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Merge branch 'dev' into no_override
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mavaylon1 authored Aug 19, 2024
2 parents bc3f336 + 316ec4b commit 56e13b8
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5 changes: 3 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -5,16 +5,17 @@
### Enhancements
- Added support to append to a dataset of references for HDMF-Zarr. @mavaylon1 [#1157](https://github.com/hdmf-dev/hdmf/pull/1157)
- Allow override of constructor args and object attrs in `hdmf.build.ObjectMapper` to return None. @rly [#1167](https://github.com/hdmf-dev/hdmf/pull/1167)
- Adjusted stacklevel of warnings to point to user code when possible. @rly [#1166](https://github.com/hdmf-dev/hdmf/pull/1166)
- Improved "already exists" error message when adding a container to a `MultiContainerInterface`. @rly [#1165](https://github.com/hdmf-dev/hdmf/pull/1165)
- Speed up loading namespaces by skipping register_type when already registered. @magland [#1102](https://github.com/hdmf-dev/hdmf/pull/1102)
- Speed up namespace loading: return a shallow copy rather than a deep copy in build_const_args. @magland [#1103](https://github.com/hdmf-dev/hdmf/pull/1103)

## HDMF 3.14.3 (July 29, 2024)

### Enhancements
- Added new attribute "dimension_labels" on `DatasetBuilder` which specifies the names of the dimensions used in the
dataset based on the shape of the dataset data and the dimension names in the spec for the data type. This attribute
is available on build (during the write process), but not on read of a dataset from a file. @rly [#1081](https://github.com/hdmf-dev/hdmf/pull/1081)
- Speed up loading namespaces by skipping register_type when already registered. @magland [#1102](https://github.com/hdmf-dev/hdmf/pull/1102)
- Speed up namespace loading: return a shallow copy rather than a deep copy in build_const_args. @magland [#1103](https://github.com/hdmf-dev/hdmf/pull/1103)

## HDMF 3.14.2 (July 7, 2024)

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8 changes: 4 additions & 4 deletions src/hdmf/backends/hdf5/h5_utils.py
Original file line number Diff line number Diff line change
Expand Up @@ -501,7 +501,7 @@ def __init__(self, **kwargs):
# Check for possible collision with other parameters
if not isinstance(getargs('data', kwargs), Dataset) and self.__link_data:
self.__link_data = False
warnings.warn('link_data parameter in H5DataIO will be ignored', stacklevel=2)
warnings.warn('link_data parameter in H5DataIO will be ignored', stacklevel=3)
# Call the super constructor and consume the data parameter
super().__init__(**kwargs)
# Construct the dict with the io args, ignoring all options that were set to None
Expand All @@ -525,7 +525,7 @@ def __init__(self, **kwargs):
self.__iosettings.pop('compression', None)
if 'compression_opts' in self.__iosettings:
warnings.warn('Compression disabled by compression=False setting. ' +
'compression_opts parameter will, therefore, be ignored.', stacklevel=2)
'compression_opts parameter will, therefore, be ignored.', stacklevel=3)
self.__iosettings.pop('compression_opts', None)
# Validate the compression options used
self._check_compression_options()
Expand All @@ -540,7 +540,7 @@ def __init__(self, **kwargs):
if isinstance(self.data, Dataset):
for k in self.__iosettings.keys():
warnings.warn("%s in H5DataIO will be ignored with H5DataIO.data being an HDF5 dataset" % k,
stacklevel=2)
stacklevel=3)

self.__dataset = None

Expand Down Expand Up @@ -618,7 +618,7 @@ def _check_compression_options(self):
if self.__iosettings['compression'] not in ['gzip', h5py_filters.h5z.FILTER_DEFLATE]:
warnings.warn(str(self.__iosettings['compression']) + " compression may not be available "
"on all installations of HDF5. Use of gzip is recommended to ensure portability of "
"the generated HDF5 files.", stacklevel=3)
"the generated HDF5 files.", stacklevel=4)

@staticmethod
def filter_available(filter, allow_plugin_filters):
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2 changes: 1 addition & 1 deletion src/hdmf/backends/hdf5/h5tools.py
Original file line number Diff line number Diff line change
Expand Up @@ -344,7 +344,7 @@ def copy_file(self, **kwargs):
warnings.warn("The copy_file class method is no longer supported and may be removed in a future version of "
"HDMF. Please use the export method or h5py.File.copy method instead.",
category=DeprecationWarning,
stacklevel=2)
stacklevel=3)

source_filename, dest_filename, expand_external, expand_refs, expand_soft = getargs('source_filename',
'dest_filename',
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2 changes: 1 addition & 1 deletion src/hdmf/common/resources.py
Original file line number Diff line number Diff line change
Expand Up @@ -628,7 +628,7 @@ def add_ref(self, **kwargs):
if entity_uri is not None:
entity_uri = entity.entity_uri
msg = 'This entity already exists. Ignoring new entity uri'
warn(msg, stacklevel=2)
warn(msg, stacklevel=3)

#################
# Validate Object
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10 changes: 5 additions & 5 deletions src/hdmf/common/table.py
Original file line number Diff line number Diff line change
Expand Up @@ -717,7 +717,7 @@ def add_row(self, **kwargs):
warn(("Data has elements with different lengths and therefore cannot be coerced into an "
"N-dimensional array. Use the 'index' argument when creating a column to add rows "
"with different lengths."),
stacklevel=2)
stacklevel=3)

def __eq__(self, other):
"""Compare if the two DynamicTables contain the same data.
Expand Down Expand Up @@ -776,7 +776,7 @@ def add_column(self, **kwargs): # noqa: C901

if isinstance(index, VectorIndex):
warn("Passing a VectorIndex in for index may lead to unexpected behavior. This functionality will be "
"deprecated in a future version of HDMF.", category=FutureWarning, stacklevel=2)
"deprecated in a future version of HDMF.", category=FutureWarning, stacklevel=3)

if name in self.__colids: # column has already been added
msg = "column '%s' already exists in %s '%s'" % (name, self.__class__.__name__, self.name)
Expand All @@ -793,7 +793,7 @@ def add_column(self, **kwargs): # noqa: C901
"Please ensure the new column complies with the spec. "
"This will raise an error in a future version of HDMF."
% (name, self.__class__.__name__, spec_table))
warn(msg, stacklevel=2)
warn(msg, stacklevel=3)

index_bool = index or not isinstance(index, bool)
spec_index = self.__uninit_cols[name].get('index', False)
Expand All @@ -803,7 +803,7 @@ def add_column(self, **kwargs): # noqa: C901
"Please ensure the new column complies with the spec. "
"This will raise an error in a future version of HDMF."
% (name, self.__class__.__name__, spec_index))
warn(msg, stacklevel=2)
warn(msg, stacklevel=3)

spec_col_cls = self.__uninit_cols[name].get('class', VectorData)
if col_cls != spec_col_cls:
Expand Down Expand Up @@ -841,7 +841,7 @@ def add_column(self, **kwargs): # noqa: C901
warn(("Data has elements with different lengths and therefore cannot be coerced into an "
"N-dimensional array. Use the 'index' argument when adding a column of data with "
"different lengths."),
stacklevel=2)
stacklevel=3)

# Check that we are asked to create an index
if (isinstance(index, bool) or isinstance(index, int)) and index > 0 and len(data) > 0:
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2 changes: 1 addition & 1 deletion src/hdmf/container.py
Original file line number Diff line number Diff line change
Expand Up @@ -894,7 +894,7 @@ def set_dataio(self, **kwargs):
warn(
"Data.set_dataio() is deprecated. Please use Data.set_data_io() instead.",
DeprecationWarning,
stacklevel=2,
stacklevel=3,
)
dataio = getargs('dataio', kwargs)
dataio.data = self.__data
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8 changes: 4 additions & 4 deletions src/hdmf/spec/namespace.py
Original file line number Diff line number Diff line change
Expand Up @@ -50,13 +50,13 @@ def __init__(self, **kwargs):
self['full_name'] = full_name
if version == str(SpecNamespace.UNVERSIONED):
# the unversioned version may be written to file as a string and read from file as a string
warn("Loaded namespace '%s' is unversioned. Please notify the extension author." % name, stacklevel=2)
warn(f"Loaded namespace '{name}' is unversioned. Please notify the extension author.")
version = SpecNamespace.UNVERSIONED
if version is None:
# version is required on write -- see YAMLSpecWriter.write_namespace -- but can be None on read in order to
# be able to read older files with extensions that are missing the version key.
warn(("Loaded namespace '%s' is missing the required key 'version'. Version will be set to '%s'. "
"Please notify the extension author.") % (name, SpecNamespace.UNVERSIONED), stacklevel=2)
warn(f"Loaded namespace '{name}' is missing the required key 'version'. Version will be set to "
f"'{SpecNamespace.UNVERSIONED}'. Please notify the extension author.")
version = SpecNamespace.UNVERSIONED
self['version'] = version
if date is not None:
Expand Down Expand Up @@ -533,7 +533,7 @@ def load_namespaces(self, **kwargs):
if ns['version'] != self.__namespaces.get(ns['name'])['version']:
# warn if the cached namespace differs from the already loaded namespace
warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
% (ns['name'], ns['version'], self.__namespaces.get(ns['name'])['version']), stacklevel=2)
% (ns['name'], ns['version'], self.__namespaces.get(ns['name'])['version']))
else:
to_load.append(ns)
# now load specs into namespace
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2 changes: 1 addition & 1 deletion src/hdmf/spec/spec.py
Original file line number Diff line number Diff line change
Expand Up @@ -321,7 +321,7 @@ def __init__(self, **kwargs):
default_name = getargs('default_name', kwargs)
if default_name:
if name is not None:
warn("found 'default_name' with 'name' - ignoring 'default_name'", stacklevel=2)
warn("found 'default_name' with 'name' - ignoring 'default_name'")
else:
self['default_name'] = default_name
self.__attributes = dict()
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