Deprecate ros3 as a streaming method (#2662)

* deprecate ros3

* remove open blas

* return ibl to streaming extractors

* add upper bound scipy

---------

Co-authored-by: Alessio Buccino <[email protected]>

.github/workflows/streaming-extractor-test.yml

@@ -29,9 +29,6 @@ jobs:
           update-conda: true
           python-version: ${{ matrix.python-version }}
           conda-channels: conda-forge
-      - run: git fetch --prune --unshallow --tags
-      - name: Install openblas
-        run: sudo apt install libopenblas-dev  # Necessary for ROS3 support
       - name: Get changed files
         id: changed-files
         uses: tj-actions/changed-files@v41
@@ -47,12 +44,6 @@ jobs:
       - name: Install package and streaming extractor dependencies
         if: ${{ steps.modules-changed.outputs.STREAMING_CHANGED == 'true' }}
         run: pip install -e .[test_core,streaming_extractors]
-      # Temporary disabled because of complicated error with path
-      # - name: Install h5py with ROS3 support and test it works
-      #   run: |
-      #     pip uninstall -y h5py
-      #     conda install -c conda-forge "h5py>=3.2"
-      #     python -c "import h5py; assert 'ros3' in h5py.registered_drivers(), f'ros3 suppport not available, failed to install'"
       - name: run tests
         if: steps.modules-changed.outputs.STREAMING_CHANGED == 'true'
-        run: pytest -m "streaming_extractors and not ros3_test" -vv -ra
+        run: pytest -m "streaming_extractors" -vv -ra

pyproject.toml

@@ -74,6 +74,8 @@ extractors = [
 streaming_extractors = [
     "ONE-api>=2.7.0", # alf sorter and streaming IBL
     "ibllib>=2.32.5", # streaming IBL
+    "scipy<1.13", # ibl has a dependency on scipy but it does not have an upper bound
+    # Remove this once https://github.com/int-brain-lab/ibllib/issues/753
     # Following dependencies are for streaming with nwb files
     "fsspec",
     "aiohttp",
@@ -113,6 +115,7 @@ qualitymetrics = [
 
 test_core = [
     "pytest",
+    "pytest-dependency",
     "psutil",
 
     # for github test : probeinterface and neo from master
@@ -200,7 +203,6 @@ markers = [
     "widgets",
     "sortingcomponents",
     "streaming_extractors: extractors that require streaming such as ross and fsspec",
-    "ros3_test"
 ]
 filterwarnings =[
     'ignore:.*distutils Version classes are deprecated.*:DeprecationWarning',

src/spikeinterface/extractors/nwbextractors.py

@@ -14,7 +14,7 @@ def read_file_from_backend(
     *,
     file_path: str | Path | None,
     file: BinaryIO | None = None,
-    stream_mode: Literal["ffspec", "ros3", "remfile"] | None = None,
+    stream_mode: Literal["ffspec", "remfile"] | None = None,
     cache: bool = False,
     stream_cache_path: str | Path | None = None,
     storage_options: dict | None = None,
@@ -98,7 +98,7 @@ def read_nwbfile(
     backend: Literal["hdf5", "zarr"],
     file_path: str | Path | None,
     file: BinaryIO | None = None,
-    stream_mode: Literal["ffspec", "ros3", "remfile", "zarr"] | None = None,
+    stream_mode: Literal["ffspec", "remfile", "zarr"] | None = None,
     cache: bool = False,
     stream_cache_path: str | Path | None = None,
     storage_options: dict | None = None,
@@ -112,7 +112,7 @@ def read_nwbfile(
         The path to the NWB file. Either provide this or file.
     file : file-like object or None
         The file-like object to read from. Either provide this or file_path.
-    stream_mode : "fsspec" | "ros3" | "remfile" | None, default: None
+    stream_mode : "fsspec" | "remfile" | None, default: None
         The streaming mode to use. If None it assumes the file is on the local disk.
     cache: bool, default: False
         If True, the file is cached in the file passed to stream_cache_path
@@ -132,12 +132,12 @@ def read_nwbfile(
 
     Notes
     -----
-    This function can stream data from the "fsspec", "ros3" and "rem" protocols.
+    This function can stream data from the "fsspec", and "rem" protocols.
 
 
     Examples
     --------
-    >>> nwbfile = read_nwbfile(file_path="data.nwb", backend="hdf5", stream_mode="ros3")
+    >>> nwbfile = read_nwbfile(file_path="data.nwb", backend="hdf5", stream_mode="fsspec")
     """
 
     if file_path is not None and file is not None:
@@ -428,7 +428,7 @@ class NwbRecordingExtractor(BaseRecording):
     samples_for_rate_estimation: int, default: 1000
         The number of timestamp samples used for estimating the sampling rate. This is relevant
         when the 'rate' attribute is not available in the ElectricalSeries.
-    stream_mode : "fsspec" | "ros3" | "remfile" | "zarr" | None, default: None
+    stream_mode : "fsspec" | "remfile" | "zarr" | None, default: None
         Determines the streaming mode for reading the file. Use this for optimized reading from
         different sources, such as local disk or remote servers.
     load_channel_properties: bool, default: True
@@ -485,7 +485,7 @@ def __init__(
         electrical_series_name: str | None = None,  # deprecated
         load_time_vector: bool = False,
         samples_for_rate_estimation: int = 1_000,
-        stream_mode: Optional[Literal["fsspec", "ros3", "remfile", "zarr"]] = None,
+        stream_mode: Optional[Literal["fsspec", "remfile", "zarr"]] = None,
         stream_cache_path: str | Path | None = None,
         electrical_series_path: str | None = None,
         load_channel_properties: bool = True,
@@ -495,6 +495,14 @@ def __init__(
         storage_options: dict | None = None,
         use_pynwb: bool = False,
     ):
+
+        if stream_mode == "ros3":
+            warnings.warn(
+                "The 'ros3' stream_mode is deprecated and will be removed in version 0.103.0. "
+                "Use 'fsspec' stream_mode instead.",
+                DeprecationWarning,
+            )
+
         if file_path is not None and file is not None:
             raise ValueError("Provide either file_path or file, not both")
         if file_path is None and file is None:
@@ -910,7 +918,7 @@ class NwbSortingExtractor(BaseSorting):
     samples_for_rate_estimation: int, default: 100000
         The number of timestamp samples to use to estimate the rate.
         Used if "rate" is not specified in the ElectricalSeries.
-    stream_mode : "fsspec" | "ros3" | "remfile" | "zarr" | None, default: None
+    stream_mode : "fsspec" | "remfile" | "zarr" | None, default: None
         The streaming mode to use. If None it assumes the file is on the local disk.
     stream_cache_path: str or Path or None, default: None
         Local path for caching. If None it uses the system temporary directory.
@@ -964,6 +972,14 @@ def __init__(
         storage_options: dict | None = None,
         use_pynwb: bool = False,
     ):
+
+        if stream_mode == "ros3":
+            warnings.warn(
+                "The 'ros3' stream_mode is deprecated and will be removed in version 0.103.0. "
+                "Use 'fsspec' stream_mode instead.",
+                DeprecationWarning,
+            )
+
         self.stream_mode = stream_mode
         self.stream_cache_path = stream_cache_path
         self.electrical_series_path = electrical_series_path

src/spikeinterface/extractors/tests/test_nwbextractors_streaming.py

@@ -12,7 +12,6 @@
 from spikeinterface.extractors import NwbRecordingExtractor, NwbSortingExtractor
 
 
-@pytest.mark.ros3_test
 @pytest.mark.streaming_extractors
 @pytest.mark.skipif("ros3" not in h5py.registered_drivers(), reason="ROS3 driver not installed")
 def test_recording_s3_nwb_ros3(tmp_path):
@@ -155,7 +154,6 @@ def test_recording_s3_nwb_remfile_file_like(tmp_path):
     check_recordings_equal(rec, rec2)
 
 
-@pytest.mark.ros3_test
 @pytest.mark.streaming_extractors
 @pytest.mark.skipif("ros3" not in h5py.registered_drivers(), reason="ROS3 driver not installed")
 def test_sorting_s3_nwb_ros3(tmp_path):