np-aind-metadata

Usage

conda create -n np_aind_metadata python>=3.10
conda activate np_aind_metadata
pip install np_aind_metadata

Python

Initialize a neuropixels rig model.

from np_aind_metadata.init import neuropixels_rig

rig_model = neuropixels_rig.init("NP3")

Update a neuropixels rig model. Currently only supports dynamic routing context.

import pathlib
from np_aind_metadata.update import dynamic_routing

dynamic_routing.update_rig(
    pathlib.Path("./examples/rig.json"),
    open_ephys_settings_sources=[
        pathlib.Path("./examples/settings.xml")
    ],
    output_path=pathlib.Path("./updated_rig.json"),
)

np-codeocean

This library can track and update rig jsons for np-codeocean. np dependency group must be installed

Initialize storage for a rig

np-aind-metadata init-rig-storage "/directory/to/store/rigs" "NP3" --date 2022/02/07

Updating via np-codeocean

import pathlib
from np_aind_metadata import np_codeocean

np_codeocean.add_rig_to_dynamic_routing_session_dir(
    pathlib.Path("/session/directory"),
    pathlib.Path("/directory/to/store/rigs"),
)

Local development

Testing

Testing intended for cloned project from source control.

Unit tests

pdm run pytest

Storage tests

pdm run pytest-storage

Onprem tests

Requires user to likely be on prem with np group dependencies installed.

Install np group dependencies

pdm install -G np

Run tests

pdm run pytest-onprem

All tests

Requires dependencies from onprem.

pdm run pytest-full

Development

See instructions in https://github.com/AllenInstitute/np-aind-metadata/CONTRIBUTING.md and the original template: https://github.com/AllenInstitute/copier-pdm-npc/blob/main/README.md