Run Notebook¶
flyvis_cli.analysis.notebook ¶
Script to run a jupyter notebook for a particular model.
usage:
flyvis notebook [-h] --notebook_path PATH [options] [hybrid_args...]
or
notebook.py [-h] --notebook_path PATH [options] [hybrid_args...]
There are three modes of operation:
1. Basic: Only requires --notebook_path
2. Per-model: Requires --notebook_per_model_path, --notebook_per_model=true, --ensemble_and_network_id
3. Per-ensemble: Requires --notebook_path, --per_ensemble=true, --task_name, --ensemble_id
Run a Jupyter notebook using papermill. Required arguments depend on the specific notebook. Pass any additional arguments as key:type=value triplets.
options:
-h, --help show this help message and exit
--notebook_path NOTEBOOK_PATH
Path of the notebook to execute, e.g.
/path/to/__main__.ipynb.
--notebook_per_model_path NOTEBOOK_PER_MODEL_PATH
Path of the notebook to execute for each model, e.g.
/path/to/__main_per_model__.ipynb.
--output_path OUTPUT_PATH
Path for the output notebook. If not provided, a
temporary file will be used and deleted after
execution.
--dry Perform a dry run without actually executing the
notebook.
Hybrid Arguments:
--notebook_per_model NOTEBOOK_PER_MODEL
notebook_per_model=value: Flag to set the output path
to the per-model notebook path. Requires
ensemble_and_network_id. (type: bool)
--ensemble_and_network_id ENSEMBLE_AND_NETWORK_ID
ensemble_and_network_id=value: Id in form of
task_name/ensemble_id/network_id, e.g., flow/0000/000.
Required if notebook_per_model is True. (type: str)
--per_ensemble PER_ENSEMBLE
per_ensemble=value: Flag to set the output path to the
per-ensemble notebook path. Requires ensemble_id and
task_name. (type: bool)
--task_name TASK_NAME
task_name=value: Name of the task, e.g. flow. Required
if per_ensemble is True. (type: str)
--ensemble_id ENSEMBLE_ID
ensemble_id=value: Id of the ensemble, e.g. 0045.
Required if per_ensemble is True. (type: int)
Examples:
# Basic usage
flyvis notebook --notebook_path notebooks/analysis.ipynb
# Per-model analysis
flyvis notebook --notebook_per_model_path notebooks/per_model.ipynb \
notebook_per_model=true \
ensemble_and_network_id=flow/0045/000
# Per-ensemble analysis
flyvis notebook --notebook_path notebooks/ensemble.ipynb \
per_ensemble=true \
task_name=flow \
ensemble_id=45
# With additional parameters passed to the notebook
flyvis notebook --notebook_path notebooks/analysis.ipynb \
param1:str=value1 \
param2:int=42