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Remove spike interface deprecations #1689

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Remove spikeinterface deprecated parameters
h-mayorquin Mar 9, 2026
954abea
Remove redundant test
h-mayorquin Mar 9, 2026
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,6 +1,10 @@
# v0.9.4 (Upcoming)

## Removals, Deprecations and Changes
* Made `nwbfile_path` a required parameter in `write_recording_to_nwbfile`, `write_sorting_to_nwbfile`, and `write_sorting_analyzer_to_nwbfile`. To add data to an in-memory NWBFile, use `add_recording_to_nwbfile`, `add_sorting_to_nwbfile`, or `add_sorting_analyzer_to_nwbfile` instead. [PR #1689](https://github.com/catalystneuro/neuroconv/pull/1689)
* `write_recording_to_nwbfile`, `write_sorting_to_nwbfile`, and `write_sorting_analyzer_to_nwbfile` now return `None` in append mode (`append_on_disk_nwbfile=True`) instead of the NWBFile object. [PR #1689](https://github.com/catalystneuro/neuroconv/pull/1689)
* Removed the deprecated `iterator_opts` parameter from `write_recording_to_nwbfile`. Use `iterator_options` instead. [PR #1689](https://github.com/catalystneuro/neuroconv/pull/1689)
* Removed stale `iterator_type='v1'` deprecation note from `BaseImagingExtractorInterface.add_to_nwbfile` docstring. [PR #1689](https://github.com/catalystneuro/neuroconv/pull/1689)
* Removed the deprecated `iterator_type='v1'` option from `_imaging_frames_to_hdmf_iterator`. Use `iterator_type='v2'` (default) instead. [PR #1679](https://github.com/catalystneuro/neuroconv/pull/1679)
* Removed support for passing `rate` in trace metadata for fluorescence traces. The rate is now always calculated automatically from the segmentation extractor's timestamps or sampling frequency. [PR #1679](https://github.com/catalystneuro/neuroconv/pull/1679)
* Removed the deprecated `stub_frames` parameter from ophys interfaces (`BaseImagingExtractorInterface`, `BaseSegmentationExtractorInterface`, `BrukerTiffMultiPlaneConverter`, `BrukerTiffSinglePlaneConverter`, `MiniscopeConverter`, `Suite2pSegmentationInterface`, `MinianSegmentationInterface`, `MiniscopeImagingDataInterface`). Use `stub_samples` instead. [PR #1676](https://github.com/catalystneuro/neuroconv/pull/1676)
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1 change: 0 additions & 1 deletion src/neuroconv/datainterfaces/ophys/baseimagingextractorinterface.py
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Expand Up @@ -203,7 +203,6 @@ def add_to_nwbfile(
The type of iterator for chunked data writing.
'v2': Uses iterative write with control over chunking and progress bars.
None: Loads all data into memory before writing (not recommended for large datasets).
Note: 'v1' is deprecated and will be removed on or after March 2026.
iterator_options : dict, optional
Options for controlling the iterative write process (buffer size, progress bars).
See the `pynwb tutorial on iterative write <https://pynwb.readthedocs.io/en/stable/tutorials/advanced_io/plot_iterative_write.html#sphx-glr-tutorials-advanced-io-plot-iterative-write-py>`_
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177 changes: 13 additions & 164 deletions src/neuroconv/tools/spikeinterface/spikeinterface.py
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Expand Up @@ -1654,7 +1654,7 @@ def add_recording_metadata_to_nwbfile(

def write_recording_to_nwbfile(
recording: BaseRecording,
nwbfile_path: FilePath | None = None,
nwbfile_path: FilePath,
nwbfile: pynwb.NWBFile | None = None,
metadata: dict | None = None,
overwrite: bool = False,
Expand All @@ -1664,7 +1664,6 @@ def write_recording_to_nwbfile(
*,
iterator_type: str | None = "v2",
iterator_options: dict | None = None,
iterator_opts: dict | None = None,
backend: Literal["hdf5", "zarr"] | None = None,
backend_configuration: HDF5BackendConfiguration | ZarrBackendConfiguration | None = None,
append_on_disk_nwbfile: bool = False,
Expand All @@ -1676,10 +1675,8 @@ def write_recording_to_nwbfile(
Parameters
----------
recording : spikeinterface.BaseRecording
nwbfile_path : FilePath, optional
nwbfile_path : FilePath
Path for where to write or load (if overwrite=False) the NWBFile.
If not provided, only adds data to the in-memory nwbfile without writing to disk.
**Deprecated**: Using this function without nwbfile_path is deprecated. Use `add_recording_to_nwbfile` instead.
nwbfile : NWBFile, optional
If passed, this function will fill the relevant fields within the NWBFile object.
E.g., calling::
Expand Down Expand Up @@ -1777,53 +1774,10 @@ def write_recording_to_nwbfile(
Returns
-------
NWBFile or None
The NWBFile object when writing a new file or using an in-memory nwbfile.
The NWBFile object when writing a new file.
Returns None when appending to an existing file on disk (append_on_disk_nwbfile=True).
**Deprecated**: Returning NWBFile in append mode is deprecated and will return None in or after March 2026.
"""

# Handle deprecated usage without nwbfile_path
if nwbfile_path is None:
warnings.warn(
"Using 'write_recording_to_nwbfile' without 'nwbfile_path' to only add data to an in-memory nwbfile is deprecated "
"and will be removed in or after March 2026. Use 'add_recording_to_nwbfile' instead.",
DeprecationWarning,
stacklevel=2,
)
if nwbfile is None:
raise ValueError(
"Either 'nwbfile_path' or 'nwbfile' must be provided. "
"To add data to an in-memory nwbfile, use 'add_recording_to_nwbfile' instead."
)
# Call add_recording_to_nwbfile for deprecated behavior
add_recording_to_nwbfile(
recording=recording,
nwbfile=nwbfile,
metadata=metadata,
write_as=write_as,
es_key=es_key,
iterator_type=iterator_type,
iterator_options=iterator_options if iterator_options is not None else iterator_opts,
null_values_for_properties=null_values_for_properties,
)
return nwbfile

# Handle deprecated iterator_opts parameter
if iterator_opts is not None:
warnings.warn(
"The 'iterator_opts' parameter is deprecated and will be removed on or after March 2026. "
"Use 'iterator_options' instead.",
FutureWarning,
stacklevel=2,
)
if iterator_options is None:
iterator_options = iterator_opts
else:
raise ValueError(
"Both 'iterator_opts' and 'iterator_options' were specified. "
"Please use only 'iterator_options' as 'iterator_opts' is deprecated."
)

appending_to_in_memory_nwbfile = nwbfile is not None
file_initially_exists = nwbfile_path.exists()
allowed_to_modify_existing = overwrite or append_on_disk_nwbfile
Expand Down Expand Up @@ -1885,13 +1839,6 @@ def write_recording_to_nwbfile(

else:
# Append mode: read existing file, add data, write back
warnings.warn(
"Returning an NWBFile object when using append_on_disk_nwbfile=True is deprecated "
"and will return None in or after March 2026.",
DeprecationWarning,
stacklevel=2,
)

IO = BACKEND_NWB_IO[backend]

with IO(path=str(nwbfile_path), mode="r+", load_namespaces=True) as io:
Expand All @@ -1918,7 +1865,7 @@ def write_recording_to_nwbfile(
if verbose:
print(f"NWB file saved at {nwbfile_path}!")

return nwbfile # Will return None in March 2026
return None


def _add_units_table_to_nwbfile(
Expand Down Expand Up @@ -2335,7 +2282,7 @@ def _add_units_table_to_nwbfile(

def write_sorting_to_nwbfile(
sorting: BaseSorting,
nwbfile_path: FilePath | None = None,
nwbfile_path: FilePath,
nwbfile: pynwb.NWBFile | None = None,
metadata: dict | None = None,
overwrite: bool = False,
Expand All @@ -2361,10 +2308,8 @@ def write_sorting_to_nwbfile(
Parameters
----------
sorting : spikeinterface.BaseSorting
nwbfile_path : FilePath, optional
nwbfile_path : FilePath
Path for where to write or load (if overwrite=False) the NWBFile.
If not provided, only adds data to the in-memory nwbfile without writing to disk.
**Deprecated**: Using this function without nwbfile_path is deprecated. Use `add_sorting_to_nwbfile` instead.
nwbfile : NWBFile, optional
If passed, this function will fill the relevant fields within the NWBFile object.
E.g., calling::
Expand Down Expand Up @@ -2421,41 +2366,10 @@ def write_sorting_to_nwbfile(
Returns
-------
NWBFile or None
The NWBFile object when writing a new file or using an in-memory nwbfile.
The NWBFile object when writing a new file.
Returns None when appending to an existing file on disk (append_on_disk_nwbfile=True).
**Deprecated**: Returning NWBFile in append mode is deprecated and will return None in or after March 2026.
"""

# Handle deprecated usage without nwbfile_path
if nwbfile_path is None:
warnings.warn(
"Using 'write_sorting_to_nwbfile' without 'nwbfile_path' to only add data to an in-memory nwbfile is deprecated "
"and will be removed in or after March 2026. Use 'add_sorting_to_nwbfile' instead.",
DeprecationWarning,
stacklevel=2,
)
if nwbfile is None:
raise ValueError(
"Either 'nwbfile_path' or 'nwbfile' must be provided. "
"To add data to an in-memory nwbfile, use 'add_sorting_to_nwbfile' instead."
)
# Call add_sorting_to_nwbfile for deprecated behavior
add_sorting_to_nwbfile(
sorting=sorting,
nwbfile=nwbfile,
unit_ids=unit_ids,
property_descriptions=property_descriptions,
skip_properties=skip_properties,
write_as=write_as,
units_name=units_name,
units_description=units_description,
waveform_means=waveform_means,
waveform_sds=waveform_sds,
unit_electrode_indices=unit_electrode_indices,
null_values_for_properties=null_values_for_properties,
)
return nwbfile

appending_to_in_memory_nwbfile = nwbfile is not None
file_initially_exists = nwbfile_path.exists()
allowed_to_modify_existing = overwrite or append_on_disk_nwbfile
Expand Down Expand Up @@ -2521,13 +2435,6 @@ def write_sorting_to_nwbfile(

else:
# Append mode: read existing file, add data, write back
warnings.warn(
"Returning an NWBFile object when using append_on_disk_nwbfile=True is deprecated "
"and will return None in or after March 2026.",
DeprecationWarning,
stacklevel=2,
)

IO = BACKEND_NWB_IO[backend]

with IO(path=str(nwbfile_path), mode="r+", load_namespaces=True) as io:
Expand Down Expand Up @@ -2557,7 +2464,7 @@ def write_sorting_to_nwbfile(
if verbose:
print(f"NWB file saved at {nwbfile_path}!")

return nwbfile # Will return None in March 2026
return None


def add_sorting_analyzer_to_nwbfile(
Expand Down Expand Up @@ -2690,7 +2597,7 @@ def add_sorting_analyzer_to_nwbfile(

def write_sorting_analyzer_to_nwbfile(
sorting_analyzer: SortingAnalyzer,
nwbfile_path: FilePath | None = None,
nwbfile_path: FilePath,
nwbfile: pynwb.NWBFile | None = None,
metadata: dict | None = None,
overwrite: bool = False,
Expand Down Expand Up @@ -2722,10 +2629,8 @@ def write_sorting_analyzer_to_nwbfile(
----------
sorting_analyzer : spikeinterface.SortingAnalyzer
The sorting analyzer object to be written to the NWBFile.
nwbfile_path : FilePath, optional
nwbfile_path : FilePath
Path for where to write or load (if overwrite=False) the NWBFile.
If not provided, only adds data to the in-memory nwbfile without writing to disk.
**Deprecated**: Using this function without nwbfile_path is deprecated. Use `add_sorting_analyzer_to_nwbfile` instead.
nwbfile : NWBFile, optional
If passed, this function will fill the relevant fields within the NWBFile object.
E.g., calling::
Expand Down Expand Up @@ -2782,60 +2687,10 @@ def write_sorting_analyzer_to_nwbfile(
Returns
-------
nwbfile : pynwb.NWBFile or None
The in-memory NWBFile object. Returns None when append_on_disk_nwbfile=True (to be implemented in or after March 2026).
The NWBFile object when writing a new file.
Returns None when appending to an existing file on disk (append_on_disk_nwbfile=True).
"""

# Handle deprecated usage without nwbfile_path
if nwbfile_path is None:
warnings.warn(
"Using 'write_sorting_analyzer_to_nwbfile' without 'nwbfile_path' to only add data to an in-memory nwbfile is deprecated "
"and will be removed in or after March 2026. Use 'add_sorting_analyzer_to_nwbfile' instead.",
DeprecationWarning,
stacklevel=2,
)
if nwbfile is None:
raise ValueError(
"Either 'nwbfile_path' or 'nwbfile' must be provided. "
"To add data to an in-memory nwbfile, use 'add_sorting_analyzer_to_nwbfile' instead."
)

# Ensure metadata exists
metadata = metadata if metadata is not None else dict()

# Get recording
if recording is None and sorting_analyzer.has_recording():
recording = sorting_analyzer.recording
assert recording is not None, (
"recording not found. To add the electrode table, the sorting_analyzer "
"needs to have a recording attached or the 'recording' argument needs to be used."
)

# Call add_sorting_analyzer_to_nwbfile for deprecated behavior
if write_electrical_series:
add_electrical_series_kwargs = add_electrical_series_kwargs or dict()
add_recording_to_nwbfile(
recording=recording,
nwbfile=nwbfile,
metadata=metadata,
null_values_for_properties=null_values_for_properties,
**add_electrical_series_kwargs,
)

add_sorting_analyzer_to_nwbfile(
sorting_analyzer=sorting_analyzer,
nwbfile=nwbfile,
metadata=metadata,
recording=recording,
unit_ids=unit_ids,
skip_properties=skip_properties,
property_descriptions=property_descriptions,
write_as=write_as,
units_name=units_name,
units_description=units_description,
null_values_for_properties=null_values_for_properties,
)
return nwbfile

# Ensure metadata exists
if metadata is None:
metadata = dict()
Expand Down Expand Up @@ -2922,12 +2777,6 @@ def write_sorting_analyzer_to_nwbfile(

else:
# Append mode: read existing file, add data, write back
warnings.warn(
"Returning an NWBFile object in append mode is deprecated and will return None in or after March 2026.",
DeprecationWarning,
stacklevel=2,
)

IO = BACKEND_NWB_IO[backend]

with IO(path=str(nwbfile_path), mode="r+", load_namespaces=True) as io:
Expand Down Expand Up @@ -2967,7 +2816,7 @@ def write_sorting_analyzer_to_nwbfile(
if verbose:
print(f"NWB file saved at {nwbfile_path}!")

return nwbfile # Will return None in March 2026
return None


def _get_electrode_group_indices(recording, nwbfile):
Expand Down
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