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NBInclude

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.

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.

Basic usage

Analogous to 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.

We also export an in_nbinclude() function, which returns true only when it is executed in code run via @nbinclude. Using this, you can selectively run code in a notebook only interactively or only via @nbinclude.

There is also a function

nbexport("myfile.jl", "myfile.ipynb")

that can be used to convert an IJulia notebook file to an ordinary Julia file, with Markdown text in the notebook converted to formatted comments in the Julia file.

Detailed features

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 (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.
• 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.
• The softscope flag mentioned below.

Note: Scoping rules differ between interactive (IJulia, REPL) and non-interactive Julia code. Running a notebook as @nbinclude("foo.ipynb"; softscope=true) will load notebooks using "soft" global scoping similar to interactive (REPL) code in Julia 1.5+ or for IJulia with any Julia version. That flag's default value, false, will load notebooks with the "hard" scoping rule that Julia uses for non-interactive code (e.g. in include); see also the SoftGlobalScope package for more details.

Key features of nbexport are:

• You can either call nbexport(filename, notebookfile) to export to a file, or nbexport(io, notebookfile) to write to an IO stream (e.g. stdout or a buffer).
• To export to a string, use sprint(nbexport, notebookfile).
• Like @nbinclude, you can pass a regex keyword to specify a subset of the notebook code cells to export.
• Markdown cells in the notebook are parsed and formatted as pretty-printed text comments with the help of Julia's Markdown standard library.
• Markdown cells can be ignored by passing markdown=false to nbexport.

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.