I have considered several options that I shall discuss below, but have yet to find a good comprehensive solution. A full solution might require some changes to IPython, or may rely on some simple external scripts. I currently use mercurial, but would like a solution that also works with git: an ideal solution would be version-control agnostic.

I have considered several options that I shall discuss below, but have yet to find a good comprehensive solution. A full solution might require some changes to IPython, or may rely on some simple external scripts. I currently use mercurial, but would like a solution that also works with git: an ideal solution would be version-control agnostic.

The notebook format is quite amenable for version control: if one wants to version control the notebook and the outputs then this works quite well. The annoyance comes when one wants only to version control the input, excluding the cell outputs (aka. "build products") which can be large binary blobs, especially for movies and plots. In particular, I am trying to find a good workflow that:

Update: I have been playing with my modified notebook version which optionally saves a .clean version with every save using Gregory Crosswhite's suggestions. This satisfies most of my constraints but leaves the following unresolved:

• When the notebook is running, one can use the Cell/All Output/Clear menu option for removing the output.
• There are some scripts for removing output, such as the script nbstripout.py which remove the output, but does not produce the same output as using the notebook interface. This was eventually included in the ipython/nbconvert repo, but this has been closed stating that the changes are now included in ipython/ipython,but the corresponding functionality seems not to have been included yet. (update) That being said, Gregory Crosswhite's solution shows that this is pretty easy to do, even without invoking ipython/nbconvert, so this approach is probably workable if it can be properly hooked in. (Attaching it to each version control system, however, does not seem like a good idea – this should somehow hook in to the notebook mechanism.)

• 1621: clear In[] prompt numbers on "Clear All Output" (Merged). (See also 2519 (Merged).)

• 1563: clear_output improvements (Merged).

• 3065: diff-ability of notebooks (Closed).

• 3291: Add the option to skip output cells when saving. (Closed). This seems extremely relevant, however was closed with the suggestion to use a "clean/smudge" filter. A relevant question what can you use if you want to strip off output before running git diff? seems not to have been answered.

• 3312: WIP: Notebook save hooks (Closed).

• 3747: ipynb -> ipynb transformer (Closed). This is rebased in 4175.

• 4175: nbconvert: Jinjaless exporter base (Merged).

• 142: Use STDIN in nbstripout if no input is given (Open).

The notebook format is quite amenable for version control: if one wants to version control the notebook and the outputs then this works quite well. The annoyance comes when one wants only to version control the input, excluding the cell outputs (aka. "build products") which can be large binary blobs, especially for movies and plots. In particular, I am trying to find a good workflow that:

Update: I have been playing with my modified notebook version which optionally saves a .clean version with every save using Gregory Crosswhite's suggestions. This satisfies most of my constraints but leaves the following unresolved:

• When the notebook is running, one can use the Cell/All Output/Clear menu option for removing the output.
• There are some scripts for removing output, such as the script nbstripout.py which remove the output, but does not produce the same output as using the notebook interface. This was eventually included in the ipython/nbconvert repo, but this has been closed stating that the changes are now included in ipython/ipython,but the corresponding functionality seems not to have been included yet. (update) That being said, Gregory Crosswhite's solution shows that this is pretty easy to do, even without invoking ipython/nbconvert, so this approach is probably workable if it can be properly hooked in. (Attaching it to each version control system, however, does not seem like a good idea — this should somehow hook in to the notebook mechanism.)

• 1621: clear In[] prompt numbers on "Clear All Output" (Merged). (See also 2519 (Merged).)
• 1563: clear_output improvements (Merged).
• 3065: diff-ability of notebooks (Closed).
• 3291: Add the option to skip output cells when saving. (Closed). This seems extremely relevant, however was closed with the suggestion to use a "clean/smudge" filter. A relevant question what can you use if you want to strip off output before running git diff? seems not to have been answered.
• 3312: WIP: Notebook save hooks (Closed).
• 3747: ipynb -> ipynb transformer (Closed). This is rebased in 4175.
• 4175: nbconvert: Jinjaless exporter base (Merged).
• 142: Use STDIN in nbstripout if no input is given (Open).