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Use latest lindi, pynwb, and hdmf with aws_region #59
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nwb_benchmarks run --bench NWBLindiFileReadRemoteReferenceFileSystemBenchmark
nwb_benchmarks run --bench NWBLindiFileCreateLocalReferenceFileSystemBenchmark
nwb_benchmarks run --bench LindiFileReadLocalReferenceFileSystemBenchmark
nwb_benchmarks run --bench NWBFileReadBenchmark
nwb_benchmarks run --bench DirectFileReadBenchmark These ran successfully. I have not yet run a full suite of benchmarks yet though. |
I defined remote benchmarks as such: lindi_remote_rfs_parameter_cases = dict(
EcephysTestCase=dict(
s3_url=get_s3_url(
is_staging=True,
dandiset_id="213889",
dandi_path="sub-IBL-ecephys/sub-IBL-ecephys_ses-3e7ae7c0_desc-18000000-frames-13653-by-384-chunking.lindi.json",
),
object_name="ElectricalSeriesAp",
slice_range=(slice(0, 30_000), slice(0, 384)),
),
OphysTestCase=dict(
s3_url=get_s3_url(
is_staging=True,
dandiset_id="213889",
dandi_path="sub-R6_ses-20200206T210000_behavior+ophys/sub-R6_ses-20200206T210000_behavior+ophys.lindi.json",
),
object_name="TwoPhotonSeries",
slice_range=(slice(0, 3), slice(0, 796), slice(0, 512)),
),
IcephysTestCase=dict(
s3_url=get_s3_url(
is_staging=True,
dandiset_id="213889",
dandi_path="sub-1214579789_ses-1214621812_icephys/sub-1214579789_ses-1214621812_icephys.lindi.json",
),
object_name="data_00002_AD0",
slice_range=(slice(0, 30_000),),
), I thought that this would create three test cases. Instead, it creates 9 - the cross of all the parameters. But all of the unintended combinations will fail. I think this is an issue within |
Well, that's cool... First time running that parameterized pattern and it's revealed that that is indeed the intended behavior of ASV: https://asv.readthedocs.io/en/v0.6.1/writing_benchmarks.html#parameterized-benchmarks There's not an easy way I can think of at the moment to resolve this at the Only way will be to break up the multilevel dict-of-dicts to separate benchmarks. I'll do that in my PR |
This fix in lindi makes the lindi ophys test case work. NeurodataWithoutBorders/lindi#71 |
Debug params behavior with multiple input arguments
Co-authored-by: Cody Baker <[email protected]>
I updated the environment file. Please remake your conda environments after merging.
I added a couple of read remote LINDI file test cases. I think the local lindi test cases still apply, though we should update those to point to the dandiset with the test NWB files that we want to use.
I'm pointing the environment to branches of HDMF and PyNWB that support the
aws_region
argument toNWBHDF5IO
so that we can specify the AWS region in ROS3 tests.Also we no longer need to say
load_namespaces=True
. That is now the default.