jupyter-runner 0.6.0

Jupyter notebook runner.

Welcome to Jupyter-Runner’s documentation

Jupyter runners allows to run multiple notebooks over multiple sets of parameters.

Notebook execution can happen in parallel with a fixed number of workers.

Installation

pip install jupyter-runner

Usage

jupyter-runner [options] <notebook>...

    --parameter-file=<PARAMETER_FILE>**    Optional parameters files containing one parameter instance by line, setting the environment.
    Example with 2 sets of 3 parameters:
        VAR1=VAL1 VAR2=VAL2 VAR3=VAL3
        VAR1=VAL5 VAR2=VAL18 VAR3=VAL42
    --workers=<workers>                    Maximum number of parallel execution [Default: 1]
    --output-directory=<OUTPUT_DIRECTORY>  Output directory [Default: .]
    --overwrite                            Overwrite output files if they already exist.
    --format=<FORMAT>                      Output format: html, notebook... [Default: html]
    --debug                                Enable debug logs
    --help                                 Display this help
    --version                              Display version
    --timeout=<TIMEOUT>                    Cell execution timeout in seconds.  [Default: -1]
    --allow-errors                         Allow errors during notebook execution.

Tutorial

Run a simple notebook

jupyter-runner notebook.ipynb

By default, the process creates output file notebook.html in current directory.

Run multiple notebooks

jupyter-runner notebookA.ipynb notebookB.ipynb

By default, the process creates output files notebookA.html and notebookB.html in current directory.

Run notebook with parameters

Use environment variables on command-line.

ENV_VAR=xxx jupyter-runner notebook.ipynb

In python notebook, variables can be retrieved using os.environ:

import os
env_var = os.environ.get('ENV_VAR', 'a_default_value')
# usage of env_var in your code

By default, the process creates output file notebook.html in current directory. The notebook variables passed by the user can impact the rendering of the output.

Run notebook with multiple sets of parameters

Create a file with multiple set of parameters, one set of parameters per line.

Example file containing 2 sets of 3 parameters:

VAR1=VAL1 VAR2=VAL2 VAR3=VAL3
VAR1=VAL5 VAR2=VAL18 VAR3='VAL42 with space'

Then run jupyter-runner specifying the path to my_parameter_file just created:

jupyter-runner --parameter-file=my_parameter_file notebook.ipynb

By default, the process creates output files notebook_1.html and notebook_2.html in current directory.

Run multiple notebooks with multiple sets of parameters

jupyter-runner can combine multiple set of parameters on multiple notebooks. When there are N sets of parameters running on M notebooks, there will be NxM distinct output files.

jupyter-runner --parameter-file=my_parameter_file notebookA.ipynb notebookB.ipynb

By default, the process creates output files notebookA_1.html, notebookA_2.html, notebookB_1.html, notebookB_2.html in current directory.

Change output directory

jupyter-runner --output-directory results notebook.ipynb

The process create output file results/notebook.html`. ``results directory is created if it does not pre-exist.

Use S3 inputs/outputs

jupyter-runner --output-directory=s3://bucket/results/ s3://bucket/notebooks/notebook.ipynb

The process create output file s3://bucket/results/notebook.html based on a notebook stored from S3.

Files are downloaded to a local temporary only available to the current user and removed at the end or in case of exceptions.

Overwrite existing outputs

By default, jupyter-runner skip the run when output file(s) already exists. To overwrite the files, use the --overwrite option:

jupyter-runner --overwrite notebook.ipynb

Use multiple workers

By default, only 1 notebook will be executed at the same time. Use --workers option to specify the number of notebooks to run in parallel.

jupyter-runner --workers 3 --parameter-file=my_parameter_file notebookA.ipynb notebookB.ipynb

The above command will start to run 3 notebook output over the 4 requested. When the first execution finishes, the 4th notebook is launched and so on.

Change output type

List of possible output types are available here: https://nbconvert.readthedocs.io/en/latest/usage.html#default-output-format-html

jupyter-runner --format notebook --output-directory results notebook.ipynb

Report mode (hide input)

jupyter-runner --hide-input notebook.ipynb

The process create output file notebook.html without any input cells. Markdown and output cells are kept, but input code cells do not show. This feature is handy to create user-friendly reports.

Change output file suffix

When multiple notebooks are run with a list of parameters, output filenames are suffixed by _1, _2, … This default can be overriden by setting parameter JUPYTER_OUTPUT_SUFFIX in parameter set.

Example my_parameter_file:

VAR1=VAL1 VAR2=VAL2 VAR3=VAL3 JUPYTER_OUTPUT_SUFFIX=AAA
VAR1=VAL5 VAR2=VAL18 VAR3='VAL42 with space' JUPYTER_OUTPUT_SUFFIX=BBB

jupyter-runner --parameter-file=my_parameter_file notebook.ipynb

This run will generate two files: notebook_AAA.html and notebook_BBB.html

Change cell execution timeout

By default, timeout is set to -1, meaning infinite. It is possible to set the cell execution timeout (in seconds) with --timeout

jupyter-runner --timeout 60 notebook.ipynb

Allow error in notebook execution

By default, errors in notebook execution stops its execution and return an error code. Setting --allow-errors option allows to ignore the error and continue the execution, returning a valid code.

jupyter-runner --allow-errors notebook.ipynb

Send e-mail containing output

You can send an e-mail containing attachments using --mail-to option. Other mail options available (subject, from, cc, bcc…) as well as attaching each output in separate file or regrouped together within a LZMA compressed zip (default).

jupyter-runner notebook.ipynb --mail-to=[e-mail]