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0.003357100002176594, + 0.0033609000020078383 + ] + } + } +} diff --git a/results/results_timestamp-2024-04-30-10-27-57_machine-Ackermann_environment-c0130a551be84e54a46ed6ebe2db18d9f31440f0.json b/results/results_timestamp-2024-04-30-10-27-57_machine-Ackermann_environment-c0130a551be84e54a46ed6ebe2db18d9f31440f0.json new file mode 100644 index 0000000..2315d95 --- /dev/null +++ b/results/results_timestamp-2024-04-30-10-27-57_machine-Ackermann_environment-c0130a551be84e54a46ed6ebe2db18d9f31440f0.json @@ -0,0 +1,16 @@ +{ + "version": 2, + "timestamp": "2024-04-30-10-27-57", + "commit_hash": "a031081af0d37dfd92b0b6101ab4b0c6198938a3", + "environment_hash": "c0130a551be84e54a46ed6ebe2db18d9f31440f0", + "machine_hash": "Ackermann", + "results": { + "time_remote_slicing.LindiFileReadRemoteReferenceFileSystemContinuousSliceBenchmark.time_slice": { + "(\"'https://kerchunk.neurosift.org/dandi/dandisets/000939/assets/11f512ba-5bcf-4230-a8cb-dc8d36db38cb/zarr.json'\", \"'accelerometer'\", '(slice(0, 30000, None), slice(0, 3, None))')": [ + 10.000524600007338, + 10.000269199998002, + 10.000371199988876 + ] + } + } +} diff --git a/src/nwb_benchmarks/command_line_interface.py b/src/nwb_benchmarks/command_line_interface.py index f1deb58..78205c0 100644 --- a/src/nwb_benchmarks/command_line_interface.py +++ b/src/nwb_benchmarks/command_line_interface.py @@ -38,9 +38,9 @@ def main() -> None: asv_root.mkdir(exist_ok=True) raw_environment_info_file_path = asv_root / ".raw_environment_info.txt" - outfile = open(raw_environment_info_file_path, "w") - environment_info_process = subprocess.Popen(["conda list"], stdout=outfile, shell=True) - environment_info_process.wait() + with open(file=raw_environment_info_file_path, mode="w") as stdout: + environment_info_process = subprocess.Popen(args=["conda", "list"], stdout=stdout, shell=True) + environment_info_process.wait() if not raw_environment_info_file_path.exists(): raise FileNotFoundError(f"Unable to create environment file at {raw_environment_info_file_path}!") @@ -59,13 +59,15 @@ def main() -> None: if bench_mode: cmd.extend(["--bench", specific_benchmark_pattern]) - process = subprocess.Popen(cmd, stdout=subprocess.PIPE) + # Run ASV with all the desired flags and reroute the output to our main console + asv_process = subprocess.Popen(cmd, stdout=subprocess.PIPE) encoding = locale.getpreferredencoding() # This is how ASV chooses to encode the output - for line in iter(process.stdout.readline, b""): + for line in iter(asv_process.stdout.readline, b""): print(line.decode(encoding).strip("\n")) - process.stdout.close() - process.wait() + asv_process.stdout.close() + asv_process.wait() + # Consider the raw ASV output as 'intermediate' and perform additional parsing globbed_json_file_paths = [ path for path in pathlib.Path(asv_root / "intermediate_results").rglob("*.json") diff --git a/src/nwb_benchmarks/core/_streaming.py b/src/nwb_benchmarks/core/_streaming.py index e6376c9..5deb396 100644 --- a/src/nwb_benchmarks/core/_streaming.py +++ b/src/nwb_benchmarks/core/_streaming.py @@ -197,9 +197,9 @@ def create_lindi_reference_file_system(s3_url: str, outfile_path: str): The output_file path should end in the '.lindi.json' extension """ # Create a read-only Zarr store as a wrapper for the h5 file - store = lindi.LindiH5ZarrStore.from_file(s3_url) + store = lindi.LindiH5ZarrStore.from_file(hdf5_file_name_or_url=s3_url) # Generate a reference file system and write it to a file - store.write_reference_file_system(outfile_path) + store.write_reference_file_system(output_file_name=outfile_path) def read_hdf5_lindi(rfs: Union[dict, str]) -> lindi.LindiH5pyFile: @@ -208,7 +208,7 @@ def read_hdf5_lindi(rfs: Union[dict, str]) -> lindi.LindiH5pyFile: :param rfs: The LINDI reference file system file. This can be a dictionary or a URL or path to a .lindi.json file. """ # Load the h5py-like client for the reference file system - client = lindi.LindiH5pyFile.from_reference_file_system(rfs) + client = lindi.LindiH5pyFile.from_reference_file_system(rfs=rfs) return client