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Merged
trexfeathers merged 12 commits into from
Jun 9, 2026
Merged

Chardata moretests #7101

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56a464e
Test with DECODE_TO_STRINGS off: WIP problem with cube contents.
pp-mo Mar 14, 2026
dd5330f
Resolve load problems with non-string read loading by skipping proble…
pp-mo May 26, 2026
a7e928a
Make cf chartostring disable work for non-owned regular datasets.
pp-mo May 27, 2026
e6bdb53
Checks for alternate encoding name.
pp-mo May 27, 2026
fa9c66d
Fix bug where nc save was removing _Encoding attributes from saved cu…
pp-mo May 28, 2026
3def8f1
Fix bug: stop cube equality failing with char/string data.
pp-mo May 28, 2026
713f631
Remove ban on string data for cubes: Extracting a scalar string cube …
pp-mo May 28, 2026
4e956e0
Tests for saving scalar strings, and a mix of encodings and lengths.
pp-mo May 28, 2026
2c276a8
Tests for some specific save/load usecases.
pp-mo May 29, 2026
6c4be38
Test save/load of a 'bad' unicode sequence as a byte array.
pp-mo May 29, 2026
5d5bedc
Remove various obsolete comments, and debug code.
pp-mo May 29, 2026
cbbaf5a
Review changes.
pp-mo Jun 8, 2026
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25 changes: 13 additions & 12 deletions lib/iris/cube.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1280,10 +1280,6 @@ def __init__(
... (longitude, 1)])

"""
# Temporary error while we transition the API.
if isinstance(data, str):
raise TypeError("Invalid data type: {!r}.".format(data))

# Configure the metadata manager.
self._metadata_manager = metadata_manager_factory(CubeMetadata)

Expand Down Expand Up @@ -4468,15 +4464,20 @@ def __eq__(self, other):

# Having checked everything else, check approximate data equality.
if result and not dataless_equality:
# TODO: why do we use allclose() here, but strict equality in
# _DimensionalMetadata (via util.array_equal())?
result = bool(
np.allclose(
self.core_data(),
other.core_data(),
equal_nan=True,
if self.dtype.kind in "if":
# numbers
# TODO: why do we use allclose() here, but strict equality in
# _DimensionalMetadata (via util.array_equal())?
result = bool(
np.allclose(
self.core_data(),
other.core_data(),
equal_nan=True,
)
)
)
else:
# non-numeric: use exact equality
result = bool(np.all(self.core_data() == other.core_data()))
return result

# Must supply __ne__, Python does not defer to __eq__ for negative equality
Expand Down
4 changes: 0 additions & 4 deletions lib/iris/fileformats/_nc_load_rules/helpers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1637,11 +1637,7 @@ def _add_auxiliary_coordinate(
# Determine the name of the dimension/s shared between the CF-netCDF data variable
# and the coordinate being built.
coord_dims = cf_coord_var.dimensions
# if cf._is_str_dtype(cf_coord_var):
# coord_dims = coord_dims[:-1]
datavar_dims = engine.cf_var.dimensions
# if cf._is_str_dtype(engine.cf_var):
# datavar_dims = datavar_dims[:-1]
common_dims = [dim for dim in coord_dims if dim in datavar_dims]
data_dims = None
if common_dims:
Expand Down
6 changes: 6 additions & 0 deletions lib/iris/fileformats/cf.py
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Expand Up @@ -1344,6 +1344,12 @@ def __init__(self, file_source, warn=False, monotonic=False):
self._with_ugrid = False

# Read the variables in the dataset only once to reduce runtime.
# Turn off *any* automatic decoding in the underlying netCDF4 dataset
ds = self._dataset
if isinstance(ds, _thread_safe_nc.DatasetWrapper):
ds._contained_instance.set_auto_chartostring(False)
else:
ds.set_auto_chartostring(False)
Comment on lines +1347 to +1352

@pp-mo pp-mo Jun 11, 2026

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link

variables = self._dataset.variables
self._translate(variables)
self._build_cf_groups(variables)
Expand Down
1 change: 0 additions & 1 deletion lib/iris/fileformats/netcdf/_bytecoding_datasets.py
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Expand Up @@ -116,7 +116,6 @@ def encode_stringarray_as_bytearray(
raise ValueError(msg) from err

n_bytes = len(bytes)
# TODO: may want to issue warning or error if we overflow the length?
if n_bytes > string_dimension_length:
from iris.exceptions import TranslationError

Expand Down
2 changes: 1 addition & 1 deletion lib/iris/fileformats/netcdf/_thread_safe_nc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -160,7 +160,7 @@ class GroupWrapper(_ThreadSafeWrapper):
# Note: will also accept a whole Dataset object, but that is OK.
_DUCKTYPE_CHECK_PROPERTIES = ["createVariable"]
# Class to use when creating variable wrappers (default=VariableWrapper).
# - needed to support _byte_encoded_data.EncodedDataset.
# - needed to support _bytecoding_datasets.EncodedDataset.
VAR_WRAPPER_CLS = VariableWrapper
GRP_WRAPPER_CLS: typing.Any | None = None # self-reference : fill in later

Expand Down
86 changes: 49 additions & 37 deletions lib/iris/fileformats/netcdf/saver.py
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Expand Up @@ -1719,20 +1719,23 @@ def add_names_attrs():
if element.units.calendar:
_setncattr(cf_var, "calendar", str(element.units.calendar))

# Take a copy so we can remove things
element_attrs = element.attributes.copy()

Comment on lines +1722 to +1724

@pp-mo pp-mo Jun 11, 2026

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# Note: when writing UGRID, "element" can be a Mesh which has no "dtype",
# and for dataless cubes it will have a 'None' dtype.
if getattr(element, "dtype", None) is not None:
# Most attributes are dealt with later. But _Encoding needs to be defined
# *before* we can write to a character variable.
if element.dtype.kind in "SU" and "_Encoding" in element.attributes:
encoding = element.attributes.pop("_Encoding")
if element.dtype.kind in "SU" and "_Encoding" in element_attrs:
encoding = element_attrs.pop("_Encoding")
_setncattr(cf_var, "_Encoding", encoding)

if not isinstance(element, Cube):
# Add any other custom coordinate attributes.
# N.B. not Cube, which has specific handling in _create_cf_data_variable
for name in sorted(element.attributes):
value = element.attributes[name]
for name in sorted(element_attrs):
value = element_attrs[name]

if name == "STASH":
# Adopting provisional Metadata Conventions for representing MO
Expand Down Expand Up @@ -1830,8 +1833,8 @@ def _create_generic_cf_array_var(
if cube is not None and data is not None and cube.shape != data.shape:
compression_kwargs = {}

if not is_dataless and np.issubdtype(data.dtype, np.str_):
# Deal with string-type variables.
if not is_dataless and data.dtype.kind == "U":
# Deal with unicode-string-type variables.
# Typically CF label variables, but also possibly ancil-vars ?

# NOTE: all we are doing here is to calculate the byte dimension length,
Expand All @@ -1840,37 +1843,26 @@ def _create_generic_cf_array_var(
# being a _bytecoding_datasets.EncodedVariable.
string_dimension_depth = data.dtype.itemsize

if data.dtype.kind == "U":
# String content (U) instead of bytes (S).
# For numpy strings, itemsize is **always** a multiple of 4
if string_dimension_depth % 4 != 0:
msg = (
"Unexpected numpy string 'itemsize' for element "
f"{cube_or_mesh.name()}: "
f"'dtype.itemsize = {string_dimension_depth}, expected "
"a multiple of four (always)."
)
raise ValueError(msg)
nchars = string_dimension_depth // 4

encoding_attr = element.attributes.get("_Encoding", "ascii")
# Look this up + return a supported encoding name
# NB implements defaults and raises a warning if given not recognised.
encoding = bytecoding_datasets._identify_encoding(
encoding=encoding_attr, var_name=cf_name, writing=True
# String content (U) instead of bytes (S).
# For numpy strings, itemsize is **always** a multiple of 4
if string_dimension_depth % 4 != 0:
msg = (
"Unexpected numpy string 'itemsize' for element "
f"{cube_or_mesh.name()}: "
f"'dtype.itemsize = {string_dimension_depth}, expected "
"a multiple of four (always)."
)
width_fns = bytecoding_datasets._ENCODING_WIDTH_TRANSLATIONS[encoding]
string_dimension_depth = width_fns.nchars_2_nbytes(nchars)
else:
if data.dtype.kind != "S" or data.dtype.itemsize != 1:
# Some type of data we don't "understand".
# NB this includes "Sxx" types other than "S1" : It seems that
# netCDF4 saves Sxx as variable-length strings. But we don't support that type in Iris.
msg = (
f"Variable {cf_name!r} has unexpected string/character dtype, "
f"{data.dtype} -- should be either 'S' or 'U' type."
)
raise ValueError(msg)

@pp-mo pp-mo Jun 11, 2026

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logic changed + code moved elsewhere : see here

raise ValueError(msg)
nchars = string_dimension_depth // 4

encoding_attr = element.attributes.get("_Encoding", "ascii")
# Look this up + return a supported encoding name
# NB implements defaults and raises a warning if given not recognised.
encoding = bytecoding_datasets._identify_encoding(
encoding=encoding_attr, var_name=cf_name, writing=True
)
width_fns = bytecoding_datasets._ENCODING_WIDTH_TRANSLATIONS[encoding]
string_dimension_depth = width_fns.nchars_2_nbytes(nchars)

string_dimension_name = "string%d" % string_dimension_depth

Expand All @@ -1890,12 +1882,32 @@ def _create_generic_cf_array_var(
# Create the label coordinate variable.
cf_var = self._dataset.createVariable(cf_name, "|S1", element_dims)
else:
# A normal (numeric) variable.
# A non-string variable.
# ensure a valid datatype for the file format.
if is_dataless:
dtype = self._DATALESS_DTYPE
fill_value = self._DATALESS_FILLVALUE
else:
# Normal non-string data.
# NOTE: this includes byte-arrays (S1 only) : however these must
# use an actual cube dimension for the 'string dimension', which
# seriously limits the utility of DECODE_TO_STRINGS_ON_READ.
# TODO: also support netCDF variable-length strings ("string" type).
# Currently hit a **write error here**, being numpy object dtype ("O").
if data.dtype.kind not in "iufSU" or (
data.dtype.kind == "S" and data.dtype.itemsize != 1
):
# This is a type of data we don't "understand".
# NB this includes "Sxx" types other than "S1" : It seems that
# netCDF4 saves Sxx as variable-length strings.
# But we don't support that type in Iris.
msg = (
f"Variable {cf_name!r} has unexpected dtype, {data.dtype!r}."
f"Data content arrays must be numeric, or contain "
"single-bytes (dtype 'S1'), or unicode strings (dtype 'U<n>')."
)
raise ValueError(msg)
Comment on lines +1897 to +1909

@pp-mo pp-mo Jun 11, 2026

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moved from above, following dtype testing logic change


element_type = type(element).__name__
data = self._ensure_valid_dtype(data, element_type, element)
if not packing_controls:
Expand Down
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