f, blosc2_ufuncs)
 
 # GENERATE additional_funcs.rst
-blosc2_addfuncs = sorted(["conj", "real", "imag", "contains", "where", "clip", "round"])
+blosc2_addfuncs = sorted(set(elementwise_funcs) - set(blosc2_ufuncs))
 blosc2_dtypefuncs = sorted(["astype", "can_cast", "result_type", "isdtype"])
 
 with open("reference/additional_funcs.rst", "w") as f:
@@ -133,7 +134,9 @@ def genbody(f, func_list, lib="blosc2"):
     )
     genbody(f, blosc2_addfuncs)
     f.write(
-        """Type Utilities
+        """
+
+Type Utilities
 --------------
 
 The following functions are useful for working with datatypes.
@@ -158,12 +161,14 @@ def genbody(f, func_list, lib="blosc2"):
         "broadcast_to",
         "meshgrid",
         "indices",
+        "concat",
+        "stack",
     ]
 )
 
 with open("reference/index_funcs.rst", "w") as f:
     f.write(
-        """Indexing Functions and Utilities
+        """Indexing and Manipulation Functions and Utilities
 =======================================
 
 The following functions are useful for performing indexing and other associated operations.
@@ -195,7 +200,68 @@ def genbody(f, func_list, lib="blosc2"):
 
 """
     )
-    genbody(f, linalg_funcs, "blosc2.linalg")
+    genbody(f, sorted(linalg_funcs), "blosc2.linalg")
+
+with open("reference/reduction_functions.rst", "w") as f:
+    f.write(
+        """Reduction Functions
+-------------------
+
+Contrarily to lazy functions, reduction functions are evaluated eagerly, and the result is always a NumPy array (although this can be converted internally into an :ref:`NDArray <NDArray>` if you pass any :func:`blosc2.empty` arguments in ``kwargs``).
+
+Reduction operations can be used with any of :ref:`NDArray <NDArray>`, :ref:`C2Array <C2Array>`, :ref:`NDField <NDField>` and :ref:`LazyExpr <LazyExpr>`. Again, although these can be part of a :ref:`LazyExpr <LazyExpr>`, you must be aware that they are not lazy, but will be evaluated eagerly during the construction of a LazyExpr instance (this might change in the future). When the input is a :ref:`LazyExpr`, reductions accept ``fp_accuracy`` to control floating-point accuracy, and it is forwarded to :func:`LazyExpr.compute`.
+
+.. currentmodule:: blosc2
+
+.. autosummary::
+
+"""
+    )
+    genbody(f, sorted(reducers))
+
+with open("reference/ndarray.rst", "w") as f:
+    f.write(
+        """.. _NDArray:
+
+NDArray
+=======
+
+The multidimensional data array class. Instances may be constructed using the constructor functions in the list below `NDArrayConstructors`_.
+In addition, all the functions from the :ref:`Lazy Functions <lazy_functions>` section can be used with NDArray instances.
+
+.. currentmodule:: blosc2
+
+.. autoclass:: NDArray
+    :members:
+    :inherited-members:
+    :exclude-members: get_slice, set_slice, get_slice_numpy, get_oindex_numpy, set_oindex_numpy
+    :member-order: groupwise
+
+    :Special Methods:
+
+    .. autosummary::
+
+        __iter__
+        __len__
+        __getitem__
+        __setitem__
+
+    Utility Methods
+    ---------------
+
+    .. automethod:: __iter__
+    .. automethod:: __len__
+    .. automethod:: __getitem__
+    .. automethod:: __setitem__
+
+Constructors
+------------
+.. _NDArrayConstructors:
+.. autosummary::
+
+"""
+    )
+    genbody(f, sorted(constructors))
 
 hidden = "_ignore_multiple_size"
 

doc/reference/additional_funcs.rst

@@ -12,8 +12,8 @@ Their result is typically a :ref:`LazyExpr` instance, which can be evaluated (wi
 
 .. autosummary::
 
+    broadcast_to
     clip
-    conj
     contains
     imag
     real
@@ -22,13 +22,15 @@ Their result is typically a :ref:`LazyExpr` instance, which can be evaluated (wi
 
 
 
+.. autofunction:: blosc2.broadcast_to
 .. autofunction:: blosc2.clip
-.. autofunction:: blosc2.conj
 .. autofunction:: blosc2.contains
 .. autofunction:: blosc2.imag
 .. autofunction:: blosc2.real
 .. autofunction:: blosc2.round
 .. autofunction:: blosc2.where
+
+
 Type Utilities
 --------------
 

doc/reference/index_funcs.rst

@@ -1,4 +1,4 @@
-Indexing Functions and Utilities
+Indexing and Manipulation Functions and Utilities
 =======================================
 
 The following functions are useful for performing indexing and other associated operations.

doc/reference/linalg.rst

@@ -6,22 +6,22 @@ The following functions can be used for computing linear algebra operations with
 
 .. autosummary::
 
+    diagonal
     matmul
-    tensordot
-    vecdot
-    permute_dims
-    transpose
     matrix_transpose
-    diagonal
     outer
+    permute_dims
+    tensordot
+    transpose
+    vecdot
 
 
 
+.. autofunction:: blosc2.linalg.diagonal
 .. autofunction:: blosc2.linalg.matmul
-.. autofunction:: blosc2.linalg.tensordot
-.. autofunction:: blosc2.linalg.vecdot
-.. autofunction:: blosc2.linalg.permute_dims
-.. autofunction:: blosc2.linalg.transpose
 .. autofunction:: blosc2.linalg.matrix_transpose
-.. autofunction:: blosc2.linalg.diagonal
 .. autofunction:: blosc2.linalg.outer
+.. autofunction:: blosc2.linalg.permute_dims
+.. autofunction:: blosc2.linalg.tensordot
+.. autofunction:: blosc2.linalg.transpose
+.. autofunction:: blosc2.linalg.vecdot

doc/reference/misc.rst

@@ -7,6 +7,7 @@ This page documents the miscellaneous members of the ``blosc2`` module that do n
     :members:
     :exclude-members: LazyArray,
         LazyExpr,
+        LazyUDF,
         lazyexpr,
         lazyudf,
         evaluate,
@@ -227,4 +228,6 @@ This page documents the miscellaneous members of the ``blosc2`` module that do n
         round,
         are_partitions_aligned,
         are_partitions_behaved,
-        indices
+        indices,
+        cumulative_sum,
+        cumulative_prod,

doc/reference/ndarray.rst

@@ -38,14 +38,13 @@ Constructors
 
     arange
     asarray
-    concat
     copy
     empty
     empty_like
-    expand_dims
     eye
     frombuffer
     fromiter
+    fromiter
     full
     full_like
     linspace
@@ -55,31 +54,30 @@ Constructors
     ones
     ones_like
     reshape
-    stack
-    squeeze
     uninit
     zeros
     zeros_like
 
-.. autofunction:: arange
-.. autofunction:: asarray
-.. autofunction:: concat
-.. autofunction:: copy
-.. autofunction:: empty
-.. autofunction:: empty_like
-.. autofunction:: expand_dims
-.. autofunction:: eye
-.. autofunction:: frombuffer
-.. autofunction:: fromiter
-.. autofunction:: full
-.. autofunction:: full_like
-.. autofunction:: linspace
-.. autofunction:: nans
-.. autofunction:: ndarray_from_cframe
-.. autofunction:: ones
-.. autofunction:: ones_like
-.. autofunction:: reshape
-.. autofunction:: stack
-.. autofunction:: uninit
-.. autofunction:: zeros
-.. autofunction:: zeros_like
+
+
+.. autofunction:: blosc2.arange
+.. autofunction:: blosc2.asarray
+.. autofunction:: blosc2.copy
+.. autofunction:: blosc2.empty
+.. autofunction:: blosc2.empty_like
+.. autofunction:: blosc2.eye
+.. autofunction:: blosc2.frombuffer
+.. autofunction:: blosc2.fromiter
+.. autofunction:: blosc2.fromiter
+.. autofunction:: blosc2.full
+.. autofunction:: blosc2.full_like
+.. autofunction:: blosc2.linspace
+.. autofunction:: blosc2.meshgrid
+.. autofunction:: blosc2.nans
+.. autofunction:: blosc2.ndarray_from_cframe
+.. autofunction:: blosc2.ones
+.. autofunction:: blosc2.ones_like
+.. autofunction:: blosc2.reshape
+.. autofunction:: blosc2.uninit
+.. autofunction:: blosc2.zeros
+.. autofunction:: blosc2.zeros_like

doc/reference/reduction_functions.rst

@@ -11,24 +11,32 @@ Reduction operations can be used with any of :ref:`NDArray <NDArray>`, :ref:`C2A
 
     all
     any
-    sum
-    prod
+    argmax
+    argmin
+    count_nonzero
+    cumulative_prod
+    cumulative_sum
+    max
     mean
+    min
+    prod
     std
+    sum
     var
-    min
-    max
-    argmin
-    argmax
 
-.. autofunction:: all
-.. autofunction:: any
-.. autofunction:: sum
-.. autofunction:: prod
-.. autofunction:: mean
-.. autofunction:: std
-.. autofunction:: var
-.. autofunction:: min
-.. autofunction:: max
-.. autofunction:: argmin
-.. autofunction:: argmax
+
+
+.. autofunction:: blosc2.all
+.. autofunction:: blosc2.any
+.. autofunction:: blosc2.argmax
+.. autofunction:: blosc2.argmin
+.. autofunction:: blosc2.count_nonzero
+.. autofunction:: blosc2.cumulative_prod
+.. autofunction:: blosc2.cumulative_sum
+.. autofunction:: blosc2.max
+.. autofunction:: blosc2.mean
+.. autofunction:: blosc2.min
+.. autofunction:: blosc2.prod
+.. autofunction:: blosc2.std
+.. autofunction:: blosc2.sum
+.. autofunction:: blosc2.var

doc/reference/ufuncs.rst

@@ -5,7 +5,7 @@ The following elementwise functions can be used for computing with any of :ref:`
 
 Their result is always a :ref:`LazyExpr` instance, which can be evaluated (with ``compute`` or ``__getitem__``) to get the actual values of the computation.
 
-Note: The functions ``conj``, ``real``, ``imag``, ``contains``, ``where`` are not technically ufuncs.
+Note: The functions ``real``, ``imag``, ``contains``, ``where`` are not technically ufuncs.
 
 .. currentmodule:: blosc2
 

src/blosc2/__init__.py

@@ -556,6 +556,8 @@ def _raise(exc):
     cos,
     cosh,
     count_nonzero,
+    cumulative_prod,
+    cumulative_sum,
     divide,
     equal,
     exp,
@@ -719,6 +721,8 @@ def _raise(exc):
     "count_nonzero",
     "cparams_dflts",
     "cpu_info",
+    "cumulative_prod",
+    "cumulative_sum",
     "decompress",
     "decompress2",
     "detect_number_of_cores",