Merge pull request #59 from NeurodataWithoutBorders/lindi_update

Use latest lindi, pynwb, and hdmf with aws_region
NeurodataWithoutBorders · May 20, 2024 · 16bb196 · 16bb196
2 parents 66b8d92 + 4d25721
commit 16bb196
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Showing 19 changed files with 1,843 additions and 828 deletions.
diff --git a/docs/writing_benchmarks.rst b/docs/writing_benchmarks.rst
@@ -112,7 +112,7 @@ Notice how the ``read_hdf5_nwbfile_remfile`` function (which reads an HDF5-backe
     def read_hdf5_nwbfile_remfile(s3_url: str) -> Tuple[pynwb.NWBFile, pynwb.NWBHDF5IO, h5py.File, remfile.File]:
         """Read an HDF5 NWB file from an S3 URL using the ROS3 driver from h5py."""
         (file, byte_stream) = read_hdf5_remfile(s3_url=s3_url)
-        io = pynwb.NWBHDF5IO(file=file, load_namespaces=True)
+        io = pynwb.NWBHDF5IO(file=file, aws_region="us-east-2")
         nwbfile = io.read()
         return (nwbfile, io, file, byte_stream)
 

diff --git a/environments/nwb_benchmarks.yaml b/environments/nwb_benchmarks.yaml
@@ -9,15 +9,14 @@ dependencies:
       - asv == 0.6.1
       - numba>=0.58.1  # Pin to specific version for cuda import
       - psutil
-      - pynwb
       - dandi
       - fsspec
       - requests
       - aiohttp
       - remfile
       - pyshark
-      - lindi
-      - hdmf @ git+https://github.com/hdmf-dev/hdmf.git@9b3282aa4999d2922f003f1b79ec7458ea3ddc5e  # required until PyNWB propagates changes
-      #- hdmf @ git+https://github.com/hdmf-dev/hdmf.git@expose_aws_region  # required until region fix is released
+      - lindi>=0.3.6
+      - pynwb @ git+https://github.com/NeurodataWithoutBorders/pynwb.git@expose_aws_region  # required until region fix is released
+      - hdmf @ git+https://github.com/hdmf-dev/hdmf.git@expose_aws_region  # required until region fix is released
       - hdmf-zarr
       - -e ..