A tool that supports one-button reproducible workflows with the Jupyter Notebook and Scons. Note: this currently only supports Python kernels.
UPDATE: Scons >= 3.0.0 now supports Python 3 so Python 2 isn't needed anymore! Now Nbflow and Scons are both Python 2 and 3 compatible so you can choose whichever you want.
The actual version of Scons (3.0.1) currently supports Python >= 3.5, which is the default in Ubuntu 16.04
To install, run:
pip3 install git+git://github.com/jhamrick/nbflow.git
pip install git+git://github.com/jhamrick/nbflow.git
For a complete example of how to use nbflow, check out the example in this repository.
You can now you Binder to check the example online:
- Entre in Binder here or through the badge above
- Open a terminal
- Check the results in the
Optionally you can modify the notebook in this online environment and check how the results change.
For each notebook that you want executed, you MUST include two special variables in the first code cell:
__depends__-- a list of relative paths to files that the notebook depends on
__dest__-- either a relative path, or list of relative paths, to files that the notebook produces
For example, the first cell in one of the example notebooks is:
__depends__ = ["../results/data.json"] __dest__ = "../results/stats.json"
You need a
SConstruct file in the root of you analysis directory. In this
SConstruct file you will need to import nbflow and use it to setup your scons
import os from nbflow.scons import setup env = Environment(ENV=os.environ) setup(env, ["analyses"])
The second argument of the
setup command takes a list of folder names that
contain analysis notebooks.
Once you have setup your analysis notebooks and your
SConstruct file, you can
run your notebooks by just running the
scons command from the root of your