Remove interface.run_conversion without nwbfile_path (#951)

Co-authored-by: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Co-authored-by: Ben Dichter <ben.dichter@gmail.com>

CHANGELOG.md

@@ -5,6 +5,9 @@
 * The usage of `compression` and `compression_opts` directly through the `FicTracDataInterface` is now deprecated - users should refer to the new `configure_backend` method for a general approach for setting compression. [PR #941](https://github.com/catalystneuro/neuroconv/pull/941)
 * The usage of `compression` directly through the `neuroconv.tools.neo` submodule is now deprecated - users should refer to the new `configure_backend` method for a general approach for setting compression. [PR #943](https://github.com/catalystneuro/neuroconv/pull/943)
 * The usage of `compression_options` directly through the `neuroconv.tools.ophys` submodule is now deprecated - users should refer to the new `configure_backend` method for a general approach for setting compression. [PR #940](https://github.com/catalystneuro/neuroconv/pull/940)
+* Removed the option of running `interface.run_conversion` without `nwbfile_path` argument . [PR #951](https://github.com/catalystneuro/neuroconv/pull/951)
+
+
 
 ### Features
 * Added docker image and tests for an automated Rclone configuration (with file stream passed via an environment variable). [PR #902](https://github.com/catalystneuro/neuroconv/pull/902)

src/neuroconv/basedatainterface.py

@@ -1,7 +1,6 @@
 import importlib
 import json
 import uuid
-import warnings
 from abc import ABC, abstractmethod
 from pathlib import Path
 from typing import Literal, Optional, Tuple, Union
@@ -116,7 +115,7 @@ def add_to_nwbfile(self, nwbfile: NWBFile, **conversion_options) -> None:
 
     def run_conversion(
         self,
-        nwbfile_path: Optional[str] = None,
+        nwbfile_path: str,
         nwbfile: Optional[NWBFile] = None,
         metadata: Optional[dict] = None,
         overwrite: bool = False,
@@ -133,8 +132,7 @@ def run_conversion(
         Parameters
         ----------
         nwbfile_path : FilePathType
-            Path for where to write or load (if overwrite=False) the NWBFile.
-            If specified, the context will always write to this location.
+            Path for where the data will be written or appended.
         nwbfile : NWBFile, optional
             An in-memory NWBFile object to write to the location.
         metadata : dict, optional
@@ -152,12 +150,7 @@ def run_conversion(
             BackendConfiguration object, and pass that instead.
             Otherwise, all datasets will use default configuration settings.
         """
-        if nwbfile_path is None:
-            warnings.warn(  # TODO: remove on or after 6/21/2024
-                "Using DataInterface.run_conversion without specifying nwbfile_path is deprecated. To create an "
-                "NWBFile object in memory, use DataInterface.create_nwbfile. To append to an existing NWBFile object,"
-                " use DataInterface.add_to_nwbfile."
-            )
+
         backend = _resolve_backend(backend, backend_configuration)
         no_nwbfile_provided = nwbfile is None  # Otherwise, variable reference may mutate later on inside the context
 

tests/test_ecephys/test_ecephys_interfaces.py

@@ -34,12 +34,12 @@ def setUpClass(cls):
     def test_stub_single_segment(self):
         interface = self.single_segment_recording_interface
         metadata = interface.get_metadata()
-        interface.run_conversion(stub_test=True, metadata=metadata)
+        interface.create_nwbfile(stub_test=True, metadata=metadata)
 
     def test_stub_multi_segment(self):
         interface = self.multi_segment_recording_interface
         metadata = interface.get_metadata()
-        interface.run_conversion(stub_test=True, metadata=metadata)
+        interface.create_nwbfile(stub_test=True, metadata=metadata)
 
     def test_no_slash_in_name(self):
         interface = self.single_segment_recording_interface

tests/test_ophys/test_ophys_interfaces.py

@@ -1,4 +1,6 @@
+import tempfile
 import unittest
+from pathlib import Path
 
 from pynwb.testing.mock.file import mock_NWBFile
 
@@ -10,7 +12,10 @@ def setUp(self):
         self.mock_imaging_interface = MockImagingInterface()
 
     def test_run_conversion(self):
-        self.mock_imaging_interface.run_conversion()
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            nwbfile_path = Path(tmpdir) / "test.nwb"
+            self.mock_imaging_interface.run_conversion(nwbfile_path=nwbfile_path)
 
     def test_add_to_nwbfile(self):
         nwbfile = mock_NWBFile()