From df4b70e50e7073fe4318f2df0202eb5004012adc Mon Sep 17 00:00:00 2001
From: dwest77a <daniel.westwood@stfc.ac.uk>
Date: Thu, 22 Aug 2024 09:59:25 +0100
Subject: [PATCH 1/5] Docstrings, comments, added normalize function

---
 arraypartition/__init__.py                    |   8 +-
 .../__pycache__/__init__.cpython-311.pyc      | Bin 0 -> 552 bytes
 .../__pycache__/__init__.cpython-312.pyc      | Bin 0 -> 441 bytes
 .../__pycache__/partition.cpython-311.pyc     | Bin 0 -> 31639 bytes
 .../__pycache__/partition.cpython-312.pyc     | Bin 0 -> 26753 bytes
 arraypartition/partition.py                   | 129 ++++++++++++++----
 6 files changed, 109 insertions(+), 28 deletions(-)
 create mode 100644 arraypartition/__pycache__/__init__.cpython-311.pyc
 create mode 100644 arraypartition/__pycache__/__init__.cpython-312.pyc
 create mode 100644 arraypartition/__pycache__/partition.cpython-311.pyc
 create mode 100644 arraypartition/__pycache__/partition.cpython-312.pyc

diff --git a/arraypartition/__init__.py b/arraypartition/__init__.py
index 605d422..cefb84c 100644
--- a/arraypartition/__init__.py
+++ b/arraypartition/__init__.py
@@ -1,5 +1,11 @@
 from .partition import (
     ArrayLike,
     SuperLazyArrayLike,
-    ArrayPartition
+    ArrayPartition,
+    get_chunk_extent,
+    get_chunk_positions,
+    get_chunk_shape,
+    get_chunk_space,
+    get_dask_chunks,
+    combine_slices
 )
\ No newline at end of file
diff --git a/arraypartition/__pycache__/__init__.cpython-311.pyc b/arraypartition/__pycache__/__init__.cpython-311.pyc
new file mode 100644
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diff --git a/arraypartition/__pycache__/__init__.cpython-312.pyc b/arraypartition/__pycache__/__init__.cpython-312.pyc
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HcmV?d00001

diff --git a/arraypartition/partition.py b/arraypartition/partition.py
index 19c22d3..fbc3cda 100644
--- a/arraypartition/partition.py
+++ b/arraypartition/partition.py
@@ -1,16 +1,13 @@
 __author__    = "Daniel Westwood"
 __contact__   = "daniel.westwood@stfc.ac.uk"
-__copyright__ = "Copyright 2023 United Kingdom Research and Innovation"
-
-# Chunk wrapper is common to both CFAPyX and XarrayActive
-VERSION = '1.2.1'
+__copyright__ = "Copyright 2024 United Kingdom Research and Innovation"
 
 import numpy as np
 import netCDF4
 
 from itertools import product
-from copy import deepcopy
 from dask.utils import SerializableLock
+from dask.array.core import normalize_chunks
 
 try:
     from XarrayActive import ActiveChunk
@@ -57,7 +54,8 @@ def ndim(self):
     def copy(self, **kwargs):
         """
         Return a new basic ArrayLike instance. Ignores provided kwargs
-        this class does not require, but other inheritors may."""
+        this class does not require, but other inheritors may.
+        """
         return ArrayLike(
             self.shape,
             **self.get_kwargs()
@@ -65,7 +63,8 @@ def copy(self, **kwargs):
     
     def get_kwargs(self):
         """
-        Get the kwargs provided to this class initially - for creating a copy."""
+        Get the kwargs provided to this class initially - for creating a copy.
+        """
         return {
             'units':self.units,
             'dtype':self.dtype,
@@ -76,7 +75,8 @@ class SuperLazyArrayLike(ArrayLike):
     """
     Container class for SuperLazy Array-Like behaviour. ``SuperLazy`` behaviour is
     defined as Lazy-Slicing behaviour for objects that are below the 'Dask Surface',
-    i.e for object that serve as Dask Chunks."""
+    i.e for object that serve as Dask Chunks.
+    """
 
     description = "Container class for SuperLazy Array-Like behaviour"
 
@@ -127,7 +127,35 @@ def shape(self, value):
         self._shape = value
    
     def get_extent(self):
-        return tuple(self._extent)
+        """
+        Method for getting private variable `_extent` outside of this class.
+        """
+        return tuple(self._smooth_extent(self._extent))
+    
+    def set_extent(self, extent):
+        """
+        Method for directly setting the `_extent` for this class, once it has been
+        'smoothed'."""
+        self._extent = self._smooth_extent(extent)
+
+    def _smooth_extent(self, extent):
+        """
+        Replace values of None within each provided slice of the extent with integer
+        values derived from the current shape.
+        """
+        if len(extent) != self.ndim:
+            raise ValueError(
+                'Direct assignment of truncated extent is not supported.'
+            )
+        
+        smoothextent = []
+        for x, ext in enumerate(extent):
+            start = ext.start or 0
+            stop  = ext.stop or self.shape[x]
+            step  = ext.step or 1
+            smoothextent.append(slice(start,stop,step))
+
+        return smoothextent
 
     def copy(self, extent=None):
         """
@@ -215,7 +243,7 @@ def __init__(self,
 
         if extent:
             # Apply a specific extent if given by the initiator
-            self._extent  = extent
+            self.set_extent(extent)
     
     def __array__(self, *args, **kwargs):
         """
@@ -307,9 +335,9 @@ def _correct_slice(self, array_dims):
             
     def _post_process_data(self, data):
         """
-        Perform any post-processing steps on the data here.
-        - unit correction
-        - calendar correction
+        Perform any post-processing steps on the data here. Method to be 
+        overriden by inherrited classes (CFAPyX.CFAPartition and 
+        XarrayActive.ActivePartition)
         """
         return data
 
@@ -429,11 +457,10 @@ def _identical_extents(old, new, dshape):
 
 def get_chunk_space(chunk_shape, shape):
     """
-    Derive the chunk space and shape given the user-provided ``chunks`` option. 
-    Chunk space is the number of chunks in each dimension which presents like an array 
-    shape, but is referred to as a ``space`` because it has a novel coordinate system. 
-    Chunk shape is the shape of each chunk in ``array space``, which must be regular
-    even if lower-level objects used to define the chunk are not.
+    Derive the chunk space from the ratio between the chunk shape and array shape in
+    each dimension. Chunk space is the number of chunks in each dimension which is 
+    referred to as a ``space`` because it effectively represents the lengths of the each
+    dimension in 'chunk space' rather than any particular chunk coordinate. 
 
     Example: 
         50 chunks across the time dimension of 1000 values which is represented by 8 
@@ -455,6 +482,25 @@ def get_chunk_space(chunk_shape, shape):
     return tuple([int(i/j) for i, j in zip(shape, chunk_shape)])
 
 def get_chunk_shape(chunks, shape, dims, chunk_limits=True):
+    """
+    Calculate the chunk shape from the user-provided ``chunks`` parameter,
+    the array shape and named dimensions, and apply chunk limits if enabled.
+
+    :param chunks:  (dict) The user specified chunks, which match the usual dask
+        chunks from xr.open_dataset, except these come from the ``cfa_options``.
+
+    :param shape:   (tuple) The array shape of the data array to be chunked.
+
+    :param dims:    (tuple) The names of each dimension to match to the ``chunks``
+        provided.
+
+    :param chunk_limits (bool) Option to disable, chunk limits will prevent chunking
+        to beyond a useful chunk size which is likely to be much less than the memory
+        chunk size of the source files, in which case there would be a lot of wasted 
+        data retrieval.
+
+    :returns:   A tuple of the shape of each chunk in ``array space`` for each dimension.
+    """
     chunk_shape = [i for i in shape]
 
     for dim in chunks.keys():
@@ -464,15 +510,17 @@ def get_chunk_shape(chunks, shape, dims, chunk_limits=True):
             if d == dim:
                 idim = x
 
-        if not idim:
+        if idim == None:
             raise ValueError(
                 f"Requested chunking across dimension '{dim}'"
                 f"but only '{dims}' present in the dataset"
             )
         
+        # Apply chunk limits unless disabled.
         min_size = int(shape[idim]/np.prod(shape))
         if chunk_limits:
-            min_size = int(min_size * 2e6)
+            min_size = int(min_size * 2e6) 
+            # 2M data points is the smallest total size allowed.
         
         chunk_size = chunks[dim]
         chunk_shape[idim] = max(chunk_size, min_size)
@@ -480,6 +528,10 @@ def get_chunk_shape(chunks, shape, dims, chunk_limits=True):
     return tuple(chunk_shape)
 
 def get_chunk_positions(chunk_space):
+    """
+    Get the list of chunk positions in ``chunk space`` given the size
+    of the space.
+    """
     origin = [0 for i in chunk_space]
 
     positions = [
@@ -491,9 +543,13 @@ def get_chunk_positions(chunk_space):
     return positions
 
 def get_chunk_extent(position, shape, chunk_space):
+    """
+    Get the extent of a particular chunk within the space given its position,
+    the array shape and the extent of the chunk space.
+    """
     extent = []
     for dim in range(len(position)):
-        pos_index   = position[dim]
+        pos_index  = position[dim]
         shape_size = shape[dim]
         space_size = chunk_space[dim]
 
@@ -503,6 +559,7 @@ def get_chunk_extent(position, shape, chunk_space):
             int(pos_index*conversion), int((pos_index+1)*conversion)
         )
         extent.append(ext)
+
     return extent
 
 def get_dask_chunks(
@@ -519,11 +576,13 @@ def get_dask_chunks(
 
     :param fragment_space:  (tuple) The shape of the array in ``fragment space``.
 
-    :param extent:      (dict) The global extent of each fragment - where it fits into the total array for this variable (in array space).
+    :param extent:          (dict) The global extent of each fragment - where it fits into 
+        the total array for this variable (in array space).
 
-    :param dtype:       (obj) The datatype for this variable.
+    :param dtype:           (obj) The datatype for this variable.
 
-    :param explicit_shapes:     (tuple) Set of shapes to apply to the fragments - currently not implemented outside this function.
+    :param explicit_shapes:     (tuple) Set of shapes to apply to the fragments - currently 
+        not implemented outside this function.
 
     :returns:       A tuple of the chunk sizes along each dimension.
     """
@@ -556,7 +615,8 @@ def get_dask_chunks(
     ## Handle explicit shapes for the fragments.
 
     if isinstance(explicit_shapes, (str, Number)) or explicit_shapes is None:
-        fsizes_per_dim = [ # For each dimension, use fs or explicit_shapes if the dimension is fragmented or not respectively.
+        # For each dimension, use fs or explicit_shapes if the dimension is fragmented or not respectively.
+        fsizes_per_dim = [
             fs if i in fragmented_dim_indices else explicit_shapes for i, fs in enumerate(fsizes_per_dim)
         ]
     elif isinstance(explicit_shapes, dict):
@@ -621,11 +681,26 @@ def combine_sliced_dim(old, new, dim):
         
         return slice(start, stop, step)
 
-
     if not extent:
         return newslice
     else:
         for dim in range(len(newslice)):
             if not _identical_extents(extent[dim], newslice[dim], shape[dim]):
                 extent[dim] = combine_sliced_dim(extent[dim], newslice[dim], dim)
-        return extent
\ No newline at end of file
+        return extent
+    
+def normalize_partition_chunks(chunks, shape, dtype, named_dims):
+        
+    chunk_values = []
+
+    for nd in named_dims:
+        if nd not in chunks.keys():
+            chunk_values.append('auto')
+        else:
+            chunk_values.append(int(chunks[nd]))
+
+    return normalize_chunks(
+        chunk_values,
+        shape,
+        dtype=dtype
+    )
\ No newline at end of file

From 5f878e88c283678246e3a1ea08472491576eda1f Mon Sep 17 00:00:00 2001
From: dwest77a <daniel.westwood@stfc.ac.uk>
Date: Thu, 22 Aug 2024 10:06:10 +0100
Subject: [PATCH 2/5] Added normalize function

---
 arraypartition/__init__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/arraypartition/__init__.py b/arraypartition/__init__.py
index cefb84c..136028e 100644
--- a/arraypartition/__init__.py
+++ b/arraypartition/__init__.py
@@ -7,5 +7,6 @@
     get_chunk_shape,
     get_chunk_space,
     get_dask_chunks,
-    combine_slices
+    combine_slices,
+    normalize_partition_chunks
 )
\ No newline at end of file

From ca4b353e09ab37465b18ec7a2cf30353c758dfd9 Mon Sep 17 00:00:00 2001
From: dwest77a <daniel.westwood@stfc.ac.uk>
Date: Thu, 22 Aug 2024 10:08:02 +0100
Subject: [PATCH 3/5] Fixed bug with providing 'auto' as chunk option

---
 arraypartition/partition.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/arraypartition/partition.py b/arraypartition/partition.py
index fbc3cda..42784aa 100644
--- a/arraypartition/partition.py
+++ b/arraypartition/partition.py
@@ -696,8 +696,11 @@ def normalize_partition_chunks(chunks, shape, dtype, named_dims):
     for nd in named_dims:
         if nd not in chunks.keys():
             chunk_values.append('auto')
-        else:
+            continue
+        try:
             chunk_values.append(int(chunks[nd]))
+        except ValueError:
+            chunk_values.append(chunks[nd])
 
     return normalize_chunks(
         chunk_values,

From c1d5965c8478a515cf086f5f888f87a54c5569da Mon Sep 17 00:00:00 2001
From: dwest77a <daniel.westwood@stfc.ac.uk>
Date: Thu, 22 Aug 2024 10:35:28 +0100
Subject: [PATCH 4/5] Fixed dtype bug

---
 arraypartition/partition.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/arraypartition/partition.py b/arraypartition/partition.py
index 42784aa..8965057 100644
--- a/arraypartition/partition.py
+++ b/arraypartition/partition.py
@@ -261,7 +261,7 @@ def __array__(self, *args, **kwargs):
         if args:
             dtype = args[0]
 
-        if dtype != self.dtype:
+        if dtype and dtype != self.dtype:
             raise ValueError(
                 'Requested datatype does not match this chunk'
             )

From d27daf6d3577468ac5a73aeb851fa47d2381e152 Mon Sep 17 00:00:00 2001
From: dwest77 <daniel.westwood@stfc.ac.uk>
Date: Thu, 22 Aug 2024 10:36:30 +0100
Subject: [PATCH 5/5] Examine diffs

---
 arraypartition/partition.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/arraypartition/partition.py b/arraypartition/partition.py
index 42784aa..2282cd9 100644
--- a/arraypartition/partition.py
+++ b/arraypartition/partition.py
@@ -6,6 +6,7 @@
 import netCDF4
 
 from itertools import product
+import math
 from dask.utils import SerializableLock
 from dask.array.core import normalize_chunks
 
@@ -479,7 +480,8 @@ def get_chunk_space(chunk_shape, shape):
 
     """
 
-    return tuple([int(i/j) for i, j in zip(shape, chunk_shape)])
+    space = tuple([math.ceil(i/j) for i, j in zip(shape, chunk_shape)])
+    return space
 
 def get_chunk_shape(chunks, shape, dims, chunk_limits=True):
     """