fix conflicts

CHANGELOG.md

@@ -6,6 +6,7 @@
 
 ### Features
 * Changed the `Suite2pSegmentationInterface` to support multiple plane segmentation outputs. The interface now has a `plane_name` and `channel_name` arguments to determine which plane output and channel trace add to the NWBFile. [PR #601](https://github.com/catalystneuro/neuroconv/pull/601)
+* Added tool function `configure_datasets` for configuring all datasets of an in-memory `NWBFile` to be backend specific. [PR #571](https://github.com/catalystneuro/neuroconv/pull/571)
 
 ### Improvements
 * `nwbinspector` has been removed as a minimal dependency. It becomes an extra (optional) dependency with `neuroconv[dandi]`. [PR #672](https://github.com/catalystneuro/neuroconv/pull/672)
@@ -21,9 +22,6 @@
 * Modify the filtering of traces to also filter out traces with empty values. [PR #649](https://github.com/catalystneuro/neuroconv/pull/649)
 * Added tool function `get_default_dataset_configurations` for identifying and collecting all fields of an in-memory `NWBFile` that could become datasets on disk; and return instances of the Pydantic dataset models filled with default values for chunking/buffering/compression. [PR #569](https://github.com/catalystneuro/neuroconv/pull/569)
 * Added tool function `get_default_backend_configuration` for conveniently packaging the results of `get_default_dataset_configurations` into an easy-to-modify mapping from locations of objects within the file to their correseponding dataset configuration options, as well as linking to a specific backend DataIO. [PR #570](https://github.com/catalystneuro/neuroconv/pull/570)
-<<<<<<< HEAD
-* Added tool function `configure_datasets` for configuring all datasets of an in-memory `NWBFile` to be backend specific. [PR #571](https://github.com/catalystneuro/neuroconv/pull/571)
-=======
 * Added `set_probe()` method to `BaseRecordingExtractorInterface`. [PR #639](https://github.com/catalystneuro/neuroconv/pull/639)
 * Changed default chunking of `ImagingExtractorDataChunkIterator` to select `chunk_shape` less than the chunk_mb threshold while keeping the original image size. The default `chunk_mb` changed to 10MB. [PR #667](https://github.com/catalystneuro/neuroconv/pull/667)
 
@@ -85,7 +83,6 @@
 ### Fixes
 
 * Reorganize timeintervals schema to reside in `schemas/` dir to ensure its inclusion in package build. [PR #573](https://github.com/catalystneuro/neuroconv/pull/573)
->>>>>>> main
 
 
 

setup.py

@@ -18,9 +18,13 @@
     testing_suite_dependencies = f.readlines()
 
 extras_require = defaultdict(list)
+
 extras_require["dandi"].append("dandi>=0.58.1")
 extras_require["full"].extend(extras_require["dandi"])
 
+extras_require.update(compressors=["hdf5plugin"])
+extras_require["full"].extend(["hdf5plugin"])
+
 extras_require.update(test=testing_suite_dependencies, docs=documentation_dependencies)
 for modality in ["ophys", "ecephys", "icephys", "behavior", "text"]:
     modality_path = root / "src" / "neuroconv" / "datainterfaces" / modality
@@ -44,9 +48,6 @@
                 extras_require[modality].extend(format_requirements)
                 extras_require[format_subpath.name].extend(format_requirements)
 
-extras_require.update(compressors=["hdf5plugin"])
-extras_require["full"].extend(["hdf5plugin"])
-
 # Create a local copy for the gin test configuration file based on the master file `base_gin_test_config.json`
 gin_config_file_base = Path("./base_gin_test_config.json")
 gin_config_file_local = Path("./tests/test_on_data/gin_test_config.json")

src/neuroconv/tools/nwb_helpers/_dataset_configuration.py

@@ -173,7 +173,7 @@ def configure_backend(
     data_io_class = backend_configuration.data_io_class
     for dataset_configuration in backend_configuration.datset_configurations:
         object_id = dataset_configuration.dataset_info.object_id
-        dataset_name = dataset_configuration.dataset_info.location.strip("/")[-1]
+        dataset_name = dataset_configuration.dataset_info.dataset_name
         data_io_kwargs = dataset_configuration.get_data_io_kwargs()
 
         # TODO: update buffer shape in iterator, if present

tests/test_minimal/test_tools/test_backend_and_dataset_configuration/test_helpers/test_configure_backend_defaults.py

@@ -8,10 +8,7 @@
 from pynwb.testing.mock.file import mock_NWBFile
 
 from neuroconv.tools.hdmf import SliceableDataChunkIterator
-from neuroconv.tools.nwb_helpers import (
-    configure_backend,
-    get_default_backend_configuration,
-)
+from neuroconv.tools.nwb_helpers import configure_backend, get_default_backend_configuration
 
 
 def test_unwrapped_time_series_hdf5(tmpdir):

tests/test_minimal/test_tools/test_backend_and_dataset_configuration/test_helpers/test_configure_backend_overrides.py

@@ -8,10 +8,7 @@
 from pynwb.testing.mock.file import mock_NWBFile
 
 from neuroconv.tools.hdmf import SliceableDataChunkIterator
-from neuroconv.tools.nwb_helpers import (
-    configure_backend,
-    get_default_backend_configuration,
-)
+from neuroconv.tools.nwb_helpers import configure_backend, get_default_backend_configuration
 
 
 def test_unwrapped_time_series_hdf5(tmpdir):