dev

Changelog.rst

@@ -1,22 +1,3 @@
-version NEXTVERSION + 1
------------------------
-
-**2024-??-??**
-
-* Allow access to netCDF-4 files in S3 object stores
-  (https://github.com/NCAS-CMS/cf-python/issues/712)
-* New class `cf.H5netcdfArray`
-* New class `cf.NetCDF4Array`
-* New class `cf.CFAH5netcdfArray`
-* New class `cf.CFANetCDF4Array`
-* New dependency: ``h5netcdf>=1.3.0``
-* New dependency: ``h5py>=3.10.0``
-* New dependency: ``s3fs>=2024.2.0``
-* Changed dependency: ``1.11.2.0<=cfdm<1.11.3.0``
-* Changed dependency: ``cfunits>=3.3.7``
-
-----
-
 version NEXTVERSION
 -------------------
 
@@ -33,6 +14,12 @@ version NEXTVERSION
 * New keyword parameter to `cf.Field.derivative`:
   ``ignore_coordinate_units``
   (https://github.com/NCAS-CMS/cf-python/issues/807)
+* Allow access to netCDF-4 files in S3 object stores
+  (https://github.com/NCAS-CMS/cf-python/issues/712)
+* New class `cf.H5netcdfArray`
+* New class `cf.NetCDF4Array`
+* New class `cf.CFAH5netcdfArray`
+* New class `cf.CFANetCDF4Array`
 * Fix bug that sometimes puts an incorrect ``radian-1`` or
   ``radian-2`` in the returned units of the differential operator
   methods and functions
@@ -46,6 +33,12 @@ version NEXTVERSION
 * Fix bug where `cf.normalize_slice` doesn't correctly
   handle certain cyclic slices
   (https://github.com/NCAS-CMS/cf-python/issues/774)
+* New dependency: ``h5netcdf>=1.3.0``
+* New dependency: ``h5py>=3.10.0``
+* New dependency: ``s3fs>=2024.2.0``
+* Changed dependency: ``1.11.2.0<=cfdm<1.11.3.0``
+* Changed dependency: ``cfunits>=3.3.7``
+
 
 ----
 

cf/cfimplementation.py

@@ -26,8 +26,6 @@
     TiePointIndex,
 )
 from .data import Data
-
-# REVIEW: h5: `cfimplementation.py`: import `CFAH5netcdfArray`, `CFANetCDF4Array`, `H5netcdfArray`,`NetCDF4Array`
 from .data.array import (
     BoundsFromNodesArray,
     CellConnectivityArray,
@@ -116,7 +114,6 @@ def set_construct(self, parent, construct, axes=None, copy=True, **kwargs):
             parent, construct, axes=axes, copy=copy, **kwargs
         )
 
-    # REVIEW: h5: `initialise_CFANetCDF4Array`: new method to initialise `CFANetCDF4Array`
     def initialise_CFANetCDF4Array(self, **kwargs):
         """Return a `CFANetCDF4Array` instance.
 
@@ -133,7 +130,6 @@ def initialise_CFANetCDF4Array(self, **kwargs):
         cls = self.get_class("CFANetCDF4Array")
         return cls(**kwargs)
 
-    # REVIEW: h5: `initialise_CFAH5netcdfArray`: new method to initialise `CFAH5netcdfArray`
     def initialise_CFAH5netcdfArray(self, **kwargs):
         """Return a `CFAH5netcdfArray` instance.
 

cf/constants.py

@@ -63,7 +63,6 @@
     "LOG_LEVEL": logging.getLevelName(logging.getLogger().level),
     "BOUNDS_COMBINATION_MODE": "AND",
     "CHUNKSIZE": parse_bytes(_CHUNKSIZE),
-    # REVIEW: active: `CONSTANTS`: new constants 'active_storage', 'active_storage_url', 'active_storage_max_requests'
     "active_storage": False,
     "active_storage_url": None,
     "active_storage_max_requests": 100,

cf/data/array/__init__.py

@@ -1,19 +1,11 @@
 from .boundsfromnodesarray import BoundsFromNodesArray
 from .cellconnectivityarray import CellConnectivityArray
-
-# REVIEW: h5: `__init__.py`: import `CFAH5netcdfArray`
 from .cfah5netcdfarray import CFAH5netcdfArray
-
-# REVIEW: h5: `__init__.py`: import `CFAH5netcdfArray`
 from .cfanetcdf4array import CFANetCDF4Array
 from .fullarray import FullArray
 from .gatheredarray import GatheredArray
-
-# REVIEW: h5: `__init__.py`: import `H5netcdfArray`
 from .h5netcdfarray import H5netcdfArray
 from .netcdfarray import NetCDFArray
-
-# REVIEW: h5: `__init__.py`: import `NetCDF4Array`
 from .netcdf4array import NetCDF4Array
 from .pointtopologyarray import PointTopologyArray
 from .raggedcontiguousarray import RaggedContiguousArray

cf/data/array/cfah5netcdfarray.py

@@ -1,4 +1,3 @@
-# REVIEW: h5: `CFAH5netcdfArray`: New class for accessing CFA with `h5netcdf`
 from .h5netcdfarray import H5netcdfArray
 from .mixin import CFAMixin
 

cf/data/array/cfanetcdf4array.py

@@ -1,4 +1,3 @@
-# REVIEW: h5: `CFAnetCDF4Array`: New class for accessing CFA with `netCDF4`
 from .mixin import CFAMixin
 from .netcdf4array import NetCDF4Array
 

cf/data/array/fullarray.py

@@ -16,7 +16,6 @@ class FullArray(IndexMixin, Array):
 
     """
 
-    # REVIEW: h5: `__init__`: replace units/calendar API with attributes
     def __init__(
         self,
         fill_value=None,
@@ -121,7 +120,6 @@ def __str__(self):
 
         return f"Filled with {fill_value!r}"
 
-    # REVIEW: getitem: `_get_array`: new method to convert subspace to numpy array
     def _get_array(self, index=None):
         """Returns the full array.
 
@@ -156,7 +154,6 @@ def _get_array(self, index=None):
 
         return array
 
-    # REVIEW: getitem: `array`: New property to convert subspace to numpy array
     @property
     def array(self):
         """Return an independent numpy array containing the data.

cf/data/array/h5netcdfarray.py

@@ -1,4 +1,3 @@
-# REVIEW: h5: `H5netcdfArray`: New class to access netCDF with `h5netcdf`
 import cfdm
 
 from ...mixin_container import Container

cf/data/array/locks.py

@@ -1,4 +1,3 @@
-# REVIEW: h5: `locks.py`:  New module to provide file locks
 from dask.utils import SerializableLock
 
 # Global lock for netCDF file access

cf/data/array/mixin/__init__.py

@@ -1,9 +1,6 @@
-# REVIEW: active: `__init__.py`: import `ActiveStorageMixin`
 from .activestoragemixin import ActiveStorageMixin
 from .arraymixin import ArrayMixin
 from .cfamixin import CFAMixin
 from .compressedarraymixin import CompressedArrayMixin
 from .filearraymixin import FileArrayMixin
-
-# REVIEW: getitem: `__init__.py`: import `IndexMixin`
 from .indexmixin import IndexMixin

cf/data/array/mixin/activestoragemixin.py

@@ -1,6 +1,3 @@
-# REVIEW: active: `ActiveStorageMixin`: new mixin class `ActiveStorageMixin`
-
-
 class ActiveStorageMixin:
     """Mixin class for enabling active storage operations.
 

cf/data/array/mixin/arraymixin.py

@@ -18,7 +18,6 @@ def __array_function__(self, func, types, args, kwargs):
         """
         return NotImplemented
 
-    # REVIEW: active: `_meta`: Moved to here from `FileArrayMixin`
     @property
     def _meta(self):
         """Normalise the array to an appropriate Dask meta object.

cf/data/array/mixin/cfamixin.py

@@ -35,7 +35,6 @@ def __new__(cls, *args, **kwargs):
         }
         return instance
 
-    # REVIEW: h5: `__init__`: replace units/calendar API with attributes
     def __init__(
         self,
         filename=None,
@@ -224,7 +223,6 @@ def __init__(
                 "substitutions", substitutions.copy(), copy=False
             )
 
-    # REVIEW: h5: `_parse_cfa`: Refactoring of code that used to be in `__init__`
     def _parse_cfa(self, x, term, substitutions):
         """Parse the CFA aggregation instructions.
 
@@ -465,7 +463,6 @@ def get_fragment_shape(self):
         """
         return self._get_component("fragment_shape")
 
-    # REVIEW: h5: `get_storage_options`: new method to get file access options
     def get_storage_options(self):
         """Return `s3fs.S3FileSystem` options for accessing S3 fragment files.
 

cf/data/array/mixin/indexmixin.py

@@ -7,7 +7,6 @@
 from ....functions import indices_shape, parse_indices
 
 
-# REVIEW: getitem: `IndexMixin`: new mixin class `IndexMixin`
 class IndexMixin:
     """Mixin class for lazy indexing of a data array.
 

cf/data/array/netcdf4array.py

@@ -1,4 +1,3 @@
-# REVIEW: h5: `NetCDF4Array`: New class to access netCDF with `netCDF4`, replaces `NetCDFArray`
 import cfdm
 
 from ...mixin_container import Container

cf/data/array/netcdfarray.py

@@ -1,4 +1,3 @@
-# REVIEW: h5: `NetCDFArray`: Replaced by `NetCDF4Array`
 class NetCDFArray:
     """A netCDF array accessed with `netCDF4`.
 

cf/data/dask_regrid.py

@@ -2,7 +2,6 @@
 
 import numpy as np
 
-# REVIEW: getitem: `regrid.py`: import `cf_asanyarray`
 from .dask_utils import cf_asanyarray
 
 
@@ -177,7 +176,6 @@ def regrid(
     """
     weights, dst_mask = weights_dst_mask
 
-    # REVIEW: getitem: `regrid`: convert a to a usable array
     a = cf_asanyarray(a)
     if dst_mask is not None:
         dst_mask = cf_asanyarray(dst_mask)

cf/data/dask_utils.py

@@ -398,6 +398,7 @@ def cf_rt2dt(a, units):
 
     """
     a = cfdm_asanyarray(a)
+
     if not units.iscalendartime:
         return rt2dt(a, units_in=units)
 

cf/data/fragment/__init__.py

@@ -1,9 +1,5 @@
 from .fullfragmentarray import FullFragmentArray
-
-# REVIEW: h5: `__init__.py`: import `H5netcdfFragmentArray`
 from .h5netcdffragmentarray import H5netcdfFragmentArray
 from .netcdffragmentarray import NetCDFFragmentArray
-
-# REVIEW: h5: `__init__.py`: import `NetCDF4FragmentArray`
 from .netcdf4fragmentarray import NetCDF4FragmentArray
 from .umfragmentarray import UMFragmentArray

cf/data/fragment/fullfragmentarray.py

@@ -9,7 +9,6 @@ class FullFragmentArray(FragmentArrayMixin, FullArray):
 
     """
 
-    # REVIEW: h5: `__init__`: replace units/calendar API with attributes
     def __init__(
         self,
         fill_value=None,

cf/data/fragment/h5netcdffragmentarray.py

@@ -2,7 +2,6 @@
 from .mixin import FragmentArrayMixin
 
 
-# REVIEW: h5: `H5netcdfFragmentArray`: New class to access netCDF fragment with `h5netcdf`
 class H5netcdfFragmentArray(FragmentArrayMixin, H5netcdfArray):
     """A netCDF fragment array accessed with `h5netcdf`.
 

cf/data/fragment/mixin/fragmentarraymixin.py

@@ -12,7 +12,6 @@ class FragmentArrayMixin:
 
     """
 
-    # REVIEW: getitem: `_get_array`: new method to convert subspace to numpy array
     def _get_array(self, index=None):
         """Returns a subspace of the dataset variable.
 
@@ -166,7 +165,6 @@ def _size_1_axis(self, indices):
         None
 
         """
-        # REVIEW: getitem: `_size_1_axis`: refactor to use `original_shape`
         original_shape = self.original_shape
         if original_shape.count(1):
             return original_shape.index(1)

cf/data/fragment/netcdf4fragmentarray.py

@@ -2,7 +2,6 @@
 from .mixin import FragmentArrayMixin
 
 
-# REVIEW: h5: `NetCDF4FragmentArray`: New class to access netCDF fragment with `netCDF4`
 class NetCDF4FragmentArray(FragmentArrayMixin, NetCDF4Array):
     """A netCDF fragment array accessed with `netCDF4`.
 

cf/data/fragment/netcdffragmentarray.py

@@ -7,7 +7,6 @@
 from .netcdf4fragmentarray import NetCDF4FragmentArray
 
 
-# REVIEW: getitem: `NetCDFFragmentArray`: new inheritance to allow for different netCDF backends
 class NetCDFFragmentArray(
     FragmentArrayMixin,
     IndexMixin,
@@ -24,7 +23,6 @@ class NetCDFFragmentArray(
 
     """
 
-    # REVIEW: h5: `__init__`: replace units/calendar API with attributes
     def __init__(
         self,
         filename=None,
@@ -176,7 +174,6 @@ def __init__(
         # By default, close the file after data array access
         self._set_component("close", True, copy=False)
 
-    # REVIEW: getitem: `_get_array`: new method to convert subspace to numpy array
     def _get_array(self, index=None):
         """Returns a subspace of the dataset variable.
 

cf/data/fragment/umfragmentarray.py

@@ -9,8 +9,6 @@ class UMFragmentArray(FragmentArrayMixin, UMArray):
 
     """
 
-    # REVIEW: h5: `__init__`: replace units/calendar API with attributes
-    # REVIEW: h5: `__init__`: new keyword 'storage_options'
     def __init__(
         self,
         filename=None,

cf/data/utils.py

@@ -542,7 +542,6 @@ def parse_weights(d, weights, axis=None):
     w = []
     shape = d.shape
     axes = d._axes
-
     Data = type(d)
     for key, value in weights.items():
         value = Data.asdata(value)

cf/field.py

@@ -5220,7 +5220,6 @@ def histogram(self, digitized):
         """
         raise RuntimeError("Use cf.histogram instead.")
 
-    # REVIEW: active: active storage docstring
     @_deprecated_kwarg_check("i", version="3.0.0", removed_at="4.0.0")
     @_manage_log_level_via_verbosity
     def collapse(
@@ -7101,7 +7100,6 @@ def collapse(
                     "collapse"
                 )
 
-            # REVIEW: active: `collapse`: include size 1 axes in collapse
             # Note: It is important that size 1 axes are also passed
             #       on to the Data collapse, because active storage
             #       collapses get confused if they're not there.