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NBInclude

import code from IJulia Jupyter notebooks into Julia programs

First Commit

10/10/2015

Last Touched

3 days ago

Commit Count

30 commits

Readme

NBInclude

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NBInclude is a package for the Julia language which allows you to include and execute IJulia (Julia-language Jupyter) notebook files just as you would include an ordinary Julia file. That is, analogous to doing include("myfile.jl") in Julia to execute myfile.jl, you can do

using NBInclude
nbinclude("myfile.ipynb")

to execute all of the code cells in the IJulia notebook myfile.ipynb. Similar to include, the value of the last evaluated expression in the last evaluated code cell is returned.

The goal of this package is to make notebook files just as easy to incorporate into Julia programs as ordinary Julia (.jl) files, giving you the advantages of a notebook (integrated code, formatted text, equations, graphics, and other results) while retaining the modularity and re-usability of .jl files.

Key features of NBInclude are:

  • The path of the notebook is relative to the path of the current file (if any), and nested inclusions can use paths relative to the notebook, just as for include.
  • In a module, included notebooks work fine with precompilation in Julia 0.4 (and re-compilation is automatically triggered if the notebook changes).
  • Code is associated with accurate line numbers (e.g. for backtraces when exceptions are thrown), in the form of myfile.ipynb:In[N]:M for line M in input cell N of the myfile.ipynb notebook. Un-numbered cells (e.g. unevaluated cells) are given a number +N for the N-th nonempty cell in the notebook. You can use nbinclude("myfile.ipynb", renumber=true) to automatically renumber the cells in sequence (as if you had selected Run All from the Jupyter Cell menu), without altering the file.
  • The Julia @__FILE__ macro returns /path/to/myfile.ipynb:In[N] for input cell N.
  • Like include, nbinclude works fine with parallel Julia processes, even for worker processes (from Julia's addprocs) that may not have filesystem access. (Do import NBInclude; @everywhere using NBInclude to use nbinclude on all processes.)
  • In IJulia, cells beginning with ; or ? are interpreted as shell commands or help requests, respectively. Such cells are ignored by nbinclude.
  • counters and regex keywords can be used to include a subset of notebook cells to those for which counter ∈ counters and the cell text matches regex. For example, nbinclude("notebook.ipynb"; counters=1:10, regex=r"#\s*EXECUTE") would include cells 1 to 10 from notebook.ipynb that contain comments like # EXECUTE.
  • A keyword anshook can be used to run a passed function on the return value of all the cells.
  • No Python or Jupyter dependency.

To install it, simply do Pkg.add("NBInclude") as usual for Julia packages.

Contact

NBInclude was written by Steven G. Johnson and is free/open-source software under the MIT/Expat license. Please file bug reports and feature requests at the NBInclude github page.