Merge pull request #826 from davidhassell/REVIEW

Remove REVIEW comments

cf/cfimplementation.py

@@ -27,7 +27,6 @@
 )
 from .data import Data
 
-# REVIEW: h5: `cfimplementation.py`: import `CFAH5netcdfArray`, `CFANetCDF4Array`, `H5netcdfArray`,`NetCDF4Array`
 from .data.array import (
     BoundsFromNodesArray,
     CellConnectivityArray,
@@ -116,7 +115,6 @@ 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 +131,6 @@ 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
@@ -49,8 +48,6 @@ def _lock(self):
         """
         return netcdf_lock
 
-    # REVIEW: h5: `_get_array`: Ignore this for h5 review
-    # 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/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

@@ -36,7 +36,6 @@ def __new__(cls, *args, **kwargs):
         }
         return instance
 
-    # REVIEW: h5: `__init__`: replace units/calendar API with attributes
     def __init__(
         self,
         filename=None,
@@ -225,7 +224,6 @@ 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.
 
@@ -466,7 +464,6 @@ 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
@@ -47,8 +46,6 @@ def _lock(self):
         """
         return netcdf_lock
 
-    # REVIEW: getitem: `_get_array`: Ignore this for h5 review
-    # 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/array/netcdfarray.py

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

cf/data/array/umarray.py

@@ -12,7 +12,6 @@ class UMArray(
 ):
     """A sub-array stored in a PP or UM fields file."""
 
-    # REVIEW: h5: `__init__`: replace units/calendar API with attributes
     def __init__(
         self,
         filename=None,
@@ -171,7 +170,6 @@ def __init__(
         # By default, close the UM 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.
 
@@ -272,7 +270,6 @@ def _get_rec(self, f, header_offset):
         #         if r.hdr_offset == header_offset:
         #             return r
 
-    # REVIEW: getitem: `_set_FillValue`: record _FillValue in attributes
     def _set_FillValue(self, int_hdr, real_hdr, attributes):
         """Set the ``_FillValue`` attribute.
 
@@ -367,10 +364,8 @@ def _set_units(self, int_hdr, attributes):
                 units = units0
                 break
 
-        # REVIEW: getitem: `_set_units`: record units in attributes
         attributes["units"] = units
 
-    # REVIEW: getitem: `_set_unpack`: record unpack in attributes
     def _set_unpack(self, int_hdr, real_hdr, attributes):
         """Set the ``add_offset`` and ``scale_factor`` attributes.
 

cf/data/collapse/collapse_active.py

@@ -1,4 +1,3 @@
-# REVIEW: active: `collapse_active.py`: new module for active storage functionality
 import datetime
 import logging
 import time

cf/data/collapse/dask_collapse.py

@@ -1,4 +1,3 @@
-# REVIEW: active: `dask_collapse.py`: all unlabelled changes in this module are general tidying, and should be reviewed at the same time as active storage
 """Reduction functions intended to be passed to be dask.
 
 Most of these functions are expected to be passed to
@@ -231,7 +230,6 @@ def sum_sample_sizes(pairs, axis, computing_meta=False, **kwargs):
 # --------------------------------------------------------------------
 # mean
 # --------------------------------------------------------------------
-# REVIEW: active: `cf_mean_chunk`: active storage decoration
 @actify("mean")
 def cf_mean_chunk(
     x,
@@ -378,7 +376,6 @@ def cf_mean_agg(
 # --------------------------------------------------------------------
 # maximum
 # --------------------------------------------------------------------
-# REVIEW: active: `cf_max_chunk`: active storage decoration
 @actify("max")
 def cf_max_chunk(x, dtype=None, computing_meta=False, **kwargs):
     """Chunk calculations for the maximum.
@@ -533,7 +530,6 @@ def cf_mid_range_agg(
 # --------------------------------------------------------------------
 # minimum
 # --------------------------------------------------------------------
-# REVIEW: active: `cf_min_chunk`: active storage decoration
 @actify("min")
 def cf_min_chunk(x, dtype=None, computing_meta=False, **kwargs):
     """Chunk calculations for the minimum.
@@ -640,7 +636,6 @@ def cf_min_agg(
 # --------------------------------------------------------------------
 # range
 # --------------------------------------------------------------------
-# REVIEW: active: `cf_range_chunk`: active storage decoration
 @actify("range")
 def cf_range_chunk(x, dtype=None, computing_meta=False, **kwargs):
     """Chunk calculations for the range.
@@ -754,7 +749,6 @@ def cf_range_agg(
 # --------------------------------------------------------------------
 # root mean square
 # --------------------------------------------------------------------
-# REVIEW: active: `cf_rms_chunk`: active storage decoration
 @actify("rms")
 def cf_rms_chunk(x, weights=None, dtype="f8", computing_meta=False, **kwargs):
     """Chunk calculations for the root mean square (RMS).
@@ -839,7 +833,6 @@ def cf_rms_agg(
 # --------------------------------------------------------------------
 # sample size
 # --------------------------------------------------------------------
-# REVIEW: active: `cf_sample_size_chunk`: active storage decoration
 @actify("sample_size")
 def cf_sample_size_chunk(x, dtype="i8", computing_meta=False, **kwargs):
     """Chunk calculations for the sample size.
@@ -953,7 +946,6 @@ def cf_sample_size_agg(
 # --------------------------------------------------------------------
 # sum
 # --------------------------------------------------------------------
-# REVIEW: active: `cf_sum_chunk`: active storage decoration
 @actify("sum")
 def cf_sum_chunk(
     x,
@@ -1089,7 +1081,6 @@ def cf_sum_agg(
 # --------------------------------------------------------------------
 # sum of weights
 # --------------------------------------------------------------------
-# REVIEW: active: `cf_sum_of_weights_chunk`: active storage decoration
 @actify("sum_of_weights")
 def cf_sum_of_weights_chunk(
     x, weights=None, dtype="f8", computing_meta=False, **kwargs
@@ -1133,7 +1124,6 @@ def cf_sum_of_weights_chunk(
 # --------------------------------------------------------------------
 # sum of squares of weights
 # --------------------------------------------------------------------
-# REVIEW: active: `cf_sum_of_weights2_chunk`: active storage decoration
 @actify("sum_of_weights2")
 def cf_sum_of_weights2_chunk(
     x, weights=None, dtype="f8", computing_meta=False, **kwargs
@@ -1179,7 +1169,6 @@ def cf_sum_of_weights2_chunk(
 # --------------------------------------------------------------------
 # unique
 # --------------------------------------------------------------------
-# REVIEW: active: `cf_unique_chunk`: active storage decoration
 @actify("unique")
 def cf_unique_chunk(x, dtype=None, computing_meta=False, **kwargs):
     """Chunk calculations for the unique values.
@@ -1244,7 +1233,6 @@ def cf_unique_agg(pairs, axis=None, computing_meta=False, **kwargs):
 # --------------------------------------------------------------------
 # variance
 # --------------------------------------------------------------------
-# REVIEW: active: `cf_var_chunk`: active storage decoration
 @actify("var")
 def cf_var_chunk(
     x, weights=None, dtype="f8", computing_meta=False, ddof=None, **kwargs

cf/data/creation.py

@@ -60,7 +60,6 @@ def to_dask(array, chunks, **from_array_options):
     if is_dask_collection(array):
         return array
 
-    # REVIEW: getitem: `to_dask`: set '_asanyarray'
     if hasattr(array, "to_dask_array"):
         try:
             return array.to_dask_array(chunks=chunks)
@@ -83,8 +82,6 @@ def to_dask(array, chunks, **from_array_options):
         array = np.asanyarray(array)
 
     kwargs = from_array_options
-    # REVIEW: active: `to_dask`: '_dask_meta' renamed to '_meta' for consistency with Dask
-    # REVIEW: getitem:  `to_dask`: The file lock is now on the `Array` object (in its `_get_array` method), rather than being set on the Dask array itself.
     kwargs.setdefault("meta", getattr(array, "_meta", None))
 
     try:

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)